From 12a31f4c130c551f82232d9ef7dfb608bd52c53f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 27 Sep 2016 23:00:48 +0200 Subject: Reorganise repository using standard package layout --- .Rbuildignore | 10 + ChangeLog | 392 ++ DESCRIPTION | 25 + GNUmakefile | 38 +- NAMESPACE | 28 + R/FOCUS_GW_scenarios_2012.R | 11 + R/GUS.R | 98 + R/PEC_soil.R | 215 + R/PEC_sw_drainage_UK.R | 66 + R/PEC_sw_drift.R | 65 + R/PEC_sw_sed.R | 50 + R/SFO_actual_twa.R | 36 + R/SSLRC_mobility_classification.R | 42 + R/TOXSWA_cwa.R | 380 ++ R/drift_data_JKI.R | 44 + R/endpoint.R | 109 + R/geomean.R | 38 + R/pfm_degradation.R | 48 + R/soil_scenario_data_EFSA_2015.R | 40 + data/FOCUS_GW_scenarios_2012.RData | Bin 0 -> 993 bytes data/drift_data_JKI.RData | Bin 0 -> 966 bytes data/soil_scenario_data_EFSA_2015.RData | Bin 0 -> 522 bytes docs/FOCUS_GW_scenarios_2012.html | 157 + docs/GUS.html | 171 + docs/PEC_soil.html | 231 ++ docs/PEC_sw_drainage_UK.html | 127 + docs/PEC_sw_drift.html | 134 + 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inst/web/img/glyphicons-halflings.png | Bin 0 -> 13826 bytes inst/web/index.html | 182 + inst/web/js/bootstrap.js | 1825 +++++++++ inst/web/js/bootstrap.min.js | 6 + inst/web/pfm_degradation.html | 119 + inst/web/plot.TOXSWA_cwa-2.png | Bin 0 -> 7409 bytes inst/web/plot.TOXSWA_cwa-4.png | Bin 0 -> 7409 bytes inst/web/plot.TOXSWA_cwa.html | 119 + inst/web/read.TOXSWA_cwa.html | 138 + inst/web/soil_DT50.html | 104 + inst/web/soil_Kfoc.html | 100 + inst/web/soil_N.html | 98 + inst/web/soil_scenario_data_EFSA_2015.html | 141 + inst/web/soil_sorption.html | 98 + man/FOCUS_GW_scenarios_2012.Rd | 17 + man/GUS.Rd | 81 + man/PEC_soil.Rd | 119 + man/PEC_sw_drainage_UK.Rd | 39 + man/PEC_sw_drift.Rd | 45 + man/PEC_sw_sed.Rd | 42 + man/SFO_actual_twa.Rd | 29 + man/SSLRC_mobility_classification.Rd | 26 + man/TOXSWA_cwa.Rd | 58 + man/drift_data_JKI.Rd | 50 + man/endpoint.Rd | 75 + man/geomean.Rd | 31 + man/pfm_degradation.Rd | 35 + man/plot.TOXSWA_cwa.Rd | 42 + man/read.TOXSWA_cwa.Rd | 56 + man/soil_scenario_data_EFSA_2015.Rd | 46 + pkg/.Rbuildignore | 3 - pkg/DESCRIPTION | 25 - pkg/NAMESPACE | 29 - pkg/R/FOCUS_GW_scenarios_2012.R | 11 - pkg/R/GUS.R | 98 - pkg/R/PEC_soil.R | 215 - pkg/R/PEC_sw_drainage_UK.R | 66 - pkg/R/PEC_sw_drift.R | 65 - pkg/R/PEC_sw_sed.R | 50 - pkg/R/SFO_actual_twa.R | 36 - pkg/R/SSLRC_mobility_classification.R | 42 - pkg/R/TOXSWA_cwa.R | 380 -- pkg/R/drift_data_JKI.R | 44 - pkg/R/endpoint.R | 110 - pkg/R/geomean.R | 38 - pkg/R/pfm_degradation.R | 48 - pkg/R/soil_scenario_data_EFSA_2015.R | 40 - pkg/data/FOCUS_GW_scenarios_2012.RData | Bin 993 -> 0 bytes pkg/data/drift_data_JKI.RData | Bin 966 -> 0 bytes pkg/data/soil_scenario_data_EFSA_2015.RData | Bin 522 -> 0 bytes pkg/inst/extdata/FOCUS_GW_scenarios_2012.R | 59 - pkg/inst/staticdocs/index.r | 42 - pkg/inst/testdata/SwashProjects.zip | Bin 7989179 -> 0 bytes pkg/inst/web/FOCUS_GW_scenarios_2012.html | 154 - pkg/inst/web/GUS.html | 160 - pkg/inst/web/PEC_soil.html | 228 -- 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tests/testthat/test_PEC_soil.R create mode 100644 tests/testthat/test_PEC_sw_drift.R create mode 100644 tests/testthat/test_SFO_actual_twa.R create mode 100644 tests/testthat/test_TOXSWA_cwa.R create mode 100644 tests/testthat/test_UK_drainage.R create mode 100644 tests/testthat/test_geomean.R diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..48acd64 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,10 @@ +^pfm_.*.tar.gz +^GNUmakefile$ +^README.rmd$ +^00003s_pa.cwa$ +^README_files$ +^README.html$ +^build.log$ +^test.log$ +^inst/extdata/Tabelle\ der\ Abdrifteckwerte.xls$ +^docs$ diff --git a/ChangeLog b/ChangeLog new file mode 100644 index 0000000..fdd1006 --- /dev/null +++ b/ChangeLog @@ -0,0 +1,392 @@ +commit 0d958ab6f84b569b5437f231c56004890c4ae23b +Author: Johannes Ranke +Date: 2016-09-27 17:50:34 +0200 + + Make the chents package optional + +commit 399383adcdb37c4a3e32f1a2133a2fa3663618d0 +Author: Johannes Ranke +Date: 2016-09-23 18:23:00 +0200 + + Keep the graph for the markdown file + + The markdown file is not self-contained as the html file... + +commit 9fb69b042924045df90119e47ad4dc666dbc8b4d +Author: Johannes Ranke +Date: 2016-09-23 18:16:51 +0200 + + Slightly update the README + +commit 2f618da8cfbeb0379f4d38af6f608a69c6d54bd5 +Author: Johannes Ranke +Date: 2016-07-30 11:29:09 +0200 + + Update static documentation + +commit 3b8730a58f7846b5261922ec90e582e0158a54c7 +Author: Johannes Ranke +Date: 2016-07-30 11:09:47 +0200 + + Add 'methods' to dependecies + +commit 3260b0e875b7af24f2aef7bc2464418525a192df +Author: Johannes Ranke +Date: 2016-07-30 11:08:05 +0200 + + Fix the TOXSWA reading test + + Since a recent commit we are reading the concentrations at the end + of each hour, so the test needed to be updated accordingly + +commit b8f953d04e4094c79b4f860d99f3c1466ed3ad6a +Author: Johannes Ranke +Date: 2016-07-30 11:06:53 +0200 + + Import 'is' from methods + +commit 1ceb226d999d56276c9e361f359368287a0749c4 +Author: Johannes Ranke +Date: 2016-07-30 10:42:48 +0200 + + Read cwas from .out files with metabolites + + TOXSWA 4 stores the detailed output for SWASH runs with metabolites + in its .out files. With this commit it is possible to read in + .out files from such runs with metabolites. Default is to read in + the concentrations for the parent, a newly gained "substance" argument + makes it possible to specify the metabolite for which the data should + be read. + +commit d6b230cd1b415a112009227bc9e0ff50316c42f7 +Author: Johannes Ranke +Date: 2016-07-15 15:05:22 +0200 + + Fix calculation of t_firstjan + + There is an inconsistency in (some?) output files, so the first + datetime needs to be fixed before reading it into a data frame + +commit b45c9bfae9e5578dd455ed417363b4996cffd46a +Author: Johannes Ranke +Date: 2016-06-08 08:36:48 +0200 + + Clean up remainders of NL drift calculation function + +commit 234a20018fe9fe9824bcfaae2c391e59d09f9871 +Author: Johannes Ranke +Date: 2016-06-08 08:29:39 +0200 + + Use the concentration at the end of the hour + + This is also what TOXSWA presents in the summary files + +commit 4284c57c7d53a9aef0c917a050ccf2ab779cfce3 +Author: Johannes Ranke +Date: 2016-06-08 08:29:39 +0200 + + Use the concentration at the end of the hour + + This is also what TOXSWA presents in the summary files + +commit 057d53d0faed7b297bbb99de8cd4bf3e3e448538 +Author: Johannes Ranke +Date: 2016-03-10 05:28:03 +0100 + + Merge the NL drift calculations based on percentages into PEC_sw_drift + +commit 527d927371083e784ad583a6b3c7465c49a53cdc +Author: Johannes Ranke +Date: 2016-03-10 05:17:45 +0100 + + Add NL specific drift calculations + +commit 1ab6d4c9f186fb7ea9bb8b968e47a9f1eab64583 +Author: Johannes Ranke +Date: 2016-03-02 17:51:21 +0100 + + Fix the name of the Chateadun scenario + +commit d14923ae1ac023c8f8f5ae8b5c0884f4247f764b +Author: Johannes Ranke +Date: 2016-02-04 18:06:15 +0100 + + Test reading .out files and close connections + +commit 98a706373107188496a1df295697e739e51d6b06 +Author: Johannes Ranke +Date: 2016-02-04 17:45:02 +0100 + + Improve reading spead for new TOXSWA format + +commit 057ba40426d49e09c06db26fb7d4072741b4cb8d +Author: Johannes Ranke +Date: 2016-02-04 12:21:02 +0100 + + Read cwa data from TOXSWA 4.4.2 .out files + +commit e7f8a0e82b24d28b74681dafc97f1cf8a4662b51 +Author: Johannes Ranke +Date: 2015-12-27 12:30:20 +0100 + + Fix rounding of endpoint retrieval functions + +commit f9373e361dde232b08fe7431e85bf367a1cfc269 +Author: Johannes Ranke +Date: 2015-12-27 12:29:37 +0100 + + Another useless variant to avoid warnings in staticdoc plots + +commit 3a579d87820ccbec514f1be5eb090e874fd87eec +Author: Johannes Ranke +Date: 2015-12-22 19:32:54 +0100 + + EFSA 2015 tier 1 PEC soil, clean up, add static docs + +commit 9851a97ec915ddbfc8357f1a7e2cabae56c89f7d +Author: Johannes Ranke +Date: 2015-12-18 14:45:24 +0100 + + Documentation fixes, chents is currently a hard dependency + +commit 6b4e342b240baaf18150360986d15895fc80a937 +Author: Johannes Ranke +Date: 2015-10-15 14:41:26 +0200 + + Add endpoint and GUS functions, roxygenize + +commit c43b4947007b3c26bc56260499af51c41b8cd702 +Author: Johannes Ranke +Date: 2015-10-01 14:42:14 +0200 + + Add some soil data for FOCUS groundwater scenarios + +commit 697e0554bf89a63f23b9ab5548e31f218bc483e9 +Author: Johannes Ranke +Date: 2015-09-11 10:07:53 +0200 + + Added PEC soil for products as defined in chents v0.1-2 + +commit 634d4a0a93882a3b2d3961abbdd33694fd93dcc6 +Author: Johannes Ranke +Date: 2015-09-10 16:18:17 +0200 + + Add PEC soil for product with serveral ais + +commit 1ec3ee4a03d4e47fdd3be1bcbe754e478353410b +Author: Johannes Ranke +Date: 2015-08-22 12:10:06 +0200 + + Updates of DESCRIPTION and NAMESPACE + +commit 51aa1a77c9b9b9a6becdb2a5a85213946719b051 +Author: Johannes Ranke +Date: 2015-08-22 12:06:37 +0200 + + Add README.html for cgit on jrwb.de + +commit 83c8575e2abde12208584b9c80935d4a873689fd +Author: Johannes Ranke +Date: 2015-08-22 12:01:57 +0200 + + Small documentation updates + +commit 5038ba57fef6cc386566ec30f3d5dd67e62decff +Author: Johannes Ranke +Date: 2015-08-21 15:10:42 +0200 + + Adapt the description to R CMD check requirements + +commit 4477e69b46e88c196f354463190753650157ea0d +Author: Johannes Ranke +Date: 2015-08-21 15:01:10 +0200 + + Updates to pass checks and tests + +commit ad4cd5d9a1f8c3976d08048a441129b1fb49a62b +Author: Johannes Ranke +Date: 2015-07-02 16:05:59 +0200 + + Changes to pass R CMD check --as-cran, roxygen run + +commit fef0bb7fe916f91dcff089c17aa3290c0ea1ab1f +Author: Johannes Ranke +Date: 2015-06-12 02:19:38 +0200 + + Add sediment PEC calculations using the percentage method + +commit 5b32c30549bfa3cb42ffde7e13f75608b98c79c2 +Author: Johannes Ranke +Date: 2015-06-12 02:19:01 +0200 + + Make UK drainage with non-SFO soil degradation work + +commit 9b8e5cb80ba4a89578d979bee134f8342ca0a527 +Author: Johannes Ranke +Date: 2015-06-11 17:38:01 +0200 + + Now we pass R CMD check + +commit dd803b191062925eda830543236836e7822fd884 +Author: Johannes Ranke +Date: 2015-06-11 16:57:43 +0200 + + Add UK tier 1 drainage PEC calculations + +commit 09cf970942706cfab43753d298b42e8d85216d80 +Author: Johannes Ranke +Date: 2015-06-11 15:25:22 +0200 + + Now there is enough content to warrant 0.2-x + +commit 3aa5fb86772c28402047c7ebd07841061dbcdbba +Author: Johannes Ranke +Date: 2015-06-11 15:23:22 +0200 + + Add facilities to calculate decline curves + +commit d3daa7b73fa5d0508ff51a843247d126c2a11691 +Author: Johannes Ranke +Date: 2015-06-11 13:17:13 +0200 + + Generate README.md with current pfm version + +commit cb0d72e2c2d431bd32ffb129b62ea1a522cbdfeb +Author: Johannes Ranke +Date: 2015-06-11 13:09:10 +0200 + + Rename PEC_sw_drift() to PEC_sw_drift_ini() + +commit ea9b75183bcf41fcdd6f61ec6060e94c4bc321a2 +Author: Johannes Ranke +Date: 2015-06-11 12:13:47 +0200 + + Add simple drift PEC ini calculations + + These are tested for field crops with the CRD spreadsheet + +commit cbba81d73faa83c63a33afc61be5efc1964925bb +Author: Johannes Ranke +Date: 2015-06-11 12:12:40 +0200 + + Use devtools for roxygenizing, improve logging + +commit 6e4a152925011528c21937f12bc53042a53f72de +Author: Johannes Ranke +Date: 2015-06-11 10:13:18 +0200 + + JKI drift percentage data for field crops and pome/stone fruit + +commit 53099978c971ee8e5c94e67bf972f51629d67fd3 +Author: Johannes Ranke +Date: 2015-06-11 10:04:22 +0200 + + and the incomplete documentation + +commit 372ab2f2f59f0baaee759ce966a705f9f754cf6d +Author: Johannes Ranke +Date: 2015-06-11 10:03:32 +0200 + + Intermediate stage for pfm_chent + +commit 586b248f5d249f4ebaad2175c9f78fcae8646636 +Author: Johannes Ranke +Date: 2015-06-11 09:54:57 +0200 + + Formatting + +commit fd1609aafd2f40266c1e29d8dfdf5e08e8838d35 +Author: Johannes Ranke +Date: 2015-05-24 03:52:28 +0200 + + Start of a pfm_chent data object + +commit e2b1d510e921f7721647b0df6602c2618937c1da +Author: Johannes Ranke +Date: 2015-05-08 08:47:11 +0200 + + Update the Figure in the README + +commit 8021c7cb9aac06e961227a3c0e0b013ec2d2d501 +Author: Johannes Ranke +Date: 2015-05-07 16:15:23 +0200 + + Bugfix: Reset maximum event concentration for each event + +commit 508d883f7689d617d15915dbd26a27f1613bb857 +Author: Johannes Ranke +Date: 2015-05-07 12:04:28 +0200 + + Make quarterly labels for plot.TOXSWA_cwa + +commit c6e57ab29170266b3038b01c54bf161ab361d440 +Author: Johannes Ranke +Date: 2015-04-24 02:22:21 +0200 + + Do not test the path to the zip file + +commit 7d2096855edcc196629c1c7a9983a56ec6addd1e +Author: Johannes Ranke +Date: 2015-04-24 02:21:04 +0200 + + Add a geometric mean function + +commit bcfe0af7970efe36c3aa661e89953fbe3689c310 +Author: Johannes Ranke +Date: 2015-04-24 02:20:21 +0200 + + Clean the Makefile a bit + +commit 768a043848dd84b9e699916657d0a23b2f3b9e83 +Author: Johannes Ranke +Date: 2015-04-22 13:48:42 +0200 + + Fix header formatting + +commit 04502ca0c658a6c929debd61aee87be8c7eceb04 +Author: Johannes Ranke +Date: 2015-04-22 13:46:32 +0200 + + Update markdown version of README + +commit ec79637749d300ab4ca170805c673905e52d67dd +Author: Johannes Ranke +Date: 2015-04-22 13:42:10 +0200 + + Add simplest PEC soil calcs, use testthat + +commit 8ffbc49b3f01deac6f9e83aaa6d318d4e2f8552b +Author: Johannes Ranke +Date: 2015-01-23 16:44:04 +0100 + + Add option to plot relative to maximum + +commit 8975dc148d0a6f222174980eb60314054be9b6cf +Author: Johannes Ranke +Date: 2015-01-13 14:54:58 +0100 + + Fix warning in README + +commit 891af5d0f1ee8d45cd4403af43293463d23ba96b +Author: Johannes Ranke +Date: 2015-01-13 14:05:31 +0100 + + README.rmd with example, fix reading unzipped files + +commit 4d74570f1ca4a94d894c6c5169684a8246d0a51c +Author: Johannes Ranke +Date: 2015-01-13 12:58:26 +0100 + + Correctly initialize R6 fields, read from zip files + +commit ee070c11f7c7faff2f573d27cf32aafab78971a8 +Author: Johannes Ranke +Date: 2015-01-07 23:56:54 +0100 + + Pass ... parameters to added cwa lines + +commit 92d97ba99d7b90d95a67796cb5e68f28f752b70b +Author: Johannes Ranke +Date: 2014-12-17 21:39:42 +0100 + + Initial commit: R6 class for TOXSWA cwa files diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..fc76480 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,25 @@ +Package: pfm +Type: Package +Title: Utilities for Pesticide Fate Modelling +Version: 0.3-8 +Date: 2016-09-27 +Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", + role = c("aut", "cre", "cph")) +Description: Utilities for simple calculations of predicted environmental + concentrations (PECs) and for dealing with data from some FOCUS pesticide + fate modelling software packages. +Depends: + R6, + mkin +Imports: + graphics, + readr, + methods +Suggests: + testthat, + chents +License: GPL +LazyLoad: yes +LazyData: yes +Encoding: UTF-8 +RoxygenNote: 5.0.1 diff --git a/GNUmakefile b/GNUmakefile index d6a2dd3..9d34c37 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -1,7 +1,6 @@ -PKGSRC := $(shell basename $(CURDIR)) -PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" pkg/DESCRIPTION) -PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" pkg/DESCRIPTION) -TGZ := $(PKGSRC)_$(PKGVERS).tar.gz +PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION) +PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION) +TGZ := $(PKGNAME)_$(PKGVERS).tar.gz R_HOME ?= $(shell R RHOME) DATE := $(shell date +%Y-%m-%d) @@ -17,38 +16,39 @@ usage: @echo " check - Run CRAN check on the package." @echo " install - Install the package." -pkgfiles = pkg/DESCRIPTION \ +pkgfiles = DESCRIPTION \ README.html \ - pkg/inst/testdata/* \ - pkg/inst/staticdocs/index.r \ - pkg/tests/testthat.R \ - pkg/tests/testthat/* \ - pkg/data/* \ - pkg/R/* + .Rbuildignore \ + inst/testdata/* \ + inst/staticdocs/index.r \ + tests/testthat.R \ + tests/testthat/* \ + data/* \ + R/* clean: @echo "Cleaning up..." - rm -fR pkg.Rcheck + rm -fR pfm.Rcheck @echo "DONE." roxygen: @echo "Roxygenizing package..." - "$(R_HOME)/bin/Rscript" -e 'library(devtools); document("pkg")' + "$(R_HOME)/bin/Rscript" -e 'library(devtools); document()' @echo "DONE." sd: roxygen @echo "Building static documentation..." # suppressWarnings to get rid of mbcsToSbcs warnings when plotting the 'µ' character - cd pkg; "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(staticdocs::build_site())' + "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(staticdocs::build_site())' @echo "DONE." $(TGZ): $(pkgfiles) - sed -i -e "s/Date:.*/Date: $(DATE)/" pkg/DESCRIPTION + sed -i -e "s/Date:.*/Date: $(DATE)/" DESCRIPTION @echo "Roxygenizing package..." - "$(R_HOME)/bin/Rscript" -e 'library(devtools); document("pkg")' + "$(R_HOME)/bin/Rscript" -e 'library(devtools); document()' @echo "Building package..." - git log --no-merges -M --date=iso pkg/ > pkg/ChangeLog - "$(R_HOME)/bin/R" CMD build pkg > build.log 2>&1 + git log --no-merges -M --date=iso > ChangeLog + "$(R_HOME)/bin/R" CMD build . > build.log 2>&1 @echo "DONE." README.html: README.rmd @@ -60,7 +60,7 @@ build: $(TGZ) test: build @echo "Running testthat tests..." - "$(R_HOME)/bin/Rscript" -e 'library(devtools); devtools::test("pkg")' 2>&1 | tee test.log + "$(R_HOME)/bin/Rscript" -e 'library(devtools); devtools::test()' 2>&1 | tee test.log @echo "DONE." quickcheck: build diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..3777574 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,28 @@ +# Generated by roxygen2: do not edit by hand + +S3method(GUS,chent) +S3method(GUS,numeric) +S3method(plot,TOXSWA_cwa) +S3method(print,GUS_result) +export(GUS) +export(PEC_soil) +export(PEC_sw_drainage_UK) +export(PEC_sw_drift) +export(PEC_sw_sed) +export(SFO_actual_twa) +export(SSLRC_mobility_classification) +export(TOXSWA_cwa) +export(endpoint) +export(geomean) +export(pfm_degradation) +export(read.TOXSWA_cwa) +export(soil_DT50) +export(soil_Kfoc) +export(soil_N) +export(soil_sorption) +import(graphics) +import(mkin) +importFrom(R6,R6Class) +importFrom(methods,is) +importFrom(readr,fwf_empty) +importFrom(readr,read_fwf) diff --git a/R/FOCUS_GW_scenarios_2012.R b/R/FOCUS_GW_scenarios_2012.R new file mode 100644 index 0000000..49cf7dd --- /dev/null +++ b/R/FOCUS_GW_scenarios_2012.R @@ -0,0 +1,11 @@ +#' A very small subset of the FOCUS Groundwater scenario defitions +#' +#' Currently, only a small subset of the soil definitions are provided. +#' +#' @name FOCUS_GW_scenarios_2012 +#' @references FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. +#' FOrum for the Co-ordination of pesticde fate models and their USe. +#' http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf +#' @examples +#' FOCUS_GW_scenarios_2012 +NULL diff --git a/R/GUS.R b/R/GUS.R new file mode 100644 index 0000000..4a6532d --- /dev/null +++ b/R/GUS.R @@ -0,0 +1,98 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' Groundwater ubiquity score based on Gustafson (1989) +#' +#' The groundwater ubiquity score GUS is calculated according to +#' the following equation +#' \deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)} +#' +#' @references Gustafson, David I. (1989) Groundwater ubiquity score: a simple +#' method for assessing pesticide leachability. \emph{Environmental +#' toxicology and chemistry} \bold{8}(4) 339–57. +#' @inheritParams endpoint +#' @param DT50 Half-life of the chemical in soil. Should be a field +#' half-life according to Gustafson (1989). However, leaching to the sub-soil +#' can not completely be excluded in field dissipation experiments and Gustafson +#' did not refer to any normalisation procedure, but says the field study should +#' be conducted under use conditions. +#' @param Koc The sorption constant normalised to organic carbon. Gustafson +#' does not mention the nonlinearity of the sorption constant commonly +#' found and usually described by Freundlich sorption, therefore it is +#' unclear at which reference concentration the Koc should be observed +#' (and if the reference concentration would be in soil or in porewater). +#' @param chent If a chent is given with appropriate information present in its +#' chyaml field, this information is used, with defaults specified below. +#' @param degradation_value Which of the available degradation values should +#' be used? +#' @param lab_field Should laboratory or field half-lives be used? This +#' defaults to lab in this implementation, in order to avoid +#' double-accounting for mobility. If comparability with the original GUS +#' values given by Gustafson (1989) is desired, non-normalised first-order +#' field half-lives obtained under actual use conditions should be used. +#' @param redox Aerobic or anaerobic degradation data +#' @param sorption_value Which of the available sorption values should be used? +#' Defaults to Kfoc as this is what is generally available from the European +#' pesticide peer review process. These values generally use a reference +#' concentration of 1 mg/L in porewater, that means they would be expected to +#' be Koc values at a concentration of 1 mg/L in the water phase. +#' @param degradation_aggregator Function for aggregating half-lives +#' @param sorption_aggregator Function for aggregation Koc values +#' @param ... Included in the generic to allow for further arguments later. Therefore +#' this also had to be added to the specific methods. +#' @return A list with the DT50 and Koc used as well as the resulting score +#' of class GUS_result +#' @author Johannes Ranke +#' @export +GUS <- function(...) UseMethod("GUS") + +#' @rdname GUS +#' @export +GUS.numeric <- function(DT50, Koc, ...) { + score <- log10(DT50) * (4 - log10(Koc)) + res <- list(DT50 = DT50, Koc = Koc, score = score) + class(res) <- "GUS_result" + return(res) +} + +#' @rdname GUS +#' @export +GUS.chent <- function(chent, + degradation_value = "DT50ref", + lab_field = "laboratory", + redox = "aerobic", + sorption_value = "Kfoc", + degradation_aggregator = geomean, + sorption_aggregator = geomean, + ...) +{ + DT50 = soil_DT50(chent, lab_field = lab_field, redox = redox, + value = degradation_value, + aggregator = degradation_aggregator, signif = 5) + Koc = soil_Kfoc(chent, value = sorption_value, + aggregator = sorption_aggregator, signif = 5) + GUS.numeric(DT50, Koc) +} + +#' @rdname GUS +#' @export +#' @param x An object of class GUS_result to be printed +#' @param digits The number of digits used in the print method +print.GUS_result = function(x, ..., digits = 1) { + cat("GUS: ", round(x$score, digits = 1), "\n") + cat("calculated from DT50 ", x$DT50, " and Koc ", x$Koc, "\n") +} diff --git a/R/PEC_soil.R b/R/PEC_soil.R new file mode 100644 index 0000000..0263e47 --- /dev/null +++ b/R/PEC_soil.R @@ -0,0 +1,215 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +# Register global variables +if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_type", "TP_identifier", + "soil_scenario_data_EFSA_2015")) + +#' Calculate predicted environmental concentrations in soil +#' +#' This is a basic calculation of a contaminant concentration in bulk soil +#' based on complete, instantaneous mixing. If an interval is given, an +#' attempt is made at calculating a long term maximum concentration using +#' the concepts layed out for example in the PPR panel opinion (EFSA 2012). +#' +#' This assumes that the complete load to soil during the time specified by +#' 'interval' (typically 365 days) is dosed at once. As in the PPR panel +#' opinion cited below (PPR panel 2012), only temperature correction using the +#' Arrhenius equation is performed. +#' +#' Total soil and porewater PEC values for the scenarios as defined in the EFSA +#' guidance (2015, p. 13) can easily be calculated. +#' +#' @note If temperature information is available in the selected scenarios, as +#' e.g. in the EFSA scenarios, the DT50 for groundwater modelling +#' (destination 'PECgw') is taken from the chent object, otherwise the DT50 +#' with destination 'PECsoil'. +#' @importFrom methods is +#' @param rate Application rate in units specified below +#' @param rate_units Defaults to g/ha +#' @param interception The fraction of the application rate that does not reach the soil +#' @param mixing_depth Mixing depth in cm +#' @param interval Period of the deeper mixing, defaults to 365, which is a year if +#' rate units are in days +#' @param n_periods Number of periods to be considered for long term PEC calculations +#' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported +#' @param PEC_pw_units Only mg/L currently supported +#' @param tillage_depth Periodic (see interval) deeper mixing in cm +#' @param chent An optional chent object holding substance specific information. Can +#' also be a name for the substance as a character string +#' @param DT50 If specified, overrides soil DT50 endpoints from a chent object +#' If DT50 is not specified here and not available from the chent object, zero +#' degradation is assumed +#' @param Koc If specified, overrides Koc endpoints from a chent object +#' @param Kom Calculated from Koc by default, but can explicitly be specified +#' as Kom here +#' @param t_avg Averaging times for time weighted average concentrations +#' @param scenarios If this is 'default', the DT50 will be used without correction +#' and soil properties as specified in the REACH guidance (R.16, Table +#' R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", +#' the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when +#' 'chents' is specified, the DegT50 with destination 'PECgw' will be used), +#' and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also +#' model and scenario adjustment factors from the EFSA guidance are used. +#' @param porewater Should equilibrium porewater concentrations be estimated +#' based on Kom and the organic carbon fraction of the soil instead of total +#' soil concentrations? Based on equation (7) given in the PPR panel opinion +#' (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, +#' p. 13). +#' @return The predicted concentration in soil +#' @references EFSA Panel on Plant Protection Products and their Residues (2012) +#' Scientific Opinion on the science behind the guidance for scenario +#' selection and scenario parameterisation for predicting environmental +#' concentrations of plant protection products in soil. \emph{EFSA Journal} +#' \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562 +#' +#' EFSA (European Food Safety Authority) (2015) EFSA guidance document for +#' predicting environmental concentrations of active substances of plant +#' protection products and transformation products of these active substances +#' in soil. \emph{EFSA Journal} \bold{13}(4) 4093 +#' doi:10.2903/j.efsa.2015.4093 +#' @author Johannes Ranke +#' @export +#' @examples +#' PEC_soil(100, interception = 0.25) +#' +#' # This is example 1 starting at p. 79 of the EFSA guidance (2015) +#' PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), +#' scenarios = "EFSA_2015") +#' PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), +#' Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) +#' +#' # The following is from example 4 starting at p. 85 of the EFSA guidance (2015) +#' # Metabolite M2 +#' # Calculate total and porewater soil concentrations for tier 1 scenarios +#' # Relative molar mass is 100/300, formation fraction is 0.7 * 1 +#' results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), +#' scenarios = "EFSA_2015") +#' results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), +#' Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) + +PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, + mixing_depth = 5, + PEC_units = "mg/kg", PEC_pw_units = "mg/L", + interval = NA, n_periods = Inf, + tillage_depth = 20, + chent = NA, + DT50 = NA, + Koc = NA, Kom = Koc / 1.724, + t_avg = 0, + scenarios = c("default", "EFSA_2015"), + porewater = FALSE) +{ + rate_to_soil = (1 - interception) * rate + rate_units = match.arg(rate_units) + PEC_units = match.arg(PEC_units) + scenarios = match.arg(scenarios) + sce <- switch(scenarios, + default = data.frame(rho = 1.5, T_arr = NA, theta_fc = 0.2, f_oc = 0.02, + f_sce = 1, f_mod = 1, row.names = "default"), + EFSA_2015 = if (porewater) soil_scenario_data_EFSA_2015[4:6, ] + else soil_scenario_data_EFSA_2015[1:3, ] + ) + n_sce = nrow(sce) + + soil_volume = 100 * 100 * (mixing_depth/100) # in m3 + soil_mass = soil_volume * sce$rho * 1000 # in kg + + # The following is C_T,ini from EFSA 2012, p. 22, but potentially with interception > 0 + PEC_soil_ini = rate_to_soil * 1000 / soil_mass # in mg/kg + + # Decide which DT50 to take, or set degradation to zero if no DT50 available + if (is.na(DT50) & is(chent, "chent")) { + if (all(is.na(sce$T_arr))) { # No temperature correction + DT50 <- subset(chent$soil_degradation_endpoints, destination == "PECsoil")$DT50 + } else { + DT50 <- subset(chent$soil_degradation_endpoints, destination == "PECgw")$DT50 + } + if (length(DT50) > 1) stop("More than one PECsoil DT50 in chent object") + if (length(DT50) == 0) DT50 <- Inf + } + k = log(2)/DT50 + + # Temperature correction of degradation (accumulation) + if (all(is.na(sce$T_arr))) { # No temperature correction + f_T = 1 + } else { + # Temperature correction as in EFSA 2012 p. 23 + f_T = ifelse(sce$T_arr == 0, + 0, + exp(- (65.4 / 0.008314) * (1/(sce$T_arr + 273.15) - 1/293.15))) + } + + # X is the fraction left after one period (EFSA guidance p. 23) + X = exp(- k * f_T * interval) + + # f_accu is the fraction left after n periods (X + X^2 + ...) + f_accu = 0 + if (!is.na(interval)) { + if (n_periods == Inf) { + f_accu = X/(1 - X) + } else { + for (i in 1:n_periods) { + f_accu = f_accu + X^i + } + } + } + + f_tillage = mixing_depth / tillage_depth + + PEC_background = f_accu * f_tillage * PEC_soil_ini + + PEC_soil = (1 + f_accu * f_tillage) * PEC_soil_ini + + # Get porewater PEC if requested + if (porewater) { + + # If Kom is not specified, try to get K(f)oc + if (is.na(Kom)) { + # If Koc not specified, try to get K(f)oc from chent + if (is.na(Koc) & is(chent, "chent")) { + Koc <- soil_Kfoc(chent) + } + Kom <- Koc / 1.724 + } + + if (is.na(Kom)) stop("No Kom information specified") + + PEC_soil = PEC_soil/((sce$theta_fc/sce$rho) + sce$f_om * Kom) + } + + # Scenario adjustment factors + PEC_soil_sce = PEC_soil * sce$f_sce + + # Model adjustment factors + PEC_soil_sce_mod = PEC_soil_sce * sce$f_mod + + result <- matrix(NA, ncol = n_sce, nrow = length(t_avg), + dimnames = list(t_avg = t_avg, scenario = rownames(sce))) + + result[1, ] <- PEC_soil_sce_mod + + for (i in seq_along(t_avg)) { + t_av_i <- t_avg[i] + if (t_av_i > 0) { + # Equation 10 from p. 24 (EFSA 2015) + result[i, ] <- PEC_soil_sce_mod/(t_av_i * f_T * k) * (1 - exp(- f_T * k * t_av_i)) + } + } + + return(result) +} diff --git a/R/PEC_sw_drainage_UK.R b/R/PEC_sw_drainage_UK.R new file mode 100644 index 0000000..e53f179 --- /dev/null +++ b/R/PEC_sw_drainage_UK.R @@ -0,0 +1,66 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method +#' +#' This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet +#' published on the CRC website +#' +#' @param rate Application rate in g/ha +#' @param interception The fraction of the application rate that does not reach the soil +#' @param Koc The sorption coefficient normalised to organic carbon in L/kg +#' @param latest_application Latest application date, formatted as e.g. "01 July" +#' @param soil_DT50 Soil degradation half-life, if SFO kinetics are to be used +#' @param model The soil degradation model to be used. Either one of "FOMC", +#' "DFOP", "HS", or "IORE", or an mkinmod object +#' @param model_parms A named numeric vector containing the model parameters +#' @return The predicted concentration in surface water in µg/L +#' @export +#' @author Johannes Ranke +#' @examples +#' PEC_sw_drainage_UK(150, Koc = 100) +PEC_sw_drainage_UK <- function(rate, interception = 0, Koc, + latest_application = NULL, soil_DT50 = NULL, + model = NULL, model_parms = NULL) +{ + percentage_lost <- SSLRC_mobility_classification(Koc)[[2]] + amount_available <- rate * (1 - interception) # g/ha + + if (!missing(latest_application)) { + lct <- Sys.getlocale("LC_TIME") + tmp <- Sys.setlocale("LC_TIME", "C") + latest <- as.Date(paste(latest_application, "1999"), "%d %b %Y") + tmp <- Sys.setlocale("LC_TIME", lct) + degradation_time <- as.numeric(difftime(as.Date("1999-10-01"), units = "days", latest)) + if (!missing(soil_DT50)) { + k = log(2)/soil_DT50 + as.Date(paste(latest_application, "1999"), "%d %B %Y") + + amount_available <- amount_available * exp(-k * degradation_time) + if (!missing(model)) stop("You already supplied a soil_DT50 value, implying SFO kinetics") + } + if (!missing(model)) { + fraction_left <- pfm_degradation(model, parms = model_parms, + times = degradation_time)[1, "parent"] + amount_available <- fraction_left * amount_available + } + } + + volume = 130000 # L/ha + PEC = 1e6 * (percentage_lost/100) * amount_available / volume + return(PEC) +} diff --git a/R/PEC_sw_drift.R b/R/PEC_sw_drift.R new file mode 100644 index 0000000..261706c --- /dev/null +++ b/R/PEC_sw_drift.R @@ -0,0 +1,65 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' Calculate predicted environmental concentrations in surface water due to drift +#' +#' This is a basic, vectorised form of a simple calculation of a contaminant +#' concentration in surface water based on complete, instantaneous mixing +#' with input via spray drift. +#' +#' @param rate Application rate in units specified below +#' @param applications Number of applications for selection of drift percentile +#' @param drift_percentages Percentage drift values for which to calculate PECsw. +#' 'drift_data' and 'distances' if not NULL. +#' @param drift_data Source of drift percentage data +#' @param crop Crop name (use German names for JKI data), defaults to "Ackerbau" +#' @param distances The distances in m for which to get PEC values +#' @param water_depth Depth of the water body in cm +#' @param rate_units Defaults to g/ha +#' @param PEC_units Requested units for the calculated PEC. Only µg/L currently supported +#' @return The predicted concentration in surface water +#' @export +#' @author Johannes Ranke +#' @examples +#' PEC_sw_drift(100) +PEC_sw_drift <- function(rate, + applications = 1, + water_depth = 30, + drift_percentages = NULL, + drift_data = "JKI", + crop = "Ackerbau", + distances = c(1, 5, 10, 20), + rate_units = "g/ha", + PEC_units = "\u00B5g/L") +{ + rate_units <- match.arg(rate_units) + PEC_units <- match.arg(PEC_units) + drift_data <- match.arg(drift_data) + water_volume <- 100 * 100 * (water_depth/100) * 1000 # in L (for 1 ha) + PEC_sw_overspray <- rate * 1e6 / water_volume # in µg/L + dist_index <- as.character(distances) + + if (is.null(drift_percentages)) { + drift_percentages <- pfm::drift_data_JKI[[applications]][dist_index, crop] + names(drift_percentages) <- paste(dist_index, "m") + } else { + names(drift_percentages) <- paste(drift_percentages, "%") + } + + PEC_sw_drift <- PEC_sw_overspray * drift_percentages / 100 + return(PEC_sw_drift) +} diff --git a/R/PEC_sw_sed.R b/R/PEC_sw_sed.R new file mode 100644 index 0000000..a4a3d6a --- /dev/null +++ b/R/PEC_sw_sed.R @@ -0,0 +1,50 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' Calculate predicted environmental concentrations in sediment from surface +#' water concentrations +#' +#' The method 'percentage' is equivalent to what is used in the CRD spreadsheet +#' PEC calculator +#' +#' @param PEC_sw Numeric vector or matrix of surface water concentrations in µg/L for +#' which the corresponding sediment concentration is to be estimated +#' @param percentage The percentage in sediment, used for the percentage method +#' @param method The method used for the calculation +#' @param sediment_depth Depth of the sediment layer +#' @param water_depth Depth of the water body in cm +#' @param sediment_density The density of the sediment in L/kg (equivalent to +#' g/cm3) +#' @param PEC_sed_units The units of the estimated sediment PEC value +#' @return The predicted concentration in sediment +#' @export +#' @author Johannes Ranke +#' @examples +#' PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) +PEC_sw_sed <- function(PEC_sw, percentage = 100, method = "percentage", + sediment_depth = 5, water_depth = 30, + sediment_density = 1.3, + PEC_sed_units = c("\u00B5g/kg", "mg/kg")) +{ + method = match.arg(method) + PEC_sed_units = match.arg(PEC_sed_units) + if (method == "percentage") { + PEC_sed = PEC_sw * (percentage/100) * (water_depth / sediment_depth) * (1 / sediment_density) + if (PEC_sed_units == "mg/kg") PEC_sed <- PEC_sed / 1000 + } + return(PEC_sed) +} diff --git a/R/SFO_actual_twa.R b/R/SFO_actual_twa.R new file mode 100644 index 0000000..7facb6a --- /dev/null +++ b/R/SFO_actual_twa.R @@ -0,0 +1,36 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' Actual and maximum moving window time average concentrations for SFO kinetics +#' +#' @param DT50 The half-life. +#' @param times The output times, and window sizes for time weighted average concentrations +#' @export +#' @author Johannes Ranke +#' @source FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation +#' Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, +#' 18 December 2014, p. 251 +#' @examples +#' SFO_actual_twa(10) +SFO_actual_twa <- function(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100)) +{ + k = log(2)/DT50 + result <- data.frame(actual = 1 * exp(-k * times), + twa = (1 - exp(-k * times))/(k * times), + row.names = times) + return(result) +} diff --git a/R/SSLRC_mobility_classification.R b/R/SSLRC_mobility_classification.R new file mode 100644 index 0000000..deda5cf --- /dev/null +++ b/R/SSLRC_mobility_classification.R @@ -0,0 +1,42 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' Determine the SSLRC mobility classification for a chemical substance from its Koc +#' +#' This implements the method specified in the UK data requirements handbook and was +#' checked against the spreadsheet published on the CRC website +#' +#' @param Koc The sorption coefficient normalised to organic carbon in L/kg +#' @return A list containing the classification and the percentage of the +#' compound transported per 10 mm drain water +#' @export +#' @author Johannes Ranke +#' @examples +#' SSLRC_mobility_classification(100) +SSLRC_mobility_classification <- function(Koc) +{ + if (!is.numeric(Koc) | length(Koc) != 1) stop("Please give a single number") + result <- list("Non mobile", 0.01) + if (Koc < 4000) result <- list("Slightly mobile", 0.02) + if (Koc < 1000) result <- list("Slightly mobile", 0.5) + if (Koc < 500) result <- list("Moderately mobile", 0.7) + if (Koc < 75) result <- list("Mobile", 1.9) + if (Koc < 15) result <- list("Very mobile", 1.9) + names(result) <- c("Mobility classification", + "Percentage drained per mm of drain water") + return(result) +} diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R new file mode 100644 index 0000000..c5ddce9 --- /dev/null +++ b/R/TOXSWA_cwa.R @@ -0,0 +1,380 @@ +# Copyright (C) 2014,2015,2016 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' Read TOXSWA surface water concentrations +#' +#' Read TOXSWA hourly concentrations of a chemical substance in a specific +#' segment of a TOXSWA surface water body. Per default, the data for the last +#' segment are imported. As TOXSWA 4 reports the values at the end of the hour +#' (ConLiqWatLayCur) in its summary file, we use this value as well instead +#' of the hourly averages (ConLiqWatLay). +#' +#' @param filename The filename of the cwa file (TOXSWA 2.x.y or similar) or the +#' out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar). +#' @param basedir The path to the directory where the cwa file resides. +#' @param zipfile Optional path to a zip file containing the cwa file. +#' @param segment The segment for which the data should be read. Either "last", or +#' the segment number. +#' @param total Set this to TRUE in order to read total concentrations as well. This is +#' only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa +#' files. For .cwa files, the total concentration is always read as well. +#' @param substance For TOXSWA 4 .out files, the default value "parent" leads +#' to reading concentrations of the parent compound. Alternatively, the substance +#' of interested can be selected by its code name. +#' @param windows Numeric vector of width of moving windows in days, for calculating +#' maximum time weighted average concentrations and areas under the curve. +#' @param thresholds Numeric vector of threshold concentrations in µg/L for +#' generating event statistics. +#' @importFrom readr read_fwf fwf_empty +#' @return An instance of an R6 object of class +#' \code{\link{TOXSWA_cwa}}. +#' @export +#' @author Johannes Ranke +#' @examples +#' H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", +#' basedir = "SwashProjects/project_H_sw/TOXSWA", +#' zipfile = system.file("testdata/SwashProjects.zip", +#' package = "pfm")) +read.TOXSWA_cwa <- function(filename, basedir = ".", zipfile = NULL, + segment = "last", substance = "parent", + total = FALSE, + windows = NULL, thresholds = NULL) +{ + if (!missing(filename)) { + cwa <- TOXSWA_cwa$new(filename, basedir, zipfile, + substance = substance, total = total) + if (!is.null(windows[1])) cwa$moving_windows(windows) + if (!is.null(thresholds[1])) cwa$get_events(thresholds) + invisible(cwa) + } else { + message("You need to specify a filename for the cwa file to be read") + } +} + +#' Plot TOXSWA surface water concentrations +#' +#' Plot TOXSWA hourly concentrations of a chemical substance in a specific +#' segment of a TOXSWA surface water body. +#' +#' @import graphics +#' @param x The TOXSWA_cwa object to be plotted. +#' @param xlab,ylab Labels for x and y axis. +#' @param time_column What should be used for the time axis. If "t_firstjan" is chosen, +#' the time is given in days relative to the first of January in the first year. +#' @param add Should we add to an existing plot? +#' @param total Should the total concentration in water be plotted, including substance sorbed +#' to suspended matter? +#' @param LC_TIME Specification of the locale used to format dates +#' @param ... Further arguments passed to \code{plot} if we are not adding to an existing plot +#' @export +#' @author Johannes Ranke +#' @examples +#' H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", +#' basedir = "SwashProjects/project_H_sw/TOXSWA", +#' zipfile = system.file("testdata/SwashProjects.zip", +#' package = "pfm")) +#' plot(H_sw_D4_pond) +plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"), + xlab = "default", ylab = "default", + add = FALSE, + total = FALSE, LC_TIME = "C", ...) +{ + time_column = match.arg(time_column) + cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L") + lct <- Sys.getlocale("LC_TIME") + tmp <- Sys.setlocale("LC_TIME", LC_TIME) + if (xlab == "default") { + xlab = switch(time_column, + datetime = "Time", + t = "Time [days]", + t_firstjan = "Time since first of January [days]", + t_rel_to_max = "Time relative to maximum concentration [days]") + } + if (ylab == "default") { + ylab = paste( ifelse(total, "Total concentration", "Concentration"), "[\u03bcg/L]") + } + if (add) { + lines(x$cwas[c(time_column, cwa_column)], xlab = xlab, ylab = ylab, ...) + } else{ + if (time_column == "datetime") { + plot(x$cwas$datetime, x$cwas[[cwa_column]], type = "l", + xlab = xlab, ylab = ylab, xaxt = "n", ...) + seq_x <- seq(min(x$cwas$datetime), max(x$cwas$datetime), by = "quarter") + axis(1, at = seq_x, labels = format(seq_x, "%b %Y")) + } else { + plot(x$cwas[c(time_column, cwa_column)], type = "l", + xlab = xlab, ylab = ylab, ...) + } + } + tmp <- Sys.setlocale("LC_TIME", lct) +} + +#' R6 class for holding TOXSWA cwa concentration data and associated statistics +#' +#' An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +#' Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. +#' +#' @docType class +#' @importFrom R6 R6Class +#' @export +#' @format An \code{\link{R6Class}} generator object. +#' @field filename Length one character vector. +#' @field basedir Length one character vector. +#' @field segment Length one integer, specifying for which segment the cwa data were read. +#' @field cwas Dataframe holding the concentrations. +#' @field events List of dataframes holding the event statistics for each threshold. +#' @field windows Matrix of maximum time weighted average concentrations (TWAC_max) +#' and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) +#' for the requested moving window sizes in days. +#' @section Methods: +#' \describe{ +#' \item{\code{get_events(threshold, total = FALSE)}}{ +#' Populate a datataframe with event information for the specified threshold value +#' in µg/L. If \code{total = TRUE}, the total concentration including the amount +#' adsorbed to suspended matter will be used. The resulting dataframe is stored in the +#' \code{events} field of the object. +#' } +#' \item{\code{moving_windows(windows, total = FALSE)}}{ +#' Add to the \code{windows} field described above. +#' Again, if \code{total = TRUE}, the total concentration including the amount +#' adsorbed to suspended matter will be used. +#' } +#' } +#' @examples +#' H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", +#' basedir = "SwashProjects/project_H_sw/TOXSWA", +#' zipfile = system.file("testdata/SwashProjects.zip", +#' package = "pfm")) +#' H_sw_R1_stream$get_events(c(2, 10)) +#' H_sw_R1_stream$moving_windows(c(7, 21)) +#' print(H_sw_R1_stream) +#' @keywords data + +TOXSWA_cwa <- R6Class("TOXSWA_cwa", + public = list( + filename = NULL, + basedir = NULL, + zipfile = NULL, + segment = NULL, + substance = NULL, + cwas = NULL, + windows = NULL, + events = list(), + initialize = function(filename, basedir, zipfile = NULL, + segment = "last", substance = "parent", total = FALSE) { + self$filename <- filename + self$basedir <- basedir + self$zipfile <- zipfile + if (!is.null(zipfile)) { + try(file_connection <- unz(zipfile, paste0(basedir, "/", filename))) + } else { + try(file_connection <- file(file.path(basedir, filename), "rt")) + } + + + if (grepl(".cwa$", filename)) { + # cwa file from FOCUS TOXSWA 3 (TOXSWA 2.x.y) + cwa_all_segments <- try( + read.table(file_connection, + sep = "", skip = 40, + encoding = "UTF-8", + colClasses = c("character", "numeric", + "integer", rep("numeric", 5)), + col.names = c("datetime", "t", "segment", + "xcd", "cwa_tot", "cwa", "Xss", "Xmp"))) + + if (is.null(zipfile)) close(file_connection) # only needed for files + + if (!inherits(cwa_all_segments, "try-error")) { + available_segments = 1:max(cwa_all_segments$segment) + if (segment == "last") segment = max(available_segments) + if (!segment %in% available_segments) stop("Invalid segment specified") + self$segment <- segment + cwa <- subset(cwa_all_segments, segment == self$segment, + c("datetime", "t", "segment", "cwa", "cwa_tot")) + lct <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C") + cwa$datetime <- strptime(cwa$datetime, "%d-%b-%Y-%H:%M") + Sys.setlocale("LC_TIME", lct) + startyear = format(cwa$datetime[1], "%Y") + firstjan <- strptime(paste0(startyear, "-01-01"), "%Y-%m-%d") + cwa$t_firstjan <- as.numeric(difftime(cwa$datetime, + firstjan, units = "days")) + + t_max = cwa[which.max(cwa$cwa), "t"] + cwa$t_rel_to_max = cwa$t - t_max + cwa$cwa_mug_per_L <- cwa$cwa * 1000 + cwa$cwa_tot_mug_per_L <- cwa$cwa_tot * 1000 + self$cwas <- cwa[c("datetime", "t", "t_firstjan", + "t_rel_to_max", + "cwa_mug_per_L", + "cwa_tot_mug_per_L")] + } else { + stop("Could not read ", filename) + } + } else { + # out file from FOCUS TOXSWA 4 (TOXSWA 4.4.2 or similar) + outfile <- try(readLines(file_connection)) + + close(file_connection) # only needed for files + + if (inherits(outfile, "try-error")) { + stop("Could not read ", filename) + } else { + # Get the substance name(s) + sub_lines <- grep(".*0.000.*ConLiqWatLayCur_", outfile[1:50], value = TRUE) + substances <- gsub(".*ConLiqWatLayCur_(.*?) *[0-9].*", "\\1", sub_lines) + if (!substance %in% c("parent", substances)) { + stop("No data for substance ", substance, " present in the .out file.") + } + + # Generate field name for the concentrations at end of hour for the + # substance of interest + if (substance == "parent") { + cwa_string = paste0("ConLiqWatLayCur_", substances[1]) + } else { + cwa_string = paste0("ConLiqWatLayCur_", substance) + } + + cwa_lines <- grep(cwa_string, outfile, value = TRUE) + + cwa_all_segments <- read_fwf(paste(cwa_lines, collapse = "\n"), + fwf_empty(paste(tail(cwa_lines), collapse = "\n"))) + + # Append time "-00h00" to datetime in first row, as this is not (always?) present + # in the line ConLiqWatLayCur + if (nchar(cwa_all_segments[1, "X2"]) == 11) { + cwa_all_segments[1, "X2"] = paste0(cwa_all_segments[1, "X2"], "-00h00") + } + + available_segments = 1:(ncol(cwa_all_segments) - 3) + if (segment == "last") segment = max(available_segments) + if (!segment %in% available_segments) stop("Invalid segment specified") + self$segment <- segment + cwa <- data.frame( + datetime = as.character(cwa_all_segments$X2), + t = cwa_all_segments$X1, + cwa = cwa_all_segments[[3 + segment]] + ) + if (total) { + cwa_tot_lines <- outfile[grep("ConSysWatLay_", outfile)] # hourly total conc. + cwa_tot_all_segments <- read.table(text = cwa_lines) + cwa$cwa_tot = cwa_tot_all_segments[[3 + segment]] + } + lct <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C") + cwa$datetime <- strptime(cwa$datetime, "%d-%b-%Y-%Hh%M") + Sys.setlocale("LC_TIME", lct) + + startyear = format(cwa$datetime[1], "%Y") + firstjan <- strptime(paste0(startyear, "-01-01"), "%Y-%m-%d") + cwa$t_firstjan <- as.numeric(difftime(cwa$datetime, + firstjan, units = "days")) + t_max = cwa[which.max(cwa$cwa), "t"] + cwa$t_rel_to_max = cwa$t - t_max + cwa$cwa_mug_per_L <- cwa$cwa * 1000 + self$cwas <- cwa[c("datetime", "t", "t_firstjan", + "t_rel_to_max", + "cwa_mug_per_L")] + if (total) { + self$cwas$cwa_tot_mug_per_L <- cwa$cwa_tot * 1000 + } + } + } + }, + moving_windows = function(windows, total = FALSE) { + window_names = paste(windows, "days") + n = length(window_names) + self$windows <- data.frame(window = window_names, + max_TWAC = numeric(n), + max_AUC_h = numeric(n), + max_AUC_d = numeric(n)) + if (missing(windows)) { + stop("You need to specify at least one moving window size in days") + } + cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L") + for (i in seq_along(windows)) { + window_size = windows[i] + filter_size = window_size * 24 + max_TWAC = max(filter(self$cwas[cwa_column], rep(1/filter_size, filter_size), + "convolution"), na.rm = TRUE) + max_AUC_h = max_TWAC * filter_size + max_AUC_d = max_TWAC * window_size + + self$windows[i, -1] = c(max_TWAC, max_AUC_h, max_AUC_d) + } + invisible(self) + }, + get_events = function(thresholds, total = FALSE) { + if (missing(thresholds)) { + stop("You need to specify at least one threshold concentration in \u03bcg/L") + } + for (threshold in thresholds) { + events = data.frame(t_start = numeric(), cwa_max = numeric(), + duration = numeric(), pre_interval = numeric(), + AUC_h = numeric(), AUC_d = numeric()) + cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L") + + event_end = 0 + event = FALSE + event_max = 0 + event_nr = 0 + n_rows = nrow(self$cwas) + for (i in 1:n_rows) { + cwa_cur = self$cwas[i, cwa_column] + if (event == FALSE) { + if (cwa_cur > threshold) { + event_start = self$cwas[i, "t"] + pre_interval = event_start - event_end + i_start = i + event = TRUE + event_max = cwa_cur + } + } else { + if (cwa_cur > event_max) event_max = cwa_cur + if (cwa_cur < threshold || i == n_rows) { + event_nr = event_nr + 1 + i_end = i + if (i == n_rows) i_end = i + event_end = self$cwas[i_end, "t"] + event_length = event_end - event_start + event_cwas <- self$cwas[i_start:(i_end - 1), cwa_column] + event_AUC_h = sum(event_cwas) + event_AUC_d = event_AUC_h / 24 + events[event_nr, ] = c(event_start, event_max, event_length, + pre_interval, event_AUC_h, event_AUC_d) + event = FALSE + } + } + } + + self$events[[as.character(threshold)]] <- events + } + invisible(self) + }, + print = function() { + cat(" data from file", self$filename, "segment", self$segment, "\n") + print(head(self$cwas)) + cat("Moving window analysis\n") + print(self$windows) + for (threshold in names(self$events)) { + cat("Event statistics for threshold", threshold, "\n") + if (nrow(self$events[[threshold]]) == 0) cat("No events found\n") + else print(self$events[[threshold]]) + } + } + ) +) +# vim: set ts=2 sw=2 expandtab: diff --git a/R/drift_data_JKI.R b/R/drift_data_JKI.R new file mode 100644 index 0000000..888d3b5 --- /dev/null +++ b/R/drift_data_JKI.R @@ -0,0 +1,44 @@ +#' Deposition from spray drift expressed as percent of the applied dose as +#' published by the JKI +#' +#' Deposition from spray drift expressed as percent of the applied dose as +#' published by the German Julius-Kühn Institute (JKI). +#' +#' The data were extracted from the spreadsheet cited below using the R code +#' given in the example section. The spreadsheet is not included in the package +#' as its licence is not clear. +#' +#' +#' @name drift_data_JKI +#' @docType data +#' @format A list currently containing matrices with spray drift percentage +#' data for field crops (Ackerbau), and Pome/stone fruit, early and late +#' (Obstbau frueh, spaet). +#' @source JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved +#' from +#' http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html +#' on 2015-06-11 +#' @keywords datasets +#' @examples +#' +#' \dontrun{ +#' # This is the code that was used to extract the data +#' library(readxl) +#' abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" +#' JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet") +#' names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late") +#' drift_data_JKI <- list() +#' +#' for (n in 1:8) { +#' drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) +#' drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) +#' dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]), +#' crop = JKI_crops) +#' drift_data_JKI[[n]] <- drift_data +#' } +#' save(drift_data_JKI, file = "data/drift_data_JKI.RData") +#' } +#' +#' # And this is the resulting data +#' drift_data_JKI +NULL diff --git a/R/endpoint.R b/R/endpoint.R new file mode 100644 index 0000000..56a314b --- /dev/null +++ b/R/endpoint.R @@ -0,0 +1,109 @@ +#' Retrieve endpoint information from the chyaml field of a chent object +#' +#' R6 class objects of class chent represent chemical entities +#' and can hold a list of information loaded from a chemical yaml file in their +#' chyaml field. Such information is extracted and optionally aggregated by +#' this function. +#' +#' The functions \code{soil_*} are functions to extract soil specific endpoints. +#' For the Freundlich exponent, the capital letter \code{N} is used in order to +#' facilitate dealing with such data in R. In pesticide fate modelling, this +#' exponent is often called 1/n. +#' +#' @export +#' @param chent The chent object to get the information from +#' @param medium The medium for which information is sought +#' @param type The information type +#' @param lab_field If not NA, do we want laboratory or field endpoints +#' @param redox If not NA, are we looking for aerobic or anaerobic data +#' @param value The name of the value we want. The list given in the +#' usage section is not exclusive +#' @param aggregator The aggregator function. Can be mean, +#' \code{\link{geomean}}, or identity, for example. +#' @param raw Should the number(s) be returned as stored in the chent +#' object (could be a character value) to retain original information +#' about precision? +#' @param signif How many significant digits do we want +#' @return The result from applying the aggregator function to +#' the values converted to a numeric vector, rounded to the +#' given number of significant digits, or, if raw = TRUE, +#' the values as a character value, retaining any implicit +#' information on precision that may be present. +#' +endpoint <- function(chent, + medium = "soil", + type = c("degradation", "sorption"), + lab_field = c(NA, "laboratory", "field"), + redox = c(NA, "aerobic", "anaerobic"), + value = c("DT50ref", "Kfoc", "N"), + aggregator = geomean, + raw = FALSE, + signif = 3) +{ + if (!is(chent, "chent")) { + stop("Please supply a chent object as created using the package 'chents' available from jrwb.de") + } + ep_list <- chent$chyaml[[medium]][[type]] + if (!is.na(lab_field[1])) { + ep_list <- ep_list[[lab_field]] + } + if (!is.na(redox[1])) { + ep_list <- ep_list[[redox]] + } + values <- ep_list$data[[value]] + if (raw) return(values) + else return(signif(aggregator(as.numeric(values)), signif)) +} + +#' @inheritParams endpoint +#' @rdname endpoint +#' @export +soil_DT50 <- function(chent, aggregator = geomean, signif = 3, + lab_field = "laboratory", value = "DT50ref", + redox = "aerobic", raw = FALSE) { + ep <- endpoint(chent, medium = "soil", type = "degradation", + lab_field = "laboratory", redox = redox, + signif = signif, + value = value, aggregator = aggregator, raw = raw) + return(ep) +} + +#' @inheritParams endpoint +#' @rdname endpoint +#' @export +soil_Kfoc <- function(chent, aggregator = geomean, signif = 3, + value = "Kfoc", raw = FALSE) { + ep <- endpoint(chent, medium = "soil", type = "sorption", + signif = signif, + value = value, aggregator = aggregator, raw = raw) + return(ep) +} + +#' @inheritParams endpoint +#' @rdname endpoint +#' @export +soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) { + ep <- endpoint(chent, medium = "soil", type = "sorption", + signif = signif, + value = "N", aggregator = aggregator, raw = raw) + return(ep) +} + +#' @inheritParams endpoint +#' @rdname endpoint +#' @param values The values to be returned +#' @param aggregators A named vector of aggregator functions to be used +#' @export +soil_sorption <- function(chent, values = c("Kfoc", "N"), + aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), + signif = c(Kfoc = 3, N = 3), + raw = FALSE) { + res <- sapply(values, + function(x) { + endpoint(chent, medium = "soil", type = "sorption", + signif = signif[[x]], + value = x, aggregator = aggregators[[x]], raw = raw) + } + ) + return(res) +} diff --git a/R/geomean.R b/R/geomean.R new file mode 100644 index 0000000..626829b --- /dev/null +++ b/R/geomean.R @@ -0,0 +1,38 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' Calculate the geometric mean +#' +#' Based on some posts in a thread on Stackoverflow +#' \url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in} +#' This function checks for negative values, removes NA values per default and +#' returns 0 if at least one element of the vector is 0. +#' +#' @param x Vector of numbers +#' @param na.rm Should NA values be omitted? +#' @return The geometric mean +#' @export +#' @author Johannes Ranke +#' @examples +#' geomean(c(1, 3, 9)) +#' geomean(c(1, 3, NA, 9)) +#' \dontrun{geomean(c(1, -3, 9)) # returns an error} +geomean = function(x, na.rm = TRUE){ + if (any(is.na(x)) & na.rm == FALSE) stop("Removal of NA values was not requested") + if (any(x < 0, na.rm = na.rm)) stop("Only defined for positive numbers") + exp(mean(log(x), na.rm = na.rm)) +} diff --git a/R/pfm_degradation.R b/R/pfm_degradation.R new file mode 100644 index 0000000..6c8610e --- /dev/null +++ b/R/pfm_degradation.R @@ -0,0 +1,48 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de +# This file is part of the R package pfm + +# This program is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +#' Calculate a time course of relative concentrations based on an mkinmod model +#' +#' @import mkin +#' @param model The degradation model to be used. Either a parent only model like +#' 'SFO' or 'FOMC', or an mkinmod object +#' @param DT50 The half-life. This is only used when simple exponential decline +#' is calculated (SFO model). +#' @param parms The parameters used for the degradation model +#' @param years For how many years should the degradation be predicted? +#' @param step_days What step size in days should the output have? +#' @param times The output times +#' @export +#' @author Johannes Ranke +#' @examples +#' head(pfm_degradation("SFO", DT50 = 10)) +pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50), + years = 1, step_days = 1, + times = seq(0, years * 365, by = step_days)) +{ + if (model %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) { + model <- mkinmod(parent = list(type = model)) + } + initial_state = c(1, rep(0, length(model$diffs) - 1)) + names(initial_state) <- names(model$diffs) + time_course <- mkinpredict(model, odeparms = parms, + odeini = initial_state, + outtimes = times, + solution_type = ifelse(length(model$spec) == 1, + "analytical", "deSolve")) + invisible(time_course) +} diff --git a/R/soil_scenario_data_EFSA_2015.R b/R/soil_scenario_data_EFSA_2015.R new file mode 100644 index 0000000..fb096bc --- /dev/null +++ b/R/soil_scenario_data_EFSA_2015.R @@ -0,0 +1,40 @@ +#' Properties of the predefined scenarios from the EFSA guidance from 2015 +#' +#' Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +#' concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the +#' scenario and model adjustment factors from p. 15 and p. 17 are included. +#' +#' @name soil_scenario_data_EFSA_2015 +#' @docType data +#' @format A data frame with one row for each scenario. Row names are the scenario codes, +#' e.g. CTN for the Northern scenario for the total concentration in soil. Columns are +#' mostly self-explanatory. \code{rho} is the dry bulk density of the top soil. +#' @source EFSA (European Food Safety Authority) (2015) +#' EFSA guidance document for predicting environmental concentrations +#' of active substances of plant protection products and transformation products of these +#' active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 +#' doi:10.2903/j.efsa.2015.4093 +#' @keywords datasets +#' @examples +#' \dontrun{ +#' # This is the code that was used to define the data +#' soil_scenario_data_EFSA_2015 <- data.frame( +#' Zone = rep(c("North", "Central", "South"), 2), +#' Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), +#' T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), +#' T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), +#' Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), +#' f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), +#' theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), +#' rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), +#' f_sce = c(3, 2, 2, 2, 1.5, 1.5), +#' f_mod = c(2, 2, 2, 4, 4, 4), +#' stringsAsFactors = FALSE, +#' row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") +#' ) +#' save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') +#' } +#' +#' # And this is the resulting dataframe +#' soil_scenario_data_EFSA_2015 +NULL diff --git a/data/FOCUS_GW_scenarios_2012.RData b/data/FOCUS_GW_scenarios_2012.RData new file mode 100644 index 0000000..4b2622e Binary files /dev/null and b/data/FOCUS_GW_scenarios_2012.RData differ diff --git a/data/drift_data_JKI.RData b/data/drift_data_JKI.RData new file mode 100644 index 0000000..0a2f05e Binary files /dev/null and b/data/drift_data_JKI.RData differ diff --git a/data/soil_scenario_data_EFSA_2015.RData b/data/soil_scenario_data_EFSA_2015.RData new file mode 100644 index 0000000..b30076f Binary files /dev/null and b/data/soil_scenario_data_EFSA_2015.RData differ diff --git a/docs/FOCUS_GW_scenarios_2012.html b/docs/FOCUS_GW_scenarios_2012.html new file mode 100644 index 0000000..275e7e4 --- /dev/null +++ b/docs/FOCUS_GW_scenarios_2012.html @@ -0,0 +1,157 @@ + + + + +FOCUS_GW_scenarios_2012. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

A very small subset of the FOCUS Groundwater scenario defitions

+ +
+
+ +
+

Description

+ +

Currently, only a small subset of the soil definitions are provided.

+ +
+ +
+

References

+ +

FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. + FOrum for the Co-ordination of pesticde fate models and their USe. + http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf

+ +
+ +

Examples

+ 
FOCUS_GW_scenarios_2012

+
$names
+           Cha            Ham            Jok            Kre            Oke 
+  "Châteaudun"      "Hamburg"    "Jokioinen" "Kremsmünster"   "Okehampton" 
+           Pia            Por            Sev            Thi 
+    "Piacenza"        "Porto"      "Sevilla"        "Thiva" 
+
+$soils
+   location horizon number pH_H2O perc_clay perc_oc rel_deg
+1       Cha      Ap      1    8.0      30.0    1.39     1.0
+2       Cha      B1      2    8.1      31.0    0.93     0.5
+3       Cha      B2      3    8.2      25.0    0.70     0.5
+4       Cha   II C1      4    8.5      26.0    0.30     0.3
+5       Cha   II C1      5    8.5      26.0    0.30     0.0
+6       Cha   II C2      6    8.5      24.0    0.27     0.0
+7       Cha       M      7    8.3      31.0    0.21     0.0
+8       Ham      Ap      1    6.4       7.2    1.50     1.0
+9       Ham     BvI      2    5.6       6.7    1.00     0.5
+10      Ham    BvII      3    5.6       0.9    0.20     0.3
+11      Ham   Bv/Cv      4    5.7       0.0    0.00     0.3
+12      Ham      Cv      5    5.5       0.0    0.00     0.3
+13      Ham      Cv      6    5.5       0.0    0.00     0.0
+14      Jok      Ap      1    6.2       3.6    4.06     1.0
+15      Jok      Bs      2    5.6       1.8    0.84     0.5
+16      Jok     BC1      3    5.4       1.2    0.36     0.3
+17      Jok     BC2      4    5.4       1.7    0.29     0.3
+18      Jok     BC2      5    5.4       1.7    0.29     0.0
+19      Jok      Cg      6    5.3       1.9    0.21     0.0
+20      Kre    <NA>      1    7.7      14.0    3.60     1.0
+21      Kre    <NA>      2    7.0      25.0    1.00     0.5
+22      Kre    <NA>      3    7.1      27.0    0.50     0.5
+23      Kre    <NA>      4    7.1      27.0    0.50     0.3
+24      Kre    <NA>      5    7.1      27.0    0.50     0.0
+25      Oke       A      1    5.8      18.0    2.20     1.0
+26      Oke     Bw1      2    6.3      17.0    0.70     0.5
+27      Oke      BC      3    6.5      14.0    0.40     0.3
+28      Oke       C      4    6.6       9.0    0.10     0.3
+29      Oke       C      5    6.6       9.0    0.10     0.0
+30      Pia      Ap      1    7.0      15.0    1.26     1.0
+31      Pia      Ap      2    7.0      15.0    1.26     0.5
+32      Pia      Bw      3    6.3       7.0    0.47     0.5
+33      Pia      Bw      4    6.3       7.0    0.47     0.3
+34      Pia      2C      5    6.4       0.0    0.00     0.3
+35      Pia      2C      6    6.4       0.0    0.00     0.0
+36      Por    <NA>      1    4.9      10.0    1.42     1.0
+37      Por    <NA>      2    4.8       8.0    0.78     0.5
+38      Por    <NA>      3    4.8       8.0    0.78     0.3
+39      Por    <NA>      4    4.8       8.0    0.78     0.0
+40      Sev    <NA>      1    7.3      14.0    0.93     1.0
+41      Sev    <NA>      2    7.3      13.0    0.93     1.0
+42      Sev    <NA>      3    7.8      15.0    0.70     0.5
+43      Sev    <NA>      4    8.1      16.0    0.58     0.3
+44      Sev    <NA>      5    8.1      16.0    0.58     0.0
+45      Sev    <NA>      6    8.2      22.0    0.49     0.0
+46      Thi     Ap1      1    7.7      25.3    0.74     1.0
+47      Thi     Ap2      2    7.7      25.3    0.74     0.5
+48      Thi      Bw      3    7.8      29.6    0.57     0.5
+49      Thi      Bw      4    7.8      31.9    0.31     0.3
+50      Thi     Ck1      5    7.8      32.9    0.18     0.3
+51      Thi     Ck1      6    7.8      32.9    0.18     0.0
+
+
+
+
+ + + + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/GUS.html b/docs/GUS.html new file mode 100644 index 0000000..cb4e10e --- /dev/null +++ b/docs/GUS.html @@ -0,0 +1,171 @@ + + + + +GUS. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Groundwater ubiquity score based on Gustafson (1989)

+ +
+
+

Usage

+ 
GUS(...)
+
+# S3 method for numeric
+GUS(DT50, Koc, ...)
+
+# S3 method for chent
+GUS(chent, degradation_value = "DT50ref",
+  lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc",
+  degradation_aggregator = geomean, sorption_aggregator = geomean, ...)
+
+# S3 method for GUS_result
+print(x, ..., digits = 1)
+ +

Arguments

+
+
...
+
Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.
+
DT50
+
Half-life of the chemical in soil. Should be a field +half-life according to Gustafson (1989). However, leaching to the sub-soil +can not completely be excluded in field dissipation experiments and Gustafson +did not refer to any normalisation procedure, but says the field study should +be conducted under use conditions.
+
Koc
+
The sorption constant normalised to organic carbon. Gustafson +does not mention the nonlinearity of the sorption constant commonly +found and usually described by Freundlich sorption, therefore it is +unclear at which reference concentration the Koc should be observed +(and if the reference concentration would be in soil or in porewater).
+
chent
+
If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.
+
degradation_value
+
Which of the available degradation values should +be used?
+
lab_field
+
Should laboratory or field half-lives be used? This +defaults to lab in this implementation, in order to avoid +double-accounting for mobility. If comparability with the original GUS +values given by Gustafson (1989) is desired, non-normalised first-order +field half-lives obtained under actual use conditions should be used.
+
redox
+
Aerobic or anaerobic degradation data
+
sorption_value
+
Which of the available sorption values should be used? +Defaults to Kfoc as this is what is generally available from the European +pesticide peer review process. These values generally use a reference +concentration of 1 mg/L in porewater, that means they would be expected to +be Koc values at a concentration of 1 mg/L in the water phase.
+
degradation_aggregator
+
Function for aggregating half-lives
+
sorption_aggregator
+
Function for aggregation Koc values
+
x
+
An object of class GUS_result to be printed
+
digits
+
The number of digits used in the print method
+
+ +
+

Value

+ +

+A list with the DT50 and Koc used as well as the resulting score + of class GUS_result +

+ +
+ +
+

Description

+ +

The groundwater ubiquity score GUS is calculated according to +the following equation +$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$

+ +
+ +
+

References

+ +

Gustafson, David I. (1989) Groundwater ubiquity score: a simple +method for assessing pesticide leachability. Environmental +toxicology and chemistry 8(4) 339–57.

+ +
+
+
+ + + + +

Author

+ +Johannes Ranke + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/PEC_soil.html b/docs/PEC_soil.html new file mode 100644 index 0000000..9a10757 --- /dev/null +++ b/docs/PEC_soil.html @@ -0,0 +1,231 @@ + + + + +PEC_soil. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Calculate predicted environmental concentrations in soil

+ +
+
+

Usage

+ 
PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5,
+  PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA,
+  n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA,
+  Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default",
+  "EFSA_2015"), porewater = FALSE)
+ +

Arguments

+
+
rate
+
Application rate in units specified below
+
rate_units
+
Defaults to g/ha
+
interception
+
The fraction of the application rate that does not reach the soil
+
mixing_depth
+
Mixing depth in cm
+
PEC_units
+
Requested units for the calculated PEC. Only mg/kg currently supported
+
PEC_pw_units
+
Only mg/L currently supported
+
interval
+
Period of the deeper mixing, defaults to 365, which is a year if +rate units are in days
+
n_periods
+
Number of periods to be considered for long term PEC calculations
+
tillage_depth
+
Periodic (see interval) deeper mixing in cm
+
chent
+
An optional chent object holding substance specific information. Can +also be a name for the substance as a character string
+
DT50
+
If specified, overrides soil DT50 endpoints from a chent object +If DT50 is not specified here and not available from the chent object, zero +degradation is assumed
+
Koc
+
If specified, overrides Koc endpoints from a chent object
+
Kom
+
Calculated from Koc by default, but can explicitly be specified +as Kom here
+
t_avg
+
Averaging times for time weighted average concentrations
+
scenarios
+
If this is 'default', the DT50 will be used without correction +and soil properties as specified in the REACH guidance (R.16, Table +R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", +the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when +'chents' is specified, the DegT50 with destination 'PECgw' will be used), +and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also +model and scenario adjustment factors from the EFSA guidance are used.
+
porewater
+
Should equilibrium porewater concentrations be estimated +based on Kom and the organic carbon fraction of the soil instead of total +soil concentrations? Based on equation (7) given in the PPR panel opinion +(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, +p. 13).
+
+ +
+

Value

+ +

+The predicted concentration in soil +

+ +
+ +
+

Description

+ +

This is a basic calculation of a contaminant concentration in bulk soil +based on complete, instantaneous mixing. If an interval is given, an +attempt is made at calculating a long term maximum concentration using +the concepts layed out for example in the PPR panel opinion (EFSA 2012).

+ +
+ +
+

Details

+ +

This assumes that the complete load to soil during the time specified by +'interval' (typically 365 days) is dosed at once. As in the PPR panel +opinion cited below (PPR panel 2012), only temperature correction using the +Arrhenius equation is performed.

+ +

Total soil and porewater PEC values for the scenarios as defined in the EFSA +guidance (2015, p. 13) can easily be calculated.

+ +
+ +
+

Note

+ +

If temperature information is available in the selected scenarios, as + e.g. in the EFSA scenarios, the DT50 for groundwater modelling + (destination 'PECgw') is taken from the chent object, otherwise the DT50 + with destination 'PECsoil'.

+ +
+ +
+

References

+ +

EFSA Panel on Plant Protection Products and their Residues (2012) + Scientific Opinion on the science behind the guidance for scenario + selection and scenario parameterisation for predicting environmental + concentrations of plant protection products in soil. EFSA Journal + 10(2) 2562, doi:10.2903/j.efsa.2012.2562

+ +

EFSA (European Food Safety Authority) (2015) EFSA guidance document for + predicting environmental concentrations of active substances of plant + protection products and transformation products of these active substances + in soil. EFSA Journal 13(4) 4093 + doi:10.2903/j.efsa.2015.4093

+ +
+ +

Examples

+ 
PEC_soil(100, interception = 0.25)

+
     scenario
+t_avg default
+    0     0.1
+

+

+# This is example 1 starting at p. 79 of the EFSA guidance (2015)
+PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
+               scenarios = "EFSA_2015")

+
     scenario
+t_avg      CTN      CTC      CTS
+   0  21.96827 11.53750 9.145259
+   21 21.78517 11.40701 9.017370
+

+
PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21),
+               Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE)

+
     scenario
+t_avg       CLN       CLC       CLS
+   0  0.7589401 0.6674322 0.9147861
+   21 0.7506036 0.6590345 0.8987279
+

+

+# The following is from example 4 starting at p. 85 of the EFSA guidance (2015)
+# Metabolite M2
+# Calculate total and porewater soil concentrations for tier 1 scenarios
+# Relative molar mass is 100/300, formation fraction is 0.7 * 1
+results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
+                        scenarios = "EFSA_2015")
+results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21),
+                           Kom = 100, scenarios = "EFSA_2015", porewater = TRUE)
+
+
+ + + + +

Author

+ +Johannes Ranke + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/PEC_sw_drainage_UK.html b/docs/PEC_sw_drainage_UK.html new file mode 100644 index 0000000..9c28968 --- /dev/null +++ b/docs/PEC_sw_drainage_UK.html @@ -0,0 +1,127 @@ + + + + +PEC_sw_drainage_UK. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

+ +
+
+

Usage

+ 
PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL,
+  soil_DT50 = NULL, model = NULL, model_parms = NULL)
+ +

Arguments

+
+
rate
+
Application rate in g/ha
+
interception
+
The fraction of the application rate that does not reach the soil
+
Koc
+
The sorption coefficient normalised to organic carbon in L/kg
+
latest_application
+
Latest application date, formatted as e.g. "01 July"
+
soil_DT50
+
Soil degradation half-life, if SFO kinetics are to be used
+
model
+
The soil degradation model to be used. Either one of "FOMC", +"DFOP", "HS", or "IORE", or an mkinmod object
+
model_parms
+
A named numeric vector containing the model parameters
+
+ +
+

Value

+ +

+The predicted concentration in surface water in µg/L +

+ +
+ +
+

Description

+ +

This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet +published on the CRC website

+ +
+ +

Examples

+ 
PEC_sw_drainage_UK(150, Koc = 100)

+
[1] 8.076923
+
+
+
+ + + + +

Author

+ +Johannes Ranke + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/PEC_sw_drift.html b/docs/PEC_sw_drift.html new file mode 100644 index 0000000..3654d2f --- /dev/null +++ b/docs/PEC_sw_drift.html @@ -0,0 +1,134 @@ + + + + +PEC_sw_drift. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Calculate predicted environmental concentrations in surface water due to drift

+ +
+
+

Usage

+ 
PEC_sw_drift(rate, applications = 1, water_depth = 30,
+  drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau",
+  distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
+ +

Arguments

+
+
rate
+
Application rate in units specified below
+
applications
+
Number of applications for selection of drift percentile
+
water_depth
+
Depth of the water body in cm
+
drift_percentages
+
Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.
+
drift_data
+
Source of drift percentage data
+
crop
+
Crop name (use German names for JKI data), defaults to "Ackerbau"
+
distances
+
The distances in m for which to get PEC values
+
rate_units
+
Defaults to g/ha
+
PEC_units
+
Requested units for the calculated PEC. Only µg/L currently supported
+
+ +
+

Value

+ +

+The predicted concentration in surface water +

+ +
+ +
+

Description

+ +

This is a basic, vectorised form of a simple calculation of a contaminant +concentration in surface water based on complete, instantaneous mixing +with input via spray drift.

+ +
+ +

Examples

+ 
PEC_sw_drift(100)

+
       1 m        5 m       10 m       20 m 
+0.92333333 0.19000000 0.09666667 0.05000000 
+
+
+
+ + + + +

Author

+ +Johannes Ranke + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/PEC_sw_sed.html b/docs/PEC_sw_sed.html new file mode 100644 index 0000000..8161eda --- /dev/null +++ b/docs/PEC_sw_sed.html @@ -0,0 +1,131 @@ + + + + +PEC_sw_sed. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Calculate predicted environmental concentrations in sediment from surface +water concentrations

+ +
+
+

Usage

+ 
PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage",
+  sediment_depth = 5, water_depth = 30, sediment_density = 1.3,
+  PEC_sed_units = c("µg/kg", "mg/kg"))
+ +

Arguments

+
+
PEC_sw
+
Numeric vector or matrix of surface water concentrations in µg/L for +which the corresponding sediment concentration is to be estimated
+
percentage
+
The percentage in sediment, used for the percentage method
+
method
+
The method used for the calculation
+
sediment_depth
+
Depth of the sediment layer
+
water_depth
+
Depth of the water body in cm
+
sediment_density
+
The density of the sediment in L/kg (equivalent to +g/cm3)
+
PEC_sed_units
+
The units of the estimated sediment PEC value
+
+ +
+

Value

+ +

+The predicted concentration in sediment +

+ +
+ +
+

Description

+ +

The method 'percentage' is equivalent to what is used in the CRD spreadsheet +PEC calculator

+ +
+ +

Examples

+ 
PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50)

+
     1 m 
+2.130769 
+
+
+
+ + + + +

Author

+ +Johannes Ranke + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/SFO_actual_twa.html b/docs/SFO_actual_twa.html new file mode 100644 index 0000000..053457d --- /dev/null +++ b/docs/SFO_actual_twa.html @@ -0,0 +1,126 @@ + + + + +SFO_actual_twa. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Actual and maximum moving window time average concentrations for SFO kinetics

+ +
+
+

Usage

+ 
SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50,
+  100))
+ +

Arguments

+
+
DT50
+
The half-life.
+
times
+
The output times, and window sizes for time weighted average concentrations
+
+ +
+

Source

+ +

FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, + 18 December 2014, p. 251

+ +
+ +
+

Description

+ +

Actual and maximum moving window time average concentrations for SFO kinetics

+ +
+ +

Examples

+ 
SFO_actual_twa(10)

+
          actual       twa
+0   1.0000000000       NaN
+1   0.9330329915 0.9661297
+2   0.8705505633 0.9337803
+4   0.7578582833 0.8733416
+7   0.6155722067 0.7923030
+14  0.3789291416 0.6400113
+21  0.2332582479 0.5267498
+28  0.1435872944 0.4412651
+42  0.0544094102 0.3248093
+50  0.0312500000 0.2795222
+100 0.0009765625 0.1441286
+
+
+
+ + + + +

Author

+ +Johannes Ranke + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/SSLRC_mobility_classification.html b/docs/SSLRC_mobility_classification.html new file mode 100644 index 0000000..7a57c50 --- /dev/null +++ b/docs/SSLRC_mobility_classification.html @@ -0,0 +1,119 @@ + + + + +SSLRC_mobility_classification. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Determine the SSLRC mobility classification for a chemical substance from its Koc

+ +
+
+

Usage

+ 
SSLRC_mobility_classification(Koc)
+ +

Arguments

+
+
Koc
+
The sorption coefficient normalised to organic carbon in L/kg
+
+ +
+

Value

+ +

+A list containing the classification and the percentage of the + compound transported per 10 mm drain water +

+ +
+ +
+

Description

+ +

This implements the method specified in the UK data requirements handbook and was +checked against the spreadsheet published on the CRC website

+ +
+ +

Examples

+ 
SSLRC_mobility_classification(100)

+
$`Mobility classification`
+[1] "Moderately mobile"
+
+$`Percentage drained per mm of drain water`
+[1] 0.7
+
+
+
+
+ + + + +

Author

+ +Johannes Ranke + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/TOXSWA_cwa.html b/docs/TOXSWA_cwa.html new file mode 100644 index 0000000..561af84 --- /dev/null +++ b/docs/TOXSWA_cwa.html @@ -0,0 +1,179 @@ + + + + +TOXSWA_cwa. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

R6 class for holding TOXSWA cwa concentration data and associated statistics

+ +
+
+

Usage

+ 
TOXSWA_cwa
+ +
+

Format

+ +

An R6Class generator object.

+ +
+ +
+

Description

+ +

An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +Usually, an instance of this class will be generated by read.TOXSWA_cwa.

+ +
+ +
+

Fields

+ +

+ +

+
filename
Length one character vector.

+ +

basedir
Length one character vector.

+ +

segment
Length one integer, specifying for which segment the cwa data were read.

+ +

cwas
Dataframe holding the concentrations.

+ +

events
List of dataframes holding the event statistics for each threshold.

+ +

windows
Matrix of maximum time weighted average concentrations (TWAC_max) +and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) +for the requested moving window sizes in days.

+ +

+ +
+ +
+

Methods

+ +

+ +

+
get_events(threshold, total = FALSE)
+ Populate a datataframe with event information for the specified threshold value + in µg/L. If total = TRUE, the total concentration including the amount + adsorbed to suspended matter will be used. The resulting dataframe is stored in the + events field of the object. +

+ +

moving_windows(windows, total = FALSE)
+ Add to the windows field described above. + Again, if total = TRUE, the total concentration including the amount + adsorbed to suspended matter will be used. +

+ +

+ +

+ +
+ +

Examples

+ 
H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
+                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                             package = "pfm"))
+H_sw_R1_stream$get_events(c(2, 10))
+H_sw_R1_stream$moving_windows(c(7, 21))
+print(H_sw_R1_stream)

+
<TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 
+               datetime     t t_firstjan t_rel_to_max cwa_mug_per_L
+20  1978-10-01 00:00:00 0.000   273.0000      -55.333             0
+40  1978-10-01 01:00:00 0.042   273.0417      -55.291             0
+60  1978-10-01 02:00:00 0.083   273.0833      -55.250             0
+80  1978-10-01 03:00:00 0.125   273.1250      -55.208             0
+100 1978-10-01 04:00:00 0.167   273.1667      -55.166             0
+120 1978-10-01 05:00:00 0.208   273.2083      -55.125             0
+    cwa_tot_mug_per_L
+20                  0
+40                  0
+60                  0
+80                  0
+100                 0
+120                 0
+Moving window analysis
+   window  max_TWAC max_AUC_h max_AUC_d
+1  7 days 2.3926551  401.9660  16.74859
+2 21 days 0.8369248  421.8101  17.57542
+Event statistics for threshold 2 
+  t_start   cwa_max duration pre_interval     AUC_h     AUC_d
+1  44.375  4.167238    0.208       44.375  17.77202  0.740501
+2  55.042 40.584010    0.583       10.459 398.21189 16.592162
+Event statistics for threshold 10 
+  t_start  cwa_max duration pre_interval   AUC_h    AUC_d
+1  55.083 40.58401    0.459       55.083 379.433 15.80971
+
+
+
+ + + + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/css/bootstrap-responsive.css b/docs/css/bootstrap-responsive.css new file mode 100644 index 0000000..06e55c0 --- /dev/null +++ b/docs/css/bootstrap-responsive.css @@ -0,0 +1,815 @@ +/*! + * Bootstrap Responsive v2.0.4 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + */ + +.clearfix { + *zoom: 1; +} + +.clearfix:before, +.clearfix:after { + display: table; + content: ""; +} + +.clearfix:after { + clear: both; +} + +.hide-text { + font: 0/0 a; + color: transparent; + text-shadow: none; + background-color: transparent; + border: 0; +} + +.input-block-level { + display: block; + width: 100%; + min-height: 28px; + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; +} + +.hidden { + display: none; + visibility: hidden; +} + +.visible-phone { + display: none !important; +} + +.visible-tablet { + display: none !important; +} + +.hidden-desktop { + display: none !important; +} + +@media (max-width: 767px) { + .visible-phone { + display: inherit !important; + } + .hidden-phone { + display: none !important; + } + .hidden-desktop { + display: inherit !important; + } + .visible-desktop { + display: none !important; + } +} + +@media (min-width: 768px) and (max-width: 979px) { + .visible-tablet { + display: inherit !important; + } + .hidden-tablet { + display: none !important; + } + .hidden-desktop { + display: inherit !important; + } + .visible-desktop { + display: none !important ; + } +} + +@media (max-width: 480px) { + .nav-collapse { + -webkit-transform: translate3d(0, 0, 0); + } + .page-header h1 small { + display: block; + line-height: 18px; + } + input[type="checkbox"], + input[type="radio"] { + border: 1px solid #ccc; + } + .form-horizontal .control-group > label { + float: none; + width: auto; + padding-top: 0; + text-align: left; + } + .form-horizontal .controls { + margin-left: 0; + } + .form-horizontal .control-list { + padding-top: 0; + } + .form-horizontal .form-actions { + padding-right: 10px; + padding-left: 10px; + } + .modal { + position: absolute; + top: 10px; + right: 10px; + left: 10px; + width: auto; + margin: 0; + } + .modal.fade.in { + top: auto; + } + .modal-header .close { + padding: 10px; + margin: -10px; + } + .carousel-caption { + position: static; + } +} + +@media (max-width: 767px) { + body { + padding-right: 20px; + padding-left: 20px; + } + .navbar-fixed-top, + .navbar-fixed-bottom { + margin-right: -20px; + margin-left: -20px; + } + .container-fluid { + padding: 0; + } + .dl-horizontal dt { + float: none; + width: auto; + clear: none; + text-align: left; + } + .dl-horizontal dd { + margin-left: 0; + } + .container { + width: auto; + } + .row-fluid { + width: 100%; + } + .row, + .thumbnails { + margin-left: 0; + } + [class*="span"], + .row-fluid [class*="span"] { + display: block; + float: none; + width: auto; + margin-left: 0; + } + .input-large, + .input-xlarge, + .input-xxlarge, + input[class*="span"], + select[class*="span"], + textarea[class*="span"], + .uneditable-input { + display: block; + width: 100%; + min-height: 28px; + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; + } + .input-prepend input, + .input-append input, + .input-prepend input[class*="span"], + .input-append input[class*="span"] { + display: inline-block; + width: auto; + } +} + +@media (min-width: 768px) and (max-width: 979px) { + .row { + margin-left: -20px; + *zoom: 1; + } + .row:before, + .row:after { + display: table; + content: ""; + } + .row:after { + clear: both; + } + [class*="span"] { + float: left; + margin-left: 20px; + } + .container, + .navbar-fixed-top .container, + .navbar-fixed-bottom .container { + width: 724px; + } + .span12 { + width: 724px; + } + .span11 { + width: 662px; + } + .span10 { + width: 600px; + } + .span9 { + width: 538px; + } + .span8 { + width: 476px; + } + .span7 { + width: 414px; + } + .span6 { + width: 352px; + } + .span5 { + width: 290px; + } + .span4 { + width: 228px; + } + .span3 { + width: 166px; + } + .span2 { + width: 104px; + } + .span1 { + width: 42px; + } + .offset12 { + margin-left: 764px; + } + .offset11 { + margin-left: 702px; + } + .offset10 { + margin-left: 640px; + } + .offset9 { + margin-left: 578px; + } + .offset8 { + margin-left: 516px; + } + .offset7 { + margin-left: 454px; + } + .offset6 { + margin-left: 392px; + } + .offset5 { + margin-left: 330px; + } + .offset4 { + margin-left: 268px; + } + .offset3 { + margin-left: 206px; + } + .offset2 { + margin-left: 144px; + } + .offset1 { + margin-left: 82px; + } + .row-fluid { + width: 100%; + *zoom: 1; + } + .row-fluid:before, + .row-fluid:after { + display: table; + content: ""; + } + .row-fluid:after { + clear: both; + } + .row-fluid [class*="span"] { + display: block; + float: left; + width: 100%; + min-height: 28px; + margin-left: 2.762430939%; + *margin-left: 2.709239449638298%; + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; + } + .row-fluid [class*="span"]:first-child { + margin-left: 0; + } + .row-fluid .span12 { + width: 99.999999993%; + *width: 99.9468085036383%; + } + .row-fluid .span11 { + width: 91.436464082%; + *width: 91.38327259263829%; + } + .row-fluid .span10 { + width: 82.87292817100001%; + *width: 82.8197366816383%; + } + .row-fluid .span9 { + width: 74.30939226%; + *width: 74.25620077063829%; + } + .row-fluid .span8 { + width: 65.74585634900001%; + *width: 65.6926648596383%; + } + .row-fluid .span7 { + width: 57.182320438000005%; + *width: 57.129128948638304%; + } + .row-fluid .span6 { + width: 48.618784527%; + *width: 48.5655930376383%; + } + .row-fluid .span5 { + width: 40.055248616%; + *width: 40.0020571266383%; + } + .row-fluid .span4 { + width: 31.491712705%; + *width: 31.4385212156383%; + } + .row-fluid .span3 { + width: 22.928176794%; + *width: 22.874985304638297%; + } + .row-fluid .span2 { + width: 14.364640883%; + *width: 14.311449393638298%; + } + .row-fluid .span1 { + width: 5.801104972%; + *width: 5.747913482638298%; + } + input, + textarea, + .uneditable-input { + margin-left: 0; + } + input.span12, + textarea.span12, + .uneditable-input.span12 { + width: 714px; + } + input.span11, + textarea.span11, + .uneditable-input.span11 { + width: 652px; + } + input.span10, + textarea.span10, + .uneditable-input.span10 { + width: 590px; + } + input.span9, + textarea.span9, + .uneditable-input.span9 { + width: 528px; + } + input.span8, + textarea.span8, + .uneditable-input.span8 { + width: 466px; + } + input.span7, + textarea.span7, + .uneditable-input.span7 { + width: 404px; + } + input.span6, + textarea.span6, + .uneditable-input.span6 { + width: 342px; + } + input.span5, + textarea.span5, + .uneditable-input.span5 { + width: 280px; + } + input.span4, + textarea.span4, + .uneditable-input.span4 { + width: 218px; + } + input.span3, + textarea.span3, + .uneditable-input.span3 { + width: 156px; + } + input.span2, + textarea.span2, + .uneditable-input.span2 { + width: 94px; + } + input.span1, + textarea.span1, + .uneditable-input.span1 { + width: 32px; + } +} + +@media (min-width: 1200px) { + .row { + margin-left: -30px; + *zoom: 1; + } + .row:before, + .row:after { + display: table; + content: ""; + } + .row:after { + clear: both; + } + [class*="span"] { + float: left; + margin-left: 30px; + } + .container, + .navbar-fixed-top .container, + .navbar-fixed-bottom .container { + width: 1170px; + } + .span12 { + width: 1170px; + } + .span11 { + width: 1070px; + } + .span10 { + width: 970px; + } + .span9 { + width: 870px; + } + .span8 { + width: 770px; + } + .span7 { + width: 670px; + } + .span6 { + width: 570px; + } + .span5 { + width: 470px; + } + .span4 { + width: 370px; + } + .span3 { + width: 270px; + } + .span2 { + width: 170px; + } + .span1 { + width: 70px; + } + .offset12 { + margin-left: 1230px; + } + .offset11 { + margin-left: 1130px; + } + .offset10 { + margin-left: 1030px; + } + .offset9 { + margin-left: 930px; + } + .offset8 { + margin-left: 830px; + } + .offset7 { + margin-left: 730px; + } + .offset6 { + margin-left: 630px; + } + .offset5 { + margin-left: 530px; + } + .offset4 { + margin-left: 430px; + } + .offset3 { + margin-left: 330px; + } + .offset2 { + margin-left: 230px; + } + .offset1 { + margin-left: 130px; + } + .row-fluid { + width: 100%; + *zoom: 1; + } + .row-fluid:before, + .row-fluid:after { + display: table; + content: ""; + } + .row-fluid:after { + clear: both; + } + .row-fluid [class*="span"] { + display: block; + float: left; + width: 100%; + min-height: 28px; + margin-left: 2.564102564%; + *margin-left: 2.510911074638298%; + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; + } + .row-fluid [class*="span"]:first-child { + margin-left: 0; + } + .row-fluid .span12 { + width: 100%; + *width: 99.94680851063829%; + } + .row-fluid .span11 { + width: 91.45299145300001%; + *width: 91.3997999636383%; + } + .row-fluid .span10 { + width: 82.905982906%; + *width: 82.8527914166383%; + } + .row-fluid .span9 { + width: 74.358974359%; + *width: 74.30578286963829%; + } + .row-fluid .span8 { + width: 65.81196581200001%; + *width: 65.7587743226383%; + } + .row-fluid .span7 { + width: 57.264957265%; + *width: 57.2117657756383%; + } + .row-fluid .span6 { + width: 48.717948718%; + *width: 48.6647572286383%; + } + .row-fluid .span5 { + width: 40.170940171000005%; + *width: 40.117748681638304%; + } + .row-fluid .span4 { + width: 31.623931624%; + *width: 31.5707401346383%; + } + .row-fluid .span3 { + width: 23.076923077%; + *width: 23.0237315876383%; + } + .row-fluid .span2 { + width: 14.529914530000001%; + *width: 14.4767230406383%; + } + .row-fluid .span1 { + width: 5.982905983%; + *width: 5.929714493638298%; + } + input, + textarea, + .uneditable-input { + margin-left: 0; + } + input.span12, + textarea.span12, + .uneditable-input.span12 { + width: 1160px; + } + input.span11, + textarea.span11, + .uneditable-input.span11 { + width: 1060px; + } + input.span10, + textarea.span10, + .uneditable-input.span10 { + width: 960px; + } + input.span9, + textarea.span9, + .uneditable-input.span9 { + width: 860px; + } + input.span8, + textarea.span8, + .uneditable-input.span8 { + width: 760px; + } + input.span7, + textarea.span7, + .uneditable-input.span7 { + width: 660px; + } + input.span6, + textarea.span6, + .uneditable-input.span6 { + width: 560px; + } + input.span5, + textarea.span5, + .uneditable-input.span5 { + width: 460px; + } + input.span4, + textarea.span4, + .uneditable-input.span4 { + width: 360px; + } + input.span3, + textarea.span3, + .uneditable-input.span3 { + width: 260px; + } + input.span2, + textarea.span2, + .uneditable-input.span2 { + width: 160px; + } + input.span1, + textarea.span1, + .uneditable-input.span1 { + width: 60px; + } + .thumbnails { + margin-left: -30px; + } + .thumbnails > li { + margin-left: 30px; + } + .row-fluid .thumbnails { + margin-left: 0; + } +} + +@media (max-width: 979px) { + body { + padding-top: 0; + } + .navbar-fixed-top, + .navbar-fixed-bottom { + position: static; + } + .navbar-fixed-top { + margin-bottom: 18px; + } + .navbar-fixed-bottom { + margin-top: 18px; + } + .navbar-fixed-top .navbar-inner, + .navbar-fixed-bottom .navbar-inner { + padding: 5px; + } + .navbar .container { + width: auto; + padding: 0; + } + .navbar .brand { + padding-right: 10px; + padding-left: 10px; + margin: 0 0 0 -5px; + } + .nav-collapse { + clear: both; + } + .nav-collapse .nav { + float: none; + margin: 0 0 9px; + } + .nav-collapse .nav > li { + float: none; + } + .nav-collapse .nav > li > a { + margin-bottom: 2px; + } + .nav-collapse .nav > .divider-vertical { + display: none; + } + .nav-collapse .nav .nav-header { + color: #999999; + text-shadow: none; + } + .nav-collapse .nav > li > a, + .nav-collapse .dropdown-menu a { + padding: 6px 15px; + font-weight: bold; + color: #999999; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + } + .nav-collapse .btn { + padding: 4px 10px 4px; + font-weight: normal; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + } + .nav-collapse .dropdown-menu li + li a { + margin-bottom: 2px; + } + .nav-collapse .nav > li > a:hover, + .nav-collapse .dropdown-menu a:hover { + background-color: #222222; + } + .nav-collapse.in .btn-group { + padding: 0; + margin-top: 5px; + } + .nav-collapse .dropdown-menu { + position: static; + top: auto; + left: auto; + display: block; + float: none; + max-width: none; + padding: 0; + margin: 0 15px; + background-color: transparent; + border: none; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; + -webkit-box-shadow: none; + -moz-box-shadow: none; + box-shadow: none; + } + .nav-collapse .dropdown-menu:before, + .nav-collapse .dropdown-menu:after { + display: none; + } + .nav-collapse .dropdown-menu .divider { + display: none; + } + .nav-collapse .navbar-form, + .nav-collapse .navbar-search { + float: none; + padding: 9px 15px; + margin: 9px 0; + border-top: 1px solid #222222; + border-bottom: 1px solid #222222; + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1); + -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1); + } + .navbar .nav-collapse .nav.pull-right { + float: none; + margin-left: 0; + } + .nav-collapse, + .nav-collapse.collapse { + height: 0; + overflow: hidden; + } + .navbar .btn-navbar { + display: block; + } + .navbar-static .navbar-inner { + padding-right: 10px; + padding-left: 10px; + } +} + +@media (min-width: 980px) { + .nav-collapse.collapse { + height: auto !important; + overflow: visible !important; + } +} diff --git a/docs/css/bootstrap-responsive.min.css b/docs/css/bootstrap-responsive.min.css new file mode 100644 index 0000000..1f55036 --- /dev/null +++ b/docs/css/bootstrap-responsive.min.css @@ -0,0 +1,9 @@ +/*! + * Bootstrap Responsive v2.0.4 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + */.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;content:""}.clearfix:after{clear:both}.hide-text{font:0/0 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18px; + color: #555555; +} + +input, +textarea { + width: 210px; +} + +textarea { + height: auto; +} + +textarea, +input[type="text"], +input[type="password"], +input[type="datetime"], +input[type="datetime-local"], +input[type="date"], +input[type="month"], +input[type="time"], +input[type="week"], +input[type="number"], +input[type="email"], +input[type="url"], +input[type="search"], +input[type="tel"], +input[type="color"], +.uneditable-input { + background-color: #ffffff; + border: 1px solid #cccccc; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + -webkit-transition: border linear 0.2s, box-shadow linear 0.2s; + -moz-transition: border linear 0.2s, box-shadow linear 0.2s; + -ms-transition: border linear 0.2s, box-shadow linear 0.2s; + -o-transition: border linear 0.2s, box-shadow linear 0.2s; + transition: border linear 0.2s, box-shadow linear 0.2s; +} + +textarea:focus, +input[type="text"]:focus, +input[type="password"]:focus, +input[type="datetime"]:focus, +input[type="datetime-local"]:focus, +input[type="date"]:focus, +input[type="month"]:focus, +input[type="time"]:focus, +input[type="week"]:focus, +input[type="number"]:focus, +input[type="email"]:focus, +input[type="url"]:focus, +input[type="search"]:focus, +input[type="tel"]:focus, +input[type="color"]:focus, +.uneditable-input:focus { + border-color: rgba(82, 168, 236, 0.8); + outline: 0; + outline: thin dotted \9; + /* IE6-9 */ + + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6); + -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6); +} + +input[type="radio"], +input[type="checkbox"] { + margin: 3px 0; + *margin-top: 0; + /* IE7 */ + + line-height: normal; + cursor: pointer; +} + +input[type="submit"], +input[type="reset"], +input[type="button"], +input[type="radio"], +input[type="checkbox"] { + width: auto; +} + +.uneditable-textarea { + width: auto; + height: auto; +} + +select, +input[type="file"] { + height: 28px; + /* In IE7, the height of the select element cannot be changed by height, only font-size */ + + *margin-top: 4px; + /* For IE7, add top margin to align select with labels */ + + line-height: 28px; +} + +select { + width: 220px; + border: 1px solid #bbb; +} + +select[multiple], +select[size] { + height: auto; +} + +select:focus, +input[type="file"]:focus, +input[type="radio"]:focus, +input[type="checkbox"]:focus { + outline: thin dotted #333; + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} + +.radio, +.checkbox { + min-height: 18px; + padding-left: 18px; +} + +.radio input[type="radio"], +.checkbox input[type="checkbox"] { + float: left; + margin-left: -18px; +} + +.controls > .radio:first-child, +.controls > .checkbox:first-child { + padding-top: 5px; +} + +.radio.inline, +.checkbox.inline { + display: inline-block; + padding-top: 5px; + margin-bottom: 0; + vertical-align: middle; +} + +.radio.inline + .radio.inline, +.checkbox.inline + .checkbox.inline { + margin-left: 10px; +} + +.input-mini { + width: 60px; +} + +.input-small { + width: 90px; +} + +.input-medium { + width: 150px; +} + +.input-large { + width: 210px; +} + +.input-xlarge { + width: 270px; +} + +.input-xxlarge { + width: 530px; +} + +input[class*="span"], +select[class*="span"], +textarea[class*="span"], +.uneditable-input[class*="span"], +.row-fluid input[class*="span"], +.row-fluid select[class*="span"], +.row-fluid textarea[class*="span"], +.row-fluid .uneditable-input[class*="span"] { + float: none; + margin-left: 0; +} + +.input-append input[class*="span"], +.input-append .uneditable-input[class*="span"], +.input-prepend input[class*="span"], +.input-prepend .uneditable-input[class*="span"], +.row-fluid .input-prepend [class*="span"], +.row-fluid .input-append [class*="span"] { + display: inline-block; +} + +input, +textarea, +.uneditable-input { + margin-left: 0; +} + +input.span12, +textarea.span12, +.uneditable-input.span12 { + width: 930px; +} + +input.span11, +textarea.span11, +.uneditable-input.span11 { + width: 850px; +} + +input.span10, +textarea.span10, +.uneditable-input.span10 { + width: 770px; +} + +input.span9, +textarea.span9, +.uneditable-input.span9 { + width: 690px; +} + +input.span8, +textarea.span8, +.uneditable-input.span8 { + width: 610px; +} + +input.span7, +textarea.span7, +.uneditable-input.span7 { + width: 530px; +} + +input.span6, +textarea.span6, +.uneditable-input.span6 { + width: 450px; +} + +input.span5, +textarea.span5, +.uneditable-input.span5 { + width: 370px; +} + +input.span4, +textarea.span4, +.uneditable-input.span4 { + width: 290px; +} + +input.span3, +textarea.span3, +.uneditable-input.span3 { + width: 210px; +} + +input.span2, +textarea.span2, +.uneditable-input.span2 { + width: 130px; +} + +input.span1, +textarea.span1, +.uneditable-input.span1 { + width: 50px; +} + +input[disabled], +select[disabled], +textarea[disabled], +input[readonly], +select[readonly], +textarea[readonly] { + cursor: not-allowed; + background-color: #eeeeee; + border-color: #ddd; +} + +input[type="radio"][disabled], +input[type="checkbox"][disabled], +input[type="radio"][readonly], +input[type="checkbox"][readonly] { + background-color: transparent; +} + +.control-group.warning > label, +.control-group.warning .help-block, +.control-group.warning .help-inline { + color: #c09853; +} + +.control-group.warning .checkbox, +.control-group.warning .radio, +.control-group.warning input, +.control-group.warning select, +.control-group.warning textarea { + color: #c09853; + border-color: #c09853; +} + +.control-group.warning .checkbox:focus, +.control-group.warning .radio:focus, +.control-group.warning input:focus, +.control-group.warning select:focus, +.control-group.warning textarea:focus { + border-color: #a47e3c; + -webkit-box-shadow: 0 0 6px #dbc59e; + -moz-box-shadow: 0 0 6px #dbc59e; + box-shadow: 0 0 6px #dbc59e; +} + +.control-group.warning .input-prepend .add-on, +.control-group.warning .input-append .add-on { + color: #c09853; + background-color: #fcf8e3; + border-color: #c09853; +} + +.control-group.error > label, +.control-group.error .help-block, +.control-group.error .help-inline { + color: #b94a48; +} + +.control-group.error .checkbox, +.control-group.error .radio, +.control-group.error input, +.control-group.error select, +.control-group.error textarea { + color: #b94a48; + border-color: #b94a48; +} + +.control-group.error .checkbox:focus, +.control-group.error .radio:focus, +.control-group.error input:focus, +.control-group.error select:focus, +.control-group.error textarea:focus { + border-color: #953b39; + -webkit-box-shadow: 0 0 6px #d59392; + -moz-box-shadow: 0 0 6px #d59392; + box-shadow: 0 0 6px #d59392; +} + +.control-group.error .input-prepend .add-on, +.control-group.error .input-append .add-on { + color: #b94a48; + background-color: #f2dede; + border-color: #b94a48; +} + +.control-group.success > label, +.control-group.success .help-block, +.control-group.success .help-inline { + color: #468847; +} + +.control-group.success .checkbox, +.control-group.success .radio, +.control-group.success input, +.control-group.success select, +.control-group.success textarea { + color: #468847; + border-color: #468847; +} + +.control-group.success .checkbox:focus, +.control-group.success .radio:focus, +.control-group.success input:focus, +.control-group.success select:focus, +.control-group.success textarea:focus { + border-color: #356635; + -webkit-box-shadow: 0 0 6px #7aba7b; + -moz-box-shadow: 0 0 6px #7aba7b; + box-shadow: 0 0 6px #7aba7b; +} + +.control-group.success .input-prepend .add-on, +.control-group.success .input-append .add-on { + color: #468847; + background-color: #dff0d8; + border-color: #468847; +} + +input:focus:required:invalid, +textarea:focus:required:invalid, +select:focus:required:invalid { + color: #b94a48; + border-color: #ee5f5b; +} + +input:focus:required:invalid:focus, +textarea:focus:required:invalid:focus, +select:focus:required:invalid:focus { + border-color: #e9322d; + -webkit-box-shadow: 0 0 6px #f8b9b7; + -moz-box-shadow: 0 0 6px #f8b9b7; + box-shadow: 0 0 6px #f8b9b7; +} + +.form-actions { + padding: 17px 20px 18px; + margin-top: 18px; + margin-bottom: 18px; + background-color: #f5f5f5; + border-top: 1px solid #e5e5e5; + *zoom: 1; +} + +.form-actions:before, +.form-actions:after { + display: table; + content: ""; +} + +.form-actions:after { + clear: both; +} + +.uneditable-input { + overflow: hidden; + white-space: nowrap; + cursor: not-allowed; + background-color: #ffffff; + border-color: #eee; + -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.025); + -moz-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.025); + box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.025); +} + +:-moz-placeholder { + color: #999999; +} + +:-ms-input-placeholder { + color: #999999; +} + +::-webkit-input-placeholder { + color: #999999; +} + +.help-block, +.help-inline { + color: #555555; +} + +.help-block { + display: block; + margin-bottom: 9px; +} + +.help-inline { + display: inline-block; + *display: inline; + padding-left: 5px; + vertical-align: middle; + *zoom: 1; +} + +.input-prepend, +.input-append { + margin-bottom: 5px; +} + +.input-prepend input, +.input-append input, +.input-prepend select, +.input-append select, +.input-prepend .uneditable-input, +.input-append .uneditable-input { + position: relative; + margin-bottom: 0; + *margin-left: 0; + vertical-align: middle; + -webkit-border-radius: 0 3px 3px 0; + -moz-border-radius: 0 3px 3px 0; + border-radius: 0 3px 3px 0; +} + +.input-prepend input:focus, +.input-append input:focus, +.input-prepend select:focus, +.input-append select:focus, +.input-prepend .uneditable-input:focus, +.input-append .uneditable-input:focus { + z-index: 2; +} + +.input-prepend .uneditable-input, +.input-append .uneditable-input { + border-left-color: #ccc; +} + +.input-prepend .add-on, +.input-append .add-on { + display: inline-block; + width: auto; + height: 18px; + min-width: 16px; + padding: 4px 5px; + font-weight: normal; + line-height: 18px; + text-align: center; + text-shadow: 0 1px 0 #ffffff; + vertical-align: middle; + background-color: #eeeeee; + border: 1px solid #ccc; +} + +.input-prepend .add-on, +.input-append .add-on, +.input-prepend .btn, +.input-append .btn { + margin-left: -1px; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.input-prepend .active, +.input-append .active { + background-color: #a9dba9; + border-color: #46a546; +} + +.input-prepend .add-on, +.input-prepend .btn { + margin-right: -1px; +} + +.input-prepend .add-on:first-child, +.input-prepend .btn:first-child { + -webkit-border-radius: 3px 0 0 3px; + -moz-border-radius: 3px 0 0 3px; + border-radius: 3px 0 0 3px; +} + +.input-append input, +.input-append select, +.input-append .uneditable-input { + -webkit-border-radius: 3px 0 0 3px; + -moz-border-radius: 3px 0 0 3px; + border-radius: 3px 0 0 3px; +} + +.input-append .uneditable-input { + border-right-color: #ccc; + border-left-color: #eee; +} + +.input-append .add-on:last-child, +.input-append .btn:last-child { + -webkit-border-radius: 0 3px 3px 0; + -moz-border-radius: 0 3px 3px 0; + border-radius: 0 3px 3px 0; +} + +.input-prepend.input-append input, +.input-prepend.input-append select, +.input-prepend.input-append .uneditable-input { + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.input-prepend.input-append .add-on:first-child, +.input-prepend.input-append .btn:first-child { + margin-right: -1px; + -webkit-border-radius: 3px 0 0 3px; + -moz-border-radius: 3px 0 0 3px; + border-radius: 3px 0 0 3px; +} + +.input-prepend.input-append .add-on:last-child, +.input-prepend.input-append .btn:last-child { + margin-left: -1px; + -webkit-border-radius: 0 3px 3px 0; + -moz-border-radius: 0 3px 3px 0; + border-radius: 0 3px 3px 0; +} + +.search-query { + padding-right: 14px; + padding-right: 4px \9; + padding-left: 14px; + padding-left: 4px \9; + /* IE7-8 doesn't have border-radius, so don't indent the padding */ + + margin-bottom: 0; + -webkit-border-radius: 14px; + -moz-border-radius: 14px; + border-radius: 14px; +} + +.form-search input, +.form-inline input, +.form-horizontal input, +.form-search textarea, +.form-inline textarea, +.form-horizontal textarea, +.form-search select, +.form-inline select, +.form-horizontal select, +.form-search .help-inline, +.form-inline .help-inline, +.form-horizontal .help-inline, +.form-search .uneditable-input, +.form-inline .uneditable-input, +.form-horizontal .uneditable-input, +.form-search .input-prepend, +.form-inline .input-prepend, +.form-horizontal .input-prepend, +.form-search .input-append, +.form-inline .input-append, +.form-horizontal .input-append { + display: inline-block; + *display: inline; + margin-bottom: 0; + *zoom: 1; +} + +.form-search .hide, +.form-inline .hide, +.form-horizontal .hide { + display: none; +} + +.form-search label, +.form-inline label { + display: inline-block; +} + +.form-search .input-append, +.form-inline .input-append, +.form-search .input-prepend, +.form-inline .input-prepend { + margin-bottom: 0; +} + +.form-search .radio, +.form-search .checkbox, +.form-inline .radio, +.form-inline .checkbox { + padding-left: 0; + margin-bottom: 0; + vertical-align: middle; +} + +.form-search .radio input[type="radio"], +.form-search .checkbox input[type="checkbox"], +.form-inline .radio input[type="radio"], +.form-inline .checkbox input[type="checkbox"] { + float: left; + margin-right: 3px; + margin-left: 0; +} + +.control-group { + margin-bottom: 9px; +} + +legend + .control-group { + margin-top: 18px; + -webkit-margin-top-collapse: separate; +} + +.form-horizontal .control-group { + margin-bottom: 18px; + *zoom: 1; +} + +.form-horizontal .control-group:before, +.form-horizontal .control-group:after { + display: table; + content: ""; +} + +.form-horizontal .control-group:after { + clear: both; +} + +.form-horizontal .control-label { + float: left; + width: 140px; + padding-top: 5px; + text-align: right; +} + +.form-horizontal .controls { + *display: inline-block; + *padding-left: 20px; + margin-left: 160px; + *margin-left: 0; +} + +.form-horizontal .controls:first-child { + *padding-left: 160px; +} + +.form-horizontal .help-block { + margin-top: 9px; + margin-bottom: 0; +} + +.form-horizontal .form-actions { + padding-left: 160px; +} + +table { + max-width: 100%; + background-color: transparent; + border-collapse: collapse; + border-spacing: 0; +} + +.table { + width: 100%; + margin-bottom: 18px; +} + +.table th, +.table td { + padding: 8px; + line-height: 18px; + text-align: left; + vertical-align: top; + border-top: 1px solid #dddddd; +} + +.table th { + font-weight: bold; +} + +.table thead th { + vertical-align: bottom; +} + +.table caption + thead tr:first-child th, +.table caption + thead tr:first-child td, +.table colgroup + thead tr:first-child th, +.table colgroup + thead tr:first-child td, +.table thead:first-child tr:first-child th, +.table thead:first-child tr:first-child td { + border-top: 0; +} + +.table tbody + tbody { + border-top: 2px solid #dddddd; +} + +.table-condensed th, +.table-condensed td { + padding: 4px 5px; +} + +.table-bordered { + border: 1px solid #dddddd; + border-collapse: separate; + *border-collapse: collapsed; + border-left: 0; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.table-bordered th, +.table-bordered td { + border-left: 1px solid #dddddd; +} + +.table-bordered caption + thead tr:first-child th, +.table-bordered caption + tbody tr:first-child th, +.table-bordered caption + tbody tr:first-child td, +.table-bordered colgroup + thead tr:first-child th, +.table-bordered colgroup + tbody tr:first-child th, +.table-bordered colgroup + tbody tr:first-child td, +.table-bordered thead:first-child tr:first-child th, +.table-bordered tbody:first-child tr:first-child th, +.table-bordered tbody:first-child tr:first-child td { + border-top: 0; +} + +.table-bordered thead:first-child tr:first-child th:first-child, +.table-bordered tbody:first-child tr:first-child td:first-child { + -webkit-border-top-left-radius: 4px; + border-top-left-radius: 4px; + -moz-border-radius-topleft: 4px; +} + +.table-bordered thead:first-child tr:first-child th:last-child, +.table-bordered tbody:first-child tr:first-child td:last-child { + -webkit-border-top-right-radius: 4px; + border-top-right-radius: 4px; + -moz-border-radius-topright: 4px; +} + +.table-bordered thead:last-child tr:last-child th:first-child, +.table-bordered tbody:last-child tr:last-child td:first-child { + -webkit-border-radius: 0 0 0 4px; + -moz-border-radius: 0 0 0 4px; + border-radius: 0 0 0 4px; + -webkit-border-bottom-left-radius: 4px; + border-bottom-left-radius: 4px; + -moz-border-radius-bottomleft: 4px; +} + +.table-bordered thead:last-child tr:last-child th:last-child, +.table-bordered tbody:last-child tr:last-child td:last-child { + -webkit-border-bottom-right-radius: 4px; + border-bottom-right-radius: 4px; + -moz-border-radius-bottomright: 4px; +} + +.table-striped tbody tr:nth-child(odd) td, +.table-striped tbody tr:nth-child(odd) th { + background-color: #f9f9f9; +} + +.table tbody tr:hover td, +.table tbody tr:hover th { + background-color: #f5f5f5; +} + +table .span1 { + float: none; + width: 44px; + margin-left: 0; +} + +table .span2 { + float: none; + width: 124px; + margin-left: 0; +} + +table .span3 { + float: none; + width: 204px; + margin-left: 0; +} + +table .span4 { + float: none; + width: 284px; + margin-left: 0; +} + +table .span5 { + float: none; + width: 364px; + margin-left: 0; +} + +table .span6 { + float: none; + width: 444px; + margin-left: 0; +} + +table .span7 { + float: none; + width: 524px; + margin-left: 0; +} + +table .span8 { + float: none; + width: 604px; + margin-left: 0; +} + +table .span9 { + float: none; + width: 684px; + margin-left: 0; +} + +table .span10 { + float: none; + width: 764px; + margin-left: 0; +} + +table .span11 { + float: none; + width: 844px; + margin-left: 0; +} + +table .span12 { + float: none; + width: 924px; + margin-left: 0; +} + +table .span13 { + float: none; + width: 1004px; + margin-left: 0; +} + +table .span14 { + float: none; + width: 1084px; + margin-left: 0; +} + +table .span15 { + float: none; + width: 1164px; + margin-left: 0; +} + +table .span16 { + float: none; + width: 1244px; + margin-left: 0; +} + +table .span17 { + float: none; + width: 1324px; + margin-left: 0; +} + +table .span18 { + float: none; + width: 1404px; + margin-left: 0; +} + +table .span19 { + float: none; + width: 1484px; + margin-left: 0; +} + +table .span20 { + float: none; + width: 1564px; + margin-left: 0; +} + +table .span21 { + float: none; + width: 1644px; + margin-left: 0; +} + +table .span22 { + float: none; + width: 1724px; + margin-left: 0; +} + +table .span23 { + float: none; + width: 1804px; + margin-left: 0; +} + +table .span24 { + float: none; + width: 1884px; + margin-left: 0; +} + +[class^="icon-"], +[class*=" icon-"] { + display: inline-block; + width: 14px; + height: 14px; + *margin-right: .3em; + line-height: 14px; + vertical-align: text-top; + background-image: url("../img/glyphicons-halflings.png"); + background-position: 14px 14px; + background-repeat: no-repeat; +} + +[class^="icon-"]:last-child, +[class*=" icon-"]:last-child { + *margin-left: 0; +} + +.icon-white { + background-image: url("../img/glyphicons-halflings-white.png"); +} + +.icon-glass { + background-position: 0 0; +} + +.icon-music { + background-position: -24px 0; +} + +.icon-search { + background-position: -48px 0; +} + +.icon-envelope { + background-position: -72px 0; +} + +.icon-heart { + background-position: -96px 0; +} + +.icon-star { + background-position: -120px 0; +} + +.icon-star-empty { + background-position: -144px 0; +} + +.icon-user { + background-position: -168px 0; +} + +.icon-film { + background-position: -192px 0; +} + +.icon-th-large { + background-position: -216px 0; +} + +.icon-th { + background-position: -240px 0; +} + +.icon-th-list { + background-position: -264px 0; +} + +.icon-ok { + background-position: -288px 0; +} + +.icon-remove { + background-position: -312px 0; +} + +.icon-zoom-in { + background-position: -336px 0; +} + +.icon-zoom-out { + background-position: -360px 0; +} + +.icon-off { + background-position: -384px 0; +} + +.icon-signal { + background-position: -408px 0; +} + +.icon-cog { + background-position: -432px 0; +} + +.icon-trash { + background-position: -456px 0; +} + +.icon-home { + background-position: 0 -24px; +} + +.icon-file { + background-position: -24px -24px; +} + +.icon-time { + background-position: -48px -24px; +} + +.icon-road { + background-position: -72px -24px; +} + +.icon-download-alt { + background-position: -96px -24px; +} + +.icon-download { + background-position: -120px -24px; +} + +.icon-upload { + background-position: -144px -24px; +} + +.icon-inbox { + background-position: -168px -24px; +} + +.icon-play-circle { + background-position: -192px -24px; +} + +.icon-repeat { + background-position: -216px -24px; +} + +.icon-refresh { + background-position: -240px -24px; +} + +.icon-list-alt { + background-position: -264px -24px; +} + +.icon-lock { + background-position: -287px -24px; +} + +.icon-flag { + background-position: -312px -24px; +} + +.icon-headphones { + background-position: -336px -24px; +} + +.icon-volume-off { + background-position: -360px -24px; +} + +.icon-volume-down { + background-position: -384px -24px; +} + +.icon-volume-up { + background-position: -408px -24px; +} + +.icon-qrcode { + background-position: -432px -24px; +} + +.icon-barcode { + background-position: -456px -24px; +} + +.icon-tag { + background-position: 0 -48px; +} + +.icon-tags { + background-position: -25px -48px; +} + +.icon-book { + background-position: -48px -48px; +} + +.icon-bookmark { + background-position: -72px -48px; +} + +.icon-print { + background-position: -96px -48px; +} + +.icon-camera { + background-position: -120px -48px; +} + +.icon-font { + background-position: -144px -48px; +} + +.icon-bold { + background-position: -167px -48px; +} + +.icon-italic { + background-position: -192px -48px; +} + +.icon-text-height { + background-position: -216px -48px; +} + +.icon-text-width { + background-position: -240px -48px; +} + +.icon-align-left { + background-position: -264px -48px; +} + +.icon-align-center { + background-position: -288px -48px; +} + +.icon-align-right { + background-position: -312px -48px; +} + +.icon-align-justify { + background-position: -336px -48px; +} + +.icon-list { + background-position: -360px -48px; +} + +.icon-indent-left { + background-position: -384px -48px; +} + +.icon-indent-right { + background-position: -408px -48px; +} + +.icon-facetime-video { + background-position: -432px -48px; +} + +.icon-picture { + background-position: -456px -48px; +} + +.icon-pencil { + background-position: 0 -72px; +} + +.icon-map-marker { + background-position: -24px -72px; +} + +.icon-adjust { + background-position: -48px -72px; +} + +.icon-tint { + background-position: -72px -72px; +} + +.icon-edit { + background-position: -96px -72px; +} + +.icon-share { + background-position: -120px -72px; +} + +.icon-check { + background-position: -144px -72px; +} + +.icon-move { + background-position: -168px -72px; +} + +.icon-step-backward { + background-position: -192px -72px; +} + +.icon-fast-backward { + background-position: -216px -72px; +} + +.icon-backward { + background-position: -240px -72px; +} + +.icon-play { + background-position: -264px -72px; +} + +.icon-pause { + background-position: -288px -72px; +} + +.icon-stop { + background-position: -312px -72px; +} + +.icon-forward { + background-position: -336px -72px; +} + +.icon-fast-forward { + background-position: -360px -72px; +} + +.icon-step-forward { + background-position: -384px -72px; +} + +.icon-eject { + background-position: -408px -72px; +} + +.icon-chevron-left { + background-position: -432px -72px; +} + +.icon-chevron-right { + background-position: -456px -72px; +} + +.icon-plus-sign { + background-position: 0 -96px; +} + +.icon-minus-sign { + background-position: -24px -96px; +} + +.icon-remove-sign { + background-position: -48px -96px; +} + +.icon-ok-sign { + background-position: -72px -96px; +} + +.icon-question-sign { + background-position: -96px -96px; +} + +.icon-info-sign { + background-position: -120px -96px; +} + +.icon-screenshot { + background-position: -144px -96px; +} + +.icon-remove-circle { + background-position: -168px -96px; +} + +.icon-ok-circle { + background-position: -192px -96px; +} + +.icon-ban-circle { + background-position: -216px -96px; +} + +.icon-arrow-left { + background-position: -240px -96px; +} + +.icon-arrow-right { + background-position: -264px -96px; +} + +.icon-arrow-up { + background-position: -289px -96px; +} + +.icon-arrow-down { + background-position: -312px -96px; +} + +.icon-share-alt { + background-position: -336px -96px; +} + +.icon-resize-full { + background-position: -360px -96px; +} + +.icon-resize-small { + background-position: -384px -96px; +} + +.icon-plus { + background-position: -408px -96px; +} + +.icon-minus { + background-position: -433px -96px; +} + +.icon-asterisk { + background-position: -456px -96px; +} + +.icon-exclamation-sign { + background-position: 0 -120px; +} + +.icon-gift { + background-position: -24px -120px; +} + +.icon-leaf { + background-position: -48px -120px; +} + +.icon-fire { + background-position: -72px -120px; +} + +.icon-eye-open { + background-position: -96px -120px; +} + +.icon-eye-close { + background-position: -120px -120px; +} + +.icon-warning-sign { + background-position: -144px -120px; +} + +.icon-plane { + background-position: -168px -120px; +} + +.icon-calendar { + background-position: -192px -120px; +} + +.icon-random { + background-position: -216px -120px; +} + +.icon-comment { + background-position: -240px -120px; +} + +.icon-magnet { + background-position: -264px -120px; +} + +.icon-chevron-up { + background-position: -288px -120px; +} + +.icon-chevron-down { + background-position: -313px -119px; +} + +.icon-retweet { + background-position: -336px -120px; +} + +.icon-shopping-cart { + background-position: -360px -120px; +} + +.icon-folder-close { + background-position: -384px -120px; +} + +.icon-folder-open { + background-position: -408px -120px; +} + +.icon-resize-vertical { + background-position: -432px -119px; +} + +.icon-resize-horizontal { + background-position: -456px -118px; +} + +.icon-hdd { + background-position: 0 -144px; +} + +.icon-bullhorn { + background-position: -24px -144px; +} + +.icon-bell { + background-position: -48px -144px; +} + +.icon-certificate { + background-position: -72px -144px; +} + +.icon-thumbs-up { + background-position: -96px -144px; +} + +.icon-thumbs-down { + background-position: -120px -144px; +} + +.icon-hand-right { + background-position: -144px -144px; +} + +.icon-hand-left { + background-position: -168px -144px; +} + +.icon-hand-up { + background-position: -192px -144px; +} + +.icon-hand-down { + background-position: -216px -144px; +} + +.icon-circle-arrow-right { + background-position: -240px -144px; +} + +.icon-circle-arrow-left { + background-position: -264px -144px; +} + +.icon-circle-arrow-up { + background-position: -288px -144px; +} + +.icon-circle-arrow-down { + background-position: -312px -144px; +} + +.icon-globe { + background-position: -336px -144px; +} + +.icon-wrench { + background-position: -360px -144px; +} + +.icon-tasks { + background-position: -384px -144px; +} + +.icon-filter { + background-position: -408px -144px; +} + +.icon-briefcase { + background-position: -432px -144px; +} + +.icon-fullscreen { + background-position: -456px -144px; +} + +.dropup, +.dropdown { + position: relative; +} + +.dropdown-toggle { + *margin-bottom: -3px; +} + +.dropdown-toggle:active, +.open .dropdown-toggle { + outline: 0; +} + +.caret { + display: inline-block; + width: 0; + height: 0; + vertical-align: top; + border-top: 4px solid #000000; + border-right: 4px solid transparent; + border-left: 4px solid transparent; + content: ""; + opacity: 0.3; + filter: alpha(opacity=30); +} + +.dropdown .caret { + margin-top: 8px; + margin-left: 2px; +} + +.dropdown:hover .caret, +.open .caret { + opacity: 1; + filter: alpha(opacity=100); +} + +.dropdown-menu { + position: absolute; + top: 100%; + left: 0; + z-index: 1000; + display: none; + float: left; + min-width: 160px; + padding: 4px 0; + margin: 1px 0 0; + list-style: none; + background-color: #ffffff; + border: 1px solid #ccc; + border: 1px solid rgba(0, 0, 0, 0.2); + *border-right-width: 2px; + *border-bottom-width: 2px; + -webkit-border-radius: 5px; + -moz-border-radius: 5px; + border-radius: 5px; + -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); + -moz-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); + box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); + -webkit-background-clip: padding-box; + -moz-background-clip: padding; + background-clip: padding-box; +} + +.dropdown-menu.pull-right { + right: 0; + left: auto; +} + +.dropdown-menu .divider { + *width: 100%; + height: 1px; + margin: 8px 1px; + *margin: -5px 0 5px; + overflow: hidden; + background-color: #e5e5e5; + border-bottom: 1px solid #ffffff; +} + +.dropdown-menu a { + display: block; + padding: 3px 15px; + clear: both; + font-weight: normal; + line-height: 18px; + color: #333333; + white-space: nowrap; +} + +.dropdown-menu li > a:hover, +.dropdown-menu .active > a, +.dropdown-menu .active > a:hover { + color: #ffffff; + text-decoration: none; + background-color: #0088cc; +} + +.open { + *z-index: 1000; +} + +.open > .dropdown-menu { + display: block; +} + +.pull-right > .dropdown-menu { + right: 0; + left: auto; +} + +.dropup .caret, +.navbar-fixed-bottom .dropdown .caret { + border-top: 0; + border-bottom: 4px solid #000000; + content: "\2191"; +} + +.dropup .dropdown-menu, +.navbar-fixed-bottom .dropdown .dropdown-menu { + top: auto; + bottom: 100%; + margin-bottom: 1px; +} + +.typeahead { + margin-top: 2px; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.well { + min-height: 20px; + padding: 19px; + margin-bottom: 20px; + background-color: #f5f5f5; + border: 1px solid #eee; + border: 1px solid rgba(0, 0, 0, 0.05); + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05); +} + +.well blockquote { + border-color: #ddd; + border-color: rgba(0, 0, 0, 0.15); +} + +.well-large { + padding: 24px; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; +} + +.well-small { + padding: 9px; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; +} + +.fade { + opacity: 0; + -webkit-transition: opacity 0.15s linear; + -moz-transition: opacity 0.15s linear; + -ms-transition: opacity 0.15s linear; + -o-transition: opacity 0.15s linear; + transition: opacity 0.15s linear; +} + +.fade.in { + opacity: 1; +} + +.collapse { + position: relative; + height: 0; + overflow: hidden; + -webkit-transition: height 0.35s ease; + -moz-transition: height 0.35s ease; + -ms-transition: height 0.35s ease; + -o-transition: height 0.35s ease; + transition: height 0.35s ease; +} + +.collapse.in { + height: auto; +} + +.close { + float: right; + font-size: 20px; + font-weight: bold; + line-height: 18px; + color: #000000; + text-shadow: 0 1px 0 #ffffff; + opacity: 0.2; + filter: alpha(opacity=20); +} + +.close:hover { + color: #000000; + text-decoration: none; + cursor: pointer; + opacity: 0.4; + filter: alpha(opacity=40); +} + +button.close { + padding: 0; + cursor: pointer; + background: transparent; + border: 0; + -webkit-appearance: none; +} + +.btn { + display: inline-block; + *display: inline; + padding: 4px 10px 4px; + margin-bottom: 0; + *margin-left: .3em; + font-size: 13px; + line-height: 18px; + *line-height: 20px; + color: #333333; + text-align: center; + text-shadow: 0 1px 1px rgba(255, 255, 255, 0.75); + vertical-align: middle; + cursor: pointer; + background-color: #f5f5f5; + *background-color: #e6e6e6; + background-image: -ms-linear-gradient(top, #ffffff, #e6e6e6); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6)); + background-image: -webkit-linear-gradient(top, #ffffff, #e6e6e6); + background-image: -o-linear-gradient(top, #ffffff, #e6e6e6); + background-image: linear-gradient(top, #ffffff, #e6e6e6); + background-image: -moz-linear-gradient(top, #ffffff, #e6e6e6); + background-repeat: repeat-x; + border: 1px solid #cccccc; + *border: 0; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + border-color: #e6e6e6 #e6e6e6 #bfbfbf; + border-bottom-color: #b3b3b3; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); + *zoom: 1; + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.btn:hover, +.btn:active, +.btn.active, +.btn.disabled, +.btn[disabled] { + background-color: #e6e6e6; + *background-color: #d9d9d9; +} + +.btn:active, +.btn.active { + background-color: #cccccc \9; +} + +.btn:first-child { + *margin-left: 0; +} + +.btn:hover { + color: #333333; + text-decoration: none; + background-color: #e6e6e6; + *background-color: #d9d9d9; + /* Buttons in IE7 don't get borders, so darken on hover */ + + background-position: 0 -15px; + -webkit-transition: background-position 0.1s linear; + -moz-transition: background-position 0.1s linear; + -ms-transition: background-position 0.1s linear; + -o-transition: background-position 0.1s linear; + transition: background-position 0.1s linear; +} + +.btn:focus { + outline: thin dotted #333; + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} + +.btn.active, +.btn:active { + background-color: #e6e6e6; + background-color: #d9d9d9 \9; + background-image: none; + outline: 0; + -webkit-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.btn.disabled, +.btn[disabled] { + cursor: default; + background-color: #e6e6e6; + background-image: none; + opacity: 0.65; + filter: alpha(opacity=65); + -webkit-box-shadow: none; + -moz-box-shadow: none; + box-shadow: none; +} + +.btn-large { + padding: 9px 14px; + font-size: 15px; + line-height: normal; + -webkit-border-radius: 5px; + -moz-border-radius: 5px; + border-radius: 5px; +} + +.btn-large [class^="icon-"] { + margin-top: 1px; +} + +.btn-small { + padding: 5px 9px; + font-size: 11px; + line-height: 16px; +} + +.btn-small [class^="icon-"] { + margin-top: -1px; +} + +.btn-mini { + padding: 2px 6px; + font-size: 11px; + line-height: 14px; +} + +.btn-primary, +.btn-primary:hover, +.btn-warning, +.btn-warning:hover, +.btn-danger, +.btn-danger:hover, +.btn-success, +.btn-success:hover, +.btn-info, +.btn-info:hover, +.btn-inverse, +.btn-inverse:hover { + color: #ffffff; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25); +} + +.btn-primary.active, +.btn-warning.active, +.btn-danger.active, +.btn-success.active, +.btn-info.active, +.btn-inverse.active { + color: rgba(255, 255, 255, 0.75); +} + +.btn { + border-color: #ccc; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); +} + +.btn-primary { + background-color: #0074cc; + *background-color: #0055cc; + background-image: -ms-linear-gradient(top, #0088cc, #0055cc); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0055cc)); + background-image: -webkit-linear-gradient(top, #0088cc, #0055cc); + background-image: -o-linear-gradient(top, #0088cc, #0055cc); + background-image: -moz-linear-gradient(top, #0088cc, #0055cc); + background-image: linear-gradient(top, #0088cc, #0055cc); + background-repeat: repeat-x; + border-color: #0055cc #0055cc #003580; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#0088cc', endColorstr='#0055cc', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-primary:hover, +.btn-primary:active, +.btn-primary.active, +.btn-primary.disabled, +.btn-primary[disabled] { + background-color: #0055cc; + *background-color: #004ab3; +} + +.btn-primary:active, +.btn-primary.active { + background-color: #004099 \9; +} + +.btn-warning { + background-color: #faa732; + *background-color: #f89406; + background-image: -ms-linear-gradient(top, #fbb450, #f89406); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406)); + background-image: -webkit-linear-gradient(top, #fbb450, #f89406); + background-image: -o-linear-gradient(top, #fbb450, #f89406); + background-image: -moz-linear-gradient(top, #fbb450, #f89406); + background-image: linear-gradient(top, #fbb450, #f89406); + background-repeat: repeat-x; + border-color: #f89406 #f89406 #ad6704; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-warning:hover, +.btn-warning:active, +.btn-warning.active, +.btn-warning.disabled, +.btn-warning[disabled] { + background-color: #f89406; + *background-color: #df8505; +} + +.btn-warning:active, +.btn-warning.active { + background-color: #c67605 \9; +} + +.btn-danger { + background-color: #da4f49; + *background-color: #bd362f; + background-image: -ms-linear-gradient(top, #ee5f5b, #bd362f); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#bd362f)); + background-image: -webkit-linear-gradient(top, #ee5f5b, #bd362f); + background-image: -o-linear-gradient(top, #ee5f5b, #bd362f); + background-image: -moz-linear-gradient(top, #ee5f5b, #bd362f); + background-image: linear-gradient(top, #ee5f5b, #bd362f); + background-repeat: repeat-x; + border-color: #bd362f #bd362f #802420; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#bd362f', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-danger:hover, +.btn-danger:active, +.btn-danger.active, +.btn-danger.disabled, +.btn-danger[disabled] { + background-color: #bd362f; + *background-color: #a9302a; +} + +.btn-danger:active, +.btn-danger.active { + background-color: #942a25 \9; +} + +.btn-success { + background-color: #5bb75b; + *background-color: #51a351; + background-image: -ms-linear-gradient(top, #62c462, #51a351); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#51a351)); + background-image: -webkit-linear-gradient(top, #62c462, #51a351); + background-image: -o-linear-gradient(top, #62c462, #51a351); + background-image: -moz-linear-gradient(top, #62c462, #51a351); + background-image: linear-gradient(top, #62c462, #51a351); + background-repeat: repeat-x; + border-color: #51a351 #51a351 #387038; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#62c462', endColorstr='#51a351', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-success:hover, +.btn-success:active, +.btn-success.active, +.btn-success.disabled, +.btn-success[disabled] { + background-color: #51a351; + *background-color: #499249; +} + +.btn-success:active, +.btn-success.active { + background-color: #408140 \9; +} + +.btn-info { + background-color: #49afcd; + *background-color: #2f96b4; + background-image: -ms-linear-gradient(top, #5bc0de, #2f96b4); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#2f96b4)); + background-image: -webkit-linear-gradient(top, #5bc0de, #2f96b4); + background-image: -o-linear-gradient(top, #5bc0de, #2f96b4); + background-image: -moz-linear-gradient(top, #5bc0de, #2f96b4); + background-image: linear-gradient(top, #5bc0de, #2f96b4); + background-repeat: repeat-x; + border-color: #2f96b4 #2f96b4 #1f6377; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#5bc0de', endColorstr='#2f96b4', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-info:hover, +.btn-info:active, +.btn-info.active, +.btn-info.disabled, +.btn-info[disabled] { + background-color: #2f96b4; + *background-color: #2a85a0; +} + +.btn-info:active, +.btn-info.active { + background-color: #24748c \9; +} + +.btn-inverse { + background-color: #414141; + *background-color: #222222; + background-image: -ms-linear-gradient(top, #555555, #222222); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#555555), to(#222222)); + background-image: -webkit-linear-gradient(top, #555555, #222222); + background-image: -o-linear-gradient(top, #555555, #222222); + background-image: -moz-linear-gradient(top, #555555, #222222); + background-image: linear-gradient(top, #555555, #222222); + background-repeat: repeat-x; + border-color: #222222 #222222 #000000; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#555555', endColorstr='#222222', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-inverse:hover, +.btn-inverse:active, +.btn-inverse.active, +.btn-inverse.disabled, +.btn-inverse[disabled] { + background-color: #222222; + *background-color: #151515; +} + +.btn-inverse:active, +.btn-inverse.active { + background-color: #080808 \9; +} + +button.btn, +input[type="submit"].btn { + *padding-top: 2px; + *padding-bottom: 2px; +} + +button.btn::-moz-focus-inner, +input[type="submit"].btn::-moz-focus-inner { + padding: 0; + border: 0; +} + +button.btn.btn-large, +input[type="submit"].btn.btn-large { + *padding-top: 7px; + *padding-bottom: 7px; +} + +button.btn.btn-small, +input[type="submit"].btn.btn-small { + *padding-top: 3px; + *padding-bottom: 3px; +} + +button.btn.btn-mini, +input[type="submit"].btn.btn-mini { + *padding-top: 1px; + *padding-bottom: 1px; +} + +.btn-group { + position: relative; + *margin-left: .3em; + *zoom: 1; +} + +.btn-group:before, +.btn-group:after { + display: table; + content: ""; +} + +.btn-group:after { + clear: both; +} + +.btn-group:first-child { + *margin-left: 0; +} + +.btn-group + .btn-group { + margin-left: 5px; +} + +.btn-toolbar { + margin-top: 9px; + margin-bottom: 9px; +} + +.btn-toolbar .btn-group { + display: inline-block; + *display: inline; + /* IE7 inline-block hack */ + + *zoom: 1; +} + +.btn-group > .btn { + position: relative; + float: left; + margin-left: -1px; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.btn-group > .btn:first-child { + margin-left: 0; + -webkit-border-bottom-left-radius: 4px; + border-bottom-left-radius: 4px; + -webkit-border-top-left-radius: 4px; + border-top-left-radius: 4px; + -moz-border-radius-bottomleft: 4px; + -moz-border-radius-topleft: 4px; +} + +.btn-group > .btn:last-child, +.btn-group > .dropdown-toggle { + -webkit-border-top-right-radius: 4px; + border-top-right-radius: 4px; + -webkit-border-bottom-right-radius: 4px; + border-bottom-right-radius: 4px; + -moz-border-radius-topright: 4px; + -moz-border-radius-bottomright: 4px; +} + +.btn-group > .btn.large:first-child { + margin-left: 0; + -webkit-border-bottom-left-radius: 6px; + border-bottom-left-radius: 6px; + -webkit-border-top-left-radius: 6px; + border-top-left-radius: 6px; + -moz-border-radius-bottomleft: 6px; + -moz-border-radius-topleft: 6px; +} + +.btn-group > .btn.large:last-child, +.btn-group > .large.dropdown-toggle { + -webkit-border-top-right-radius: 6px; + border-top-right-radius: 6px; + -webkit-border-bottom-right-radius: 6px; + border-bottom-right-radius: 6px; + -moz-border-radius-topright: 6px; + -moz-border-radius-bottomright: 6px; +} + +.btn-group > .btn:hover, +.btn-group > .btn:focus, +.btn-group > .btn:active, +.btn-group > .btn.active { + z-index: 2; +} + +.btn-group .dropdown-toggle:active, +.btn-group.open .dropdown-toggle { + outline: 0; +} + +.btn-group > .dropdown-toggle { + *padding-top: 4px; + padding-right: 8px; + *padding-bottom: 4px; + padding-left: 8px; + -webkit-box-shadow: inset 1px 0 0 rgba(255, 255, 255, 0.125), inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 1px 0 0 rgba(255, 255, 255, 0.125), inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: inset 1px 0 0 rgba(255, 255, 255, 0.125), inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.btn-group > .btn-mini.dropdown-toggle { + padding-right: 5px; + padding-left: 5px; +} + +.btn-group > .btn-small.dropdown-toggle { + *padding-top: 4px; + *padding-bottom: 4px; +} + +.btn-group > .btn-large.dropdown-toggle { + padding-right: 12px; + padding-left: 12px; +} + +.btn-group.open .dropdown-toggle { + background-image: none; + -webkit-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.btn-group.open .btn.dropdown-toggle { + background-color: #e6e6e6; +} + +.btn-group.open .btn-primary.dropdown-toggle { + background-color: #0055cc; +} + +.btn-group.open .btn-warning.dropdown-toggle { + background-color: #f89406; +} + +.btn-group.open .btn-danger.dropdown-toggle { + background-color: #bd362f; +} + +.btn-group.open .btn-success.dropdown-toggle { + background-color: #51a351; +} + +.btn-group.open .btn-info.dropdown-toggle { + background-color: #2f96b4; +} + +.btn-group.open .btn-inverse.dropdown-toggle { + background-color: #222222; +} + +.btn .caret { + margin-top: 7px; + margin-left: 0; +} + +.btn:hover .caret, +.open.btn-group .caret { + opacity: 1; + filter: alpha(opacity=100); +} + +.btn-mini .caret { + margin-top: 5px; +} + +.btn-small .caret { + margin-top: 6px; +} + +.btn-large .caret { + margin-top: 6px; + border-top-width: 5px; + border-right-width: 5px; + border-left-width: 5px; +} + +.dropup .btn-large .caret { + border-top: 0; + border-bottom: 5px solid #000000; +} + +.btn-primary .caret, +.btn-warning .caret, +.btn-danger .caret, +.btn-info .caret, +.btn-success .caret, +.btn-inverse .caret { + border-top-color: #ffffff; + border-bottom-color: #ffffff; + opacity: 0.75; + filter: alpha(opacity=75); +} + +.alert { + padding: 8px 35px 8px 14px; + margin-bottom: 18px; + color: #c09853; + text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5); + background-color: #fcf8e3; + border: 1px solid #fbeed5; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.alert-heading { + color: inherit; +} + +.alert .close { + position: relative; + top: -2px; + right: -21px; + line-height: 18px; +} + +.alert-success { + color: #468847; + background-color: #dff0d8; + border-color: #d6e9c6; +} + +.alert-danger, +.alert-error { + color: #b94a48; + background-color: #f2dede; + border-color: #eed3d7; +} + +.alert-info { + color: #3a87ad; + background-color: #d9edf7; + border-color: #bce8f1; +} + +.alert-block { + padding-top: 14px; + padding-bottom: 14px; +} + +.alert-block > p, +.alert-block > ul { + margin-bottom: 0; +} + +.alert-block p + p { + margin-top: 5px; +} + +.nav { + margin-bottom: 18px; + margin-left: 0; + list-style: none; +} + +.nav > li > a { + display: block; +} + +.nav > li > a:hover { + text-decoration: none; + background-color: #eeeeee; +} + +.nav > .pull-right { + float: right; +} + +.nav .nav-header { + display: block; + padding: 3px 15px; + font-size: 11px; + font-weight: bold; + line-height: 18px; + color: #999999; + text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5); + text-transform: uppercase; +} + +.nav li + .nav-header { + margin-top: 9px; +} + +.nav-list { + padding-right: 15px; + padding-left: 15px; + margin-bottom: 0; +} + +.nav-list > li > a, +.nav-list .nav-header { + margin-right: -15px; + margin-left: -15px; + text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5); +} + +.nav-list > li > a { + padding: 3px 15px; +} + +.nav-list > .active > a, +.nav-list > .active > a:hover { + color: #ffffff; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.2); + background-color: #0088cc; +} + +.nav-list [class^="icon-"] { + margin-right: 2px; +} + +.nav-list .divider { + *width: 100%; + height: 1px; + margin: 8px 1px; + *margin: -5px 0 5px; + overflow: hidden; + background-color: #e5e5e5; + border-bottom: 1px solid #ffffff; +} + +.nav-tabs, +.nav-pills { + *zoom: 1; +} + +.nav-tabs:before, +.nav-pills:before, +.nav-tabs:after, +.nav-pills:after { + display: table; + content: ""; +} + +.nav-tabs:after, +.nav-pills:after { + clear: both; +} + +.nav-tabs > li, +.nav-pills > li { + float: left; +} + +.nav-tabs > li > a, +.nav-pills > li > a { + padding-right: 12px; + padding-left: 12px; + margin-right: 2px; + line-height: 14px; +} + +.nav-tabs { + border-bottom: 1px solid #ddd; +} + +.nav-tabs > li { + margin-bottom: -1px; +} + +.nav-tabs > li > a { + padding-top: 8px; + padding-bottom: 8px; + line-height: 18px; + border: 1px solid transparent; + -webkit-border-radius: 4px 4px 0 0; + -moz-border-radius: 4px 4px 0 0; + border-radius: 4px 4px 0 0; +} + +.nav-tabs > li > a:hover { + border-color: #eeeeee #eeeeee #dddddd; +} + +.nav-tabs > .active > a, +.nav-tabs > .active > a:hover { + color: #555555; + cursor: default; + background-color: #ffffff; + border: 1px solid #ddd; + border-bottom-color: transparent; +} + +.nav-pills > li > a { + padding-top: 8px; + padding-bottom: 8px; + margin-top: 2px; + margin-bottom: 2px; + -webkit-border-radius: 5px; + -moz-border-radius: 5px; + border-radius: 5px; +} + +.nav-pills > .active > a, +.nav-pills > .active > a:hover { + color: #ffffff; + background-color: #0088cc; +} + +.nav-stacked > li { + float: none; +} + +.nav-stacked > li > a { + margin-right: 0; +} + +.nav-tabs.nav-stacked { + border-bottom: 0; +} + +.nav-tabs.nav-stacked > li > a { + border: 1px solid #ddd; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.nav-tabs.nav-stacked > li:first-child > a { + -webkit-border-radius: 4px 4px 0 0; + -moz-border-radius: 4px 4px 0 0; + border-radius: 4px 4px 0 0; +} + +.nav-tabs.nav-stacked > li:last-child > a { + -webkit-border-radius: 0 0 4px 4px; + -moz-border-radius: 0 0 4px 4px; + border-radius: 0 0 4px 4px; +} + +.nav-tabs.nav-stacked > li > a:hover { + z-index: 2; + border-color: #ddd; +} + +.nav-pills.nav-stacked > li > a { + margin-bottom: 3px; +} + +.nav-pills.nav-stacked > li:last-child > a { + margin-bottom: 1px; +} + +.nav-tabs .dropdown-menu { + -webkit-border-radius: 0 0 5px 5px; + -moz-border-radius: 0 0 5px 5px; + border-radius: 0 0 5px 5px; +} + +.nav-pills .dropdown-menu { + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.nav-tabs .dropdown-toggle .caret, +.nav-pills .dropdown-toggle .caret { + margin-top: 6px; + border-top-color: #0088cc; + border-bottom-color: #0088cc; +} + +.nav-tabs .dropdown-toggle:hover .caret, +.nav-pills .dropdown-toggle:hover .caret { + border-top-color: #005580; + border-bottom-color: #005580; +} + +.nav-tabs .active .dropdown-toggle .caret, +.nav-pills .active .dropdown-toggle .caret { + border-top-color: #333333; + border-bottom-color: #333333; +} + +.nav > .dropdown.active > a:hover { + color: #000000; + cursor: pointer; +} + +.nav-tabs .open .dropdown-toggle, +.nav-pills .open .dropdown-toggle, +.nav > li.dropdown.open.active > a:hover { + color: #ffffff; + background-color: #999999; + border-color: #999999; +} + +.nav li.dropdown.open .caret, +.nav li.dropdown.open.active .caret, +.nav li.dropdown.open a:hover .caret { + border-top-color: #ffffff; + border-bottom-color: #ffffff; + opacity: 1; + filter: alpha(opacity=100); +} + +.tabs-stacked .open > a:hover { + border-color: #999999; +} + +.tabbable { + *zoom: 1; +} + +.tabbable:before, +.tabbable:after { + display: table; + content: ""; +} + +.tabbable:after { + clear: both; +} + +.tab-content { + overflow: auto; +} + +.tabs-below > .nav-tabs, +.tabs-right > .nav-tabs, +.tabs-left > .nav-tabs { + border-bottom: 0; +} + +.tab-content > .tab-pane, +.pill-content > .pill-pane { + display: none; +} + +.tab-content > .active, +.pill-content > .active { + display: block; +} + +.tabs-below > .nav-tabs { + border-top: 1px solid #ddd; +} + +.tabs-below > .nav-tabs > li { + margin-top: -1px; + margin-bottom: 0; +} + +.tabs-below > .nav-tabs > li > a { + -webkit-border-radius: 0 0 4px 4px; + -moz-border-radius: 0 0 4px 4px; + border-radius: 0 0 4px 4px; +} + +.tabs-below > .nav-tabs > li > a:hover { + border-top-color: #ddd; + border-bottom-color: transparent; +} + +.tabs-below > .nav-tabs > .active > a, +.tabs-below > .nav-tabs > .active > a:hover { + border-color: transparent #ddd #ddd #ddd; +} + +.tabs-left > .nav-tabs > li, +.tabs-right > .nav-tabs > li { + float: none; +} + +.tabs-left > .nav-tabs > li > a, +.tabs-right > .nav-tabs > li > a { + min-width: 74px; + margin-right: 0; + margin-bottom: 3px; +} + +.tabs-left > .nav-tabs { + float: left; + margin-right: 19px; + border-right: 1px solid #ddd; +} + +.tabs-left > .nav-tabs > li > a { + margin-right: -1px; + -webkit-border-radius: 4px 0 0 4px; + -moz-border-radius: 4px 0 0 4px; + border-radius: 4px 0 0 4px; +} + +.tabs-left > .nav-tabs > li > a:hover { + border-color: #eeeeee #dddddd #eeeeee #eeeeee; +} + +.tabs-left > .nav-tabs .active > a, +.tabs-left > .nav-tabs .active > a:hover { + border-color: #ddd transparent #ddd #ddd; + *border-right-color: #ffffff; +} + +.tabs-right > .nav-tabs { + float: right; + margin-left: 19px; + border-left: 1px solid #ddd; +} + +.tabs-right > .nav-tabs > li > a { + margin-left: -1px; + -webkit-border-radius: 0 4px 4px 0; + -moz-border-radius: 0 4px 4px 0; + border-radius: 0 4px 4px 0; +} + +.tabs-right > .nav-tabs > li > a:hover { + border-color: #eeeeee #eeeeee #eeeeee #dddddd; +} + +.tabs-right > .nav-tabs .active > a, +.tabs-right > .nav-tabs .active > a:hover { + border-color: #ddd #ddd #ddd transparent; + *border-left-color: #ffffff; +} + +.navbar { + *position: relative; + *z-index: 2; + margin-bottom: 18px; + overflow: visible; +} + +.navbar-inner { + min-height: 40px; + padding-right: 20px; + padding-left: 20px; + background-color: #2c2c2c; + background-image: -moz-linear-gradient(top, #333333, #222222); + background-image: -ms-linear-gradient(top, #333333, #222222); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#222222)); + background-image: -webkit-linear-gradient(top, #333333, #222222); + background-image: -o-linear-gradient(top, #333333, #222222); + background-image: linear-gradient(top, #333333, #222222); + background-repeat: repeat-x; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#333333', endColorstr='#222222', GradientType=0); + -webkit-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.25), inset 0 -1px 0 rgba(0, 0, 0, 0.1); + -moz-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.25), inset 0 -1px 0 rgba(0, 0, 0, 0.1); + box-shadow: 0 1px 3px rgba(0, 0, 0, 0.25), inset 0 -1px 0 rgba(0, 0, 0, 0.1); +} + +.navbar .container { + width: auto; +} + +.nav-collapse.collapse { + height: auto; +} + +.navbar { + color: #999999; +} + +.navbar .brand:hover { + text-decoration: none; +} + +.navbar .brand { + display: block; + float: left; + padding: 8px 20px 12px; + margin-left: -20px; + font-size: 20px; + font-weight: 200; + line-height: 1; + color: #999999; +} + +.navbar .navbar-text { + margin-bottom: 0; + line-height: 40px; +} + +.navbar .navbar-link { + color: #999999; +} + +.navbar .navbar-link:hover { + color: #ffffff; +} + +.navbar .btn, +.navbar .btn-group { + margin-top: 5px; +} + +.navbar .btn-group .btn { + margin: 0; +} + +.navbar-form { + margin-bottom: 0; + *zoom: 1; +} + +.navbar-form:before, +.navbar-form:after { + display: table; + content: ""; +} + +.navbar-form:after { + clear: both; +} + +.navbar-form input, +.navbar-form select, +.navbar-form .radio, +.navbar-form .checkbox { + margin-top: 5px; +} + +.navbar-form input, +.navbar-form select { + display: inline-block; + margin-bottom: 0; +} + +.navbar-form input[type="image"], +.navbar-form input[type="checkbox"], +.navbar-form input[type="radio"] { + margin-top: 3px; +} + +.navbar-form .input-append, +.navbar-form .input-prepend { + margin-top: 6px; + white-space: nowrap; +} + +.navbar-form .input-append input, +.navbar-form .input-prepend input { + margin-top: 0; +} + +.navbar-search { + position: relative; + float: left; + margin-top: 6px; + margin-bottom: 0; +} + +.navbar-search .search-query { + padding: 4px 9px; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 13px; + font-weight: normal; + line-height: 1; + color: #ffffff; + background-color: #626262; + border: 1px solid #151515; + -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1), 0 1px 0 rgba(255, 255, 255, 0.15); + -moz-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1), 0 1px 0 rgba(255, 255, 255, 0.15); + box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1), 0 1px 0 rgba(255, 255, 255, 0.15); + -webkit-transition: none; + -moz-transition: none; + -ms-transition: none; + -o-transition: none; + transition: none; +} + +.navbar-search .search-query:-moz-placeholder { + color: #cccccc; +} + +.navbar-search .search-query:-ms-input-placeholder { + color: #cccccc; +} + +.navbar-search .search-query::-webkit-input-placeholder { + color: #cccccc; +} + +.navbar-search .search-query:focus, +.navbar-search .search-query.focused { + padding: 5px 10px; + color: #333333; + text-shadow: 0 1px 0 #ffffff; + background-color: #ffffff; + border: 0; + outline: 0; + -webkit-box-shadow: 0 0 3px rgba(0, 0, 0, 0.15); + -moz-box-shadow: 0 0 3px rgba(0, 0, 0, 0.15); + box-shadow: 0 0 3px rgba(0, 0, 0, 0.15); +} + +.navbar-fixed-top, +.navbar-fixed-bottom { + position: fixed; + right: 0; + left: 0; + z-index: 1030; + margin-bottom: 0; +} + +.navbar-fixed-top .navbar-inner, +.navbar-fixed-bottom .navbar-inner { + padding-right: 0; + padding-left: 0; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.navbar-fixed-top .container, +.navbar-fixed-bottom .container { + width: 940px; +} + +.navbar-fixed-top { + top: 0; +} + +.navbar-fixed-bottom { + bottom: 0; +} + +.navbar .nav { + position: relative; + left: 0; + display: block; + float: left; + margin: 0 10px 0 0; +} + +.navbar .nav.pull-right { + float: right; +} + +.navbar .nav > li { + display: block; + float: left; +} + +.navbar .nav > li > a { + float: none; + padding: 9px 10px 11px; + line-height: 19px; + color: #999999; + text-decoration: none; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25); +} + +.navbar .btn { + display: inline-block; + padding: 4px 10px 4px; + margin: 5px 5px 6px; + line-height: 18px; +} + +.navbar .btn-group { + padding: 5px 5px 6px; + margin: 0; +} + +.navbar .nav > li > a:hover { + color: #ffffff; + text-decoration: none; + background-color: transparent; +} + +.navbar .nav .active > a, +.navbar .nav .active > a:hover { + color: #ffffff; + text-decoration: none; + background-color: #222222; +} + +.navbar .divider-vertical { + width: 1px; + height: 40px; + margin: 0 9px; + overflow: hidden; + background-color: #222222; + border-right: 1px solid #333333; +} + +.navbar .nav.pull-right { + margin-right: 0; + margin-left: 10px; +} + +.navbar .btn-navbar { + display: none; + float: right; + padding: 7px 10px; + margin-right: 5px; + margin-left: 5px; + background-color: #2c2c2c; + *background-color: #222222; + background-image: -ms-linear-gradient(top, #333333, #222222); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#222222)); + background-image: -webkit-linear-gradient(top, #333333, #222222); + background-image: -o-linear-gradient(top, #333333, #222222); + background-image: linear-gradient(top, #333333, #222222); + background-image: -moz-linear-gradient(top, #333333, #222222); + background-repeat: repeat-x; + border-color: #222222 #222222 #000000; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#333333', endColorstr='#222222', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.075); + -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.075); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.075); +} + +.navbar .btn-navbar:hover, +.navbar .btn-navbar:active, +.navbar .btn-navbar.active, +.navbar .btn-navbar.disabled, +.navbar .btn-navbar[disabled] { + background-color: #222222; + *background-color: #151515; +} + +.navbar .btn-navbar:active, +.navbar .btn-navbar.active { + background-color: #080808 \9; +} + +.navbar .btn-navbar .icon-bar { + display: block; + width: 18px; + height: 2px; + background-color: #f5f5f5; + -webkit-border-radius: 1px; + -moz-border-radius: 1px; + border-radius: 1px; + -webkit-box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25); + -moz-box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25); + box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25); +} + +.btn-navbar .icon-bar + .icon-bar { + margin-top: 3px; +} + +.navbar .dropdown-menu:before { + position: absolute; + top: -7px; + left: 9px; + display: inline-block; + border-right: 7px solid transparent; + border-bottom: 7px solid #ccc; + border-left: 7px solid transparent; + border-bottom-color: rgba(0, 0, 0, 0.2); + content: ''; +} + +.navbar .dropdown-menu:after { + position: absolute; + top: -6px; + left: 10px; + display: inline-block; + border-right: 6px solid transparent; + border-bottom: 6px solid #ffffff; + border-left: 6px solid transparent; + content: ''; +} + +.navbar-fixed-bottom .dropdown-menu:before { + top: auto; + bottom: -7px; + border-top: 7px solid #ccc; + border-bottom: 0; + border-top-color: rgba(0, 0, 0, 0.2); +} + +.navbar-fixed-bottom .dropdown-menu:after { + top: auto; + bottom: -6px; + border-top: 6px solid #ffffff; + border-bottom: 0; +} + +.navbar .nav li.dropdown .dropdown-toggle .caret, +.navbar .nav li.dropdown.open .caret { + border-top-color: #ffffff; + border-bottom-color: #ffffff; +} + +.navbar .nav li.dropdown.active .caret { + opacity: 1; + filter: alpha(opacity=100); +} + +.navbar .nav li.dropdown.open > .dropdown-toggle, +.navbar .nav li.dropdown.active > .dropdown-toggle, +.navbar .nav li.dropdown.open.active > .dropdown-toggle { + background-color: transparent; +} + +.navbar .nav li.dropdown.active > .dropdown-toggle:hover { + color: #ffffff; +} + +.navbar .pull-right .dropdown-menu, +.navbar .dropdown-menu.pull-right { + right: 0; + left: auto; +} + +.navbar .pull-right .dropdown-menu:before, +.navbar .dropdown-menu.pull-right:before { + right: 12px; + left: auto; +} + +.navbar .pull-right .dropdown-menu:after, +.navbar .dropdown-menu.pull-right:after { + right: 13px; + left: auto; +} + +.breadcrumb { + padding: 7px 14px; + margin: 0 0 18px; + list-style: none; + background-color: #fbfbfb; + background-image: -moz-linear-gradient(top, #ffffff, #f5f5f5); + background-image: -ms-linear-gradient(top, #ffffff, #f5f5f5); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#f5f5f5)); + background-image: -webkit-linear-gradient(top, #ffffff, #f5f5f5); + background-image: -o-linear-gradient(top, #ffffff, #f5f5f5); + background-image: linear-gradient(top, #ffffff, #f5f5f5); + background-repeat: repeat-x; + border: 1px solid #ddd; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#ffffff', endColorstr='#f5f5f5', GradientType=0); + -webkit-box-shadow: inset 0 1px 0 #ffffff; + -moz-box-shadow: inset 0 1px 0 #ffffff; + box-shadow: inset 0 1px 0 #ffffff; +} + +.breadcrumb li { + display: inline-block; + *display: inline; + text-shadow: 0 1px 0 #ffffff; + *zoom: 1; +} + +.breadcrumb .divider { + padding: 0 5px; + color: #999999; +} + +.breadcrumb .active a { + color: #333333; +} + +.pagination { + height: 36px; + margin: 18px 0; +} + +.pagination ul { + display: inline-block; + *display: inline; + margin-bottom: 0; + margin-left: 0; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + *zoom: 1; + -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.pagination li { + display: inline; +} + +.pagination a { + float: left; + padding: 0 14px; + line-height: 34px; + text-decoration: none; + border: 1px solid #ddd; + border-left-width: 0; +} + +.pagination a:hover, +.pagination .active a { + background-color: #f5f5f5; +} + +.pagination .active a { + color: #999999; + cursor: default; +} + +.pagination .disabled span, +.pagination .disabled a, +.pagination .disabled a:hover { + color: #999999; + cursor: default; + background-color: transparent; +} + +.pagination li:first-child a { + border-left-width: 1px; + -webkit-border-radius: 3px 0 0 3px; + -moz-border-radius: 3px 0 0 3px; + border-radius: 3px 0 0 3px; +} + +.pagination li:last-child a { + -webkit-border-radius: 0 3px 3px 0; + -moz-border-radius: 0 3px 3px 0; + border-radius: 0 3px 3px 0; +} + +.pagination-centered { + text-align: center; +} + +.pagination-right { + text-align: right; +} + +.pager { + margin-bottom: 18px; + margin-left: 0; + text-align: center; + list-style: none; + *zoom: 1; +} + +.pager:before, +.pager:after { + display: table; + content: ""; +} + +.pager:after { + clear: both; +} + +.pager li { + display: inline; +} + +.pager a { + display: inline-block; + padding: 5px 14px; + background-color: #fff; + border: 1px solid #ddd; + -webkit-border-radius: 15px; + -moz-border-radius: 15px; + border-radius: 15px; +} + +.pager a:hover { + text-decoration: none; + background-color: #f5f5f5; +} + +.pager .next a { + float: right; +} + +.pager .previous a { + float: left; +} + +.pager .disabled a, +.pager .disabled a:hover { + color: #999999; + cursor: default; + background-color: #fff; +} + +.modal-open .dropdown-menu { + z-index: 2050; +} + +.modal-open .dropdown.open { + *z-index: 2050; +} + +.modal-open .popover { + z-index: 2060; +} + +.modal-open .tooltip { + z-index: 2070; +} + +.modal-backdrop { + position: fixed; + top: 0; + right: 0; + bottom: 0; + left: 0; + z-index: 1040; + background-color: #000000; +} + +.modal-backdrop.fade { + opacity: 0; +} + +.modal-backdrop, +.modal-backdrop.fade.in { + opacity: 0.8; + filter: alpha(opacity=80); +} + +.modal { + position: fixed; + top: 50%; + left: 50%; + z-index: 1050; + width: 560px; + margin: -250px 0 0 -280px; + overflow: auto; + background-color: #ffffff; + border: 1px solid #999; + border: 1px solid rgba(0, 0, 0, 0.3); + *border: 1px solid #999; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; +} + +.modal.fade { + top: -25%; + -webkit-transition: opacity 0.3s linear, top 0.3s ease-out; + -moz-transition: opacity 0.3s linear, top 0.3s ease-out; + -ms-transition: opacity 0.3s linear, top 0.3s ease-out; + -o-transition: opacity 0.3s linear, top 0.3s ease-out; + transition: opacity 0.3s linear, top 0.3s ease-out; +} + +.modal.fade.in { + top: 50%; +} + +.modal-header { + padding: 9px 15px; + border-bottom: 1px solid #eee; +} + +.modal-header .close { + margin-top: 2px; +} + +.modal-body { + max-height: 400px; + padding: 15px; + overflow-y: auto; +} + +.modal-form { + margin-bottom: 0; +} + +.modal-footer { + padding: 14px 15px 15px; + margin-bottom: 0; + text-align: right; + background-color: #f5f5f5; + border-top: 1px solid #ddd; + -webkit-border-radius: 0 0 6px 6px; + -moz-border-radius: 0 0 6px 6px; + border-radius: 0 0 6px 6px; + *zoom: 1; + -webkit-box-shadow: inset 0 1px 0 #ffffff; + -moz-box-shadow: inset 0 1px 0 #ffffff; + box-shadow: inset 0 1px 0 #ffffff; +} + +.modal-footer:before, +.modal-footer:after { + display: table; + content: ""; +} + +.modal-footer:after { + clear: both; +} + +.modal-footer .btn + .btn { + margin-bottom: 0; + margin-left: 5px; +} + +.modal-footer .btn-group .btn + .btn { + margin-left: -1px; +} + +.tooltip { + position: absolute; + z-index: 1020; + display: block; + padding: 5px; + font-size: 11px; + opacity: 0; + filter: alpha(opacity=0); + visibility: visible; +} + +.tooltip.in { + opacity: 0.8; + filter: alpha(opacity=80); +} + +.tooltip.top { + margin-top: -2px; +} + +.tooltip.right { + margin-left: 2px; +} + +.tooltip.bottom { + margin-top: 2px; +} + +.tooltip.left { + margin-left: -2px; +} + +.tooltip.top .tooltip-arrow { + bottom: 0; + left: 50%; + margin-left: -5px; + border-top: 5px solid #000000; + border-right: 5px solid transparent; + border-left: 5px solid transparent; +} + +.tooltip.left .tooltip-arrow { + top: 50%; + right: 0; + margin-top: -5px; + border-top: 5px solid transparent; + border-bottom: 5px solid transparent; + border-left: 5px solid #000000; +} + +.tooltip.bottom .tooltip-arrow { + top: 0; + left: 50%; + margin-left: -5px; + border-right: 5px solid transparent; + border-bottom: 5px solid #000000; + border-left: 5px solid transparent; +} + +.tooltip.right .tooltip-arrow { + top: 50%; + left: 0; + margin-top: -5px; + border-top: 5px solid transparent; + border-right: 5px solid #000000; + border-bottom: 5px solid transparent; +} + +.tooltip-inner { + max-width: 200px; + padding: 3px 8px; + color: #ffffff; + text-align: center; + text-decoration: none; + background-color: #000000; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.tooltip-arrow { + position: absolute; + width: 0; + height: 0; +} + +.popover { + position: absolute; + top: 0; + left: 0; + z-index: 1010; + display: none; + padding: 5px; +} + +.popover.top { + margin-top: -5px; +} + +.popover.right { + margin-left: 5px; +} + +.popover.bottom { + margin-top: 5px; +} + +.popover.left { + margin-left: -5px; +} + +.popover.top .arrow { + bottom: 0; + left: 50%; + margin-left: -5px; + border-top: 5px solid #000000; + border-right: 5px solid transparent; + border-left: 5px solid transparent; +} + +.popover.right .arrow { + top: 50%; + left: 0; + margin-top: -5px; + border-top: 5px solid transparent; + border-right: 5px solid #000000; + border-bottom: 5px solid transparent; +} + +.popover.bottom .arrow { + top: 0; + left: 50%; + margin-left: -5px; + border-right: 5px solid transparent; + border-bottom: 5px solid #000000; + border-left: 5px solid transparent; +} + +.popover.left .arrow { + top: 50%; + right: 0; + margin-top: -5px; + border-top: 5px solid transparent; + border-bottom: 5px solid transparent; + border-left: 5px solid #000000; +} + +.popover .arrow { + position: absolute; + width: 0; + height: 0; +} + +.popover-inner { + width: 280px; + padding: 3px; + overflow: hidden; + background: #000000; + background: rgba(0, 0, 0, 0.8); + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); +} + +.popover-title { + padding: 9px 15px; + line-height: 1; + background-color: #f5f5f5; + border-bottom: 1px solid #eee; + -webkit-border-radius: 3px 3px 0 0; + -moz-border-radius: 3px 3px 0 0; + border-radius: 3px 3px 0 0; +} + +.popover-content { + padding: 14px; + background-color: #ffffff; + -webkit-border-radius: 0 0 3px 3px; + -moz-border-radius: 0 0 3px 3px; + border-radius: 0 0 3px 3px; + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; +} + +.popover-content p, +.popover-content ul, +.popover-content ol { + margin-bottom: 0; +} + +.thumbnails { + margin-left: -20px; + list-style: none; + *zoom: 1; +} + +.thumbnails:before, +.thumbnails:after { + display: table; + content: ""; +} + +.thumbnails:after { + clear: both; +} + +.row-fluid .thumbnails { + margin-left: 0; +} + +.thumbnails > li { + float: left; + margin-bottom: 18px; + margin-left: 20px; +} + +.thumbnail { + display: block; + padding: 4px; + line-height: 1; + border: 1px solid #ddd; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + -webkit-box-shadow: 0 1px 1px rgba(0, 0, 0, 0.075); + -moz-box-shadow: 0 1px 1px rgba(0, 0, 0, 0.075); + box-shadow: 0 1px 1px rgba(0, 0, 0, 0.075); +} + +a.thumbnail:hover { + border-color: #0088cc; + -webkit-box-shadow: 0 1px 4px rgba(0, 105, 214, 0.25); + -moz-box-shadow: 0 1px 4px rgba(0, 105, 214, 0.25); + box-shadow: 0 1px 4px rgba(0, 105, 214, 0.25); +} + +.thumbnail > img { + display: block; + max-width: 100%; + margin-right: auto; + margin-left: auto; +} + +.thumbnail .caption { + padding: 9px; +} + +.label, +.badge { + font-size: 10.998px; + font-weight: bold; + line-height: 14px; + color: #ffffff; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25); + white-space: nowrap; + vertical-align: baseline; + background-color: #999999; +} + +.label { + padding: 1px 4px 2px; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; +} + +.badge { + padding: 1px 9px 2px; + -webkit-border-radius: 9px; + -moz-border-radius: 9px; + border-radius: 9px; +} + +a.label:hover, +a.badge:hover { + color: #ffffff; + text-decoration: none; + cursor: pointer; +} + +.label-important, +.badge-important { + background-color: #b94a48; +} + +.label-important[href], +.badge-important[href] { + background-color: #953b39; +} + +.label-warning, +.badge-warning { + background-color: #f89406; +} + +.label-warning[href], +.badge-warning[href] { + background-color: #c67605; +} + +.label-success, +.badge-success { + background-color: #468847; +} + +.label-success[href], +.badge-success[href] { + background-color: #356635; +} + +.label-info, +.badge-info { + background-color: #3a87ad; +} + +.label-info[href], +.badge-info[href] { + background-color: #2d6987; +} + +.label-inverse, +.badge-inverse { + background-color: #333333; +} + +.label-inverse[href], +.badge-inverse[href] { + background-color: #1a1a1a; +} + +@-webkit-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} + +@-moz-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} + +@-ms-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} + +@-o-keyframes progress-bar-stripes { + from { + background-position: 0 0; + } + to { + background-position: 40px 0; + } +} + +@keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} + +.progress { + height: 18px; + margin-bottom: 18px; + overflow: hidden; + background-color: #f7f7f7; + background-image: -moz-linear-gradient(top, #f5f5f5, #f9f9f9); + background-image: -ms-linear-gradient(top, #f5f5f5, #f9f9f9); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9)); + background-image: -webkit-linear-gradient(top, #f5f5f5, #f9f9f9); + background-image: -o-linear-gradient(top, #f5f5f5, #f9f9f9); + background-image: linear-gradient(top, #f5f5f5, #f9f9f9); + background-repeat: repeat-x; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#f5f5f5', endColorstr='#f9f9f9', GradientType=0); + -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1); + -moz-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1); + box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1); +} + +.progress .bar { + width: 0; + height: 18px; + font-size: 12px; + color: #ffffff; + text-align: center; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25); + background-color: #0e90d2; + background-image: -moz-linear-gradient(top, #149bdf, #0480be); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be)); + background-image: -webkit-linear-gradient(top, #149bdf, #0480be); + background-image: -o-linear-gradient(top, #149bdf, #0480be); + background-image: linear-gradient(top, #149bdf, #0480be); + background-image: -ms-linear-gradient(top, #149bdf, #0480be); + background-repeat: repeat-x; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#149bdf', endColorstr='#0480be', GradientType=0); + -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15); + -moz-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15); + box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15); + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; + -webkit-transition: width 0.6s ease; + -moz-transition: width 0.6s ease; + -ms-transition: width 0.6s ease; + -o-transition: width 0.6s ease; + transition: width 0.6s ease; +} + +.progress-striped .bar { + background-color: #149bdf; + background-image: -o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent)); + background-image: linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + -webkit-background-size: 40px 40px; + -moz-background-size: 40px 40px; + -o-background-size: 40px 40px; + background-size: 40px 40px; +} + +.progress.active .bar { + -webkit-animation: progress-bar-stripes 2s linear infinite; + -moz-animation: progress-bar-stripes 2s linear infinite; + -ms-animation: progress-bar-stripes 2s linear infinite; + -o-animation: progress-bar-stripes 2s linear infinite; + animation: progress-bar-stripes 2s linear infinite; +} + +.progress-danger .bar { + background-color: #dd514c; + background-image: -moz-linear-gradient(top, #ee5f5b, #c43c35); + background-image: -ms-linear-gradient(top, #ee5f5b, #c43c35); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35)); + background-image: -webkit-linear-gradient(top, #ee5f5b, #c43c35); + background-image: -o-linear-gradient(top, #ee5f5b, #c43c35); + background-image: linear-gradient(top, #ee5f5b, #c43c35); + background-repeat: repeat-x; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0); +} + +.progress-danger.progress-striped .bar { + background-color: #ee5f5b; + background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent)); + background-image: -webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); +} + +.progress-success .bar { + background-color: #5eb95e; + background-image: -moz-linear-gradient(top, #62c462, #57a957); + background-image: -ms-linear-gradient(top, #62c462, #57a957); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957)); + background-image: -webkit-linear-gradient(top, #62c462, #57a957); + background-image: -o-linear-gradient(top, #62c462, #57a957); + background-image: linear-gradient(top, #62c462, #57a957); + background-repeat: repeat-x; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0); +} + +.progress-success.progress-striped .bar { + background-color: #62c462; + background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent)); + background-image: -webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, 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50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); +} + +.progress-warning .bar { + background-color: #faa732; + background-image: -moz-linear-gradient(top, #fbb450, #f89406); + background-image: -ms-linear-gradient(top, #fbb450, #f89406); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406)); + background-image: 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+.accordion-heading .accordion-toggle { + display: block; + padding: 8px 15px; +} + +.accordion-toggle { + cursor: pointer; +} + +.accordion-inner { + padding: 9px 15px; + border-top: 1px solid #e5e5e5; +} + +.carousel { + position: relative; + margin-bottom: 18px; + line-height: 1; +} + +.carousel-inner { + position: relative; + width: 100%; + overflow: hidden; +} + +.carousel .item { + position: relative; + display: none; + -webkit-transition: 0.6s ease-in-out left; + -moz-transition: 0.6s ease-in-out left; + -ms-transition: 0.6s ease-in-out left; + -o-transition: 0.6s ease-in-out left; + transition: 0.6s ease-in-out left; +} + +.carousel .item > img { + display: block; + line-height: 1; +} + +.carousel .active, +.carousel .next, +.carousel .prev { + display: block; +} + +.carousel .active { + left: 0; +} + +.carousel .next, +.carousel .prev { + position: absolute; + top: 0; + width: 100%; +} + +.carousel .next { + left: 100%; +} + +.carousel .prev { + left: -100%; +} + +.carousel .next.left, +.carousel .prev.right { + left: 0; +} + +.carousel .active.left { + left: -100%; +} + +.carousel .active.right { + left: 100%; +} + +.carousel-control { + position: absolute; + top: 40%; + left: 15px; + width: 40px; + height: 40px; + margin-top: -20px; + font-size: 60px; + font-weight: 100; + line-height: 30px; + color: #ffffff; + text-align: center; + background: #222222; + border: 3px solid #ffffff; + -webkit-border-radius: 23px; + -moz-border-radius: 23px; + border-radius: 23px; + opacity: 0.5; + filter: alpha(opacity=50); +} + +.carousel-control.right { + right: 15px; + left: auto; +} + +.carousel-control:hover { + color: #ffffff; + text-decoration: none; + opacity: 0.9; + filter: alpha(opacity=90); +} + +.carousel-caption { + position: absolute; + right: 0; + bottom: 0; + left: 0; + padding: 10px 15px 5px; + background: #333333; + background: rgba(0, 0, 0, 0.75); +} + +.carousel-caption h4, +.carousel-caption p { + color: #ffffff; +} + +.hero-unit { + padding: 60px; + margin-bottom: 30px; + background-color: #eeeeee; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; +} + +.hero-unit h1 { + margin-bottom: 0; + font-size: 60px; + line-height: 1; + letter-spacing: -1px; + color: inherit; +} + +.hero-unit p { + font-size: 18px; + font-weight: 200; + line-height: 27px; + color: inherit; +} + +.pull-right { + float: right; +} + +.pull-left { + float: left; +} + +.hide { + display: none; +} + +.show { + display: block; +} + +.invisible { + visibility: hidden; +} diff --git a/docs/css/bootstrap.min.css b/docs/css/bootstrap.min.css new file mode 100644 index 0000000..b74b454 --- /dev/null +++ b/docs/css/bootstrap.min.css @@ -0,0 +1,9 @@ +/*! + * Bootstrap v2.0.4 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + 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#fff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:.5;filter:alpha(opacity=50)}.carousel-control.right{right:15px;left:auto}.carousel-control:hover{color:#fff;text-decoration:none;opacity:.9;filter:alpha(opacity=90)}.carousel-caption{position:absolute;right:0;bottom:0;left:0;padding:10px 15px 5px;background:#333;background:rgba(0,0,0,0.75)}.carousel-caption h4,.carousel-caption p{color:#fff}.hero-unit{padding:60px;margin-bottom:30px;background-color:#eee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;letter-spacing:-1px;color:inherit}.hero-unit p{font-size:18px;font-weight:200;line-height:27px;color:inherit}.pull-right{float:right}.pull-left{float:left}.hide{display:none}.show{display:block}.invisible{visibility:hidden} diff --git a/docs/css/highlight.css b/docs/css/highlight.css new file mode 100644 index 0000000..cd3ead6 --- /dev/null +++ b/docs/css/highlight.css @@ -0,0 +1,28 @@ +/* Syntax highlighting ---------------------------------------------------- */ + +pre .input { + border-left: 3px solid #ccc; + padding-left: 0.5em; +} +pre .output { + background-color: #eee; +} + +.number {color:rgb(21,20,181);} +.functioncall {color:#264D66 ;} +.string {color:#375D81 ;} +.keyword {font-weight:bolder ;color:black;} +.argument {color:#264D66 ;} +.comment {color: #4C886B;} +.formalargs {color: #264D66;} +.eqformalargs {color:#264D66;} +.slot {font-style:italic;} +.symbol {color:black ;} +.prompt {color:black ;} + +pre img { + background-color: #fff; + border: 1px solid #ccc; + display: block; + margin: 0.5em auto 0.5em auto; +} diff --git a/docs/css/staticdocs.css b/docs/css/staticdocs.css new file mode 100644 index 0000000..15d7408 --- /dev/null +++ b/docs/css/staticdocs.css @@ -0,0 +1,25 @@ +h2 {padding-top: 20px} + +.icon img { + float: right; + border: 1px solid #ccc; +} +.index .internal {display: none;} +ul.index li {margin-bottom: 0.5em; clear: both;} + +footer { + margin-top: 45px; + padding: 35px 0 36px; + border-top: 1px solid #e5e5e5; +} +footer p { + margin-bottom: 0; + color: #555; +} + +.sidebar h2 { + font-size: 1.1em; + padding-top: 0.5em; +} + +.sidebar li {margin-bottom: 0.5em;} diff --git a/docs/drift_data_JKI.html b/docs/drift_data_JKI.html new file mode 100644 index 0000000..6a45077 --- /dev/null +++ b/docs/drift_data_JKI.html @@ -0,0 +1,242 @@ + + + + +drift_data_JKI. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Deposition from spray drift expressed as percent of the applied dose as +published by the JKI

+ +
+
+ +
+

Format

+ +

A list currently containing matrices with spray drift percentage +data for field crops (Ackerbau), and Pome/stone fruit, early and late +(Obstbau frueh, spaet).

+ +
+ +
+

Source

+ +

JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved +from +http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html +on 2015-06-11

+ +
+ +
+

Description

+ +

Deposition from spray drift expressed as percent of the applied dose as +published by the German Julius-Kühn Institute (JKI).

+ +
+ +
+

Details

+ +

The data were extracted from the spreadsheet cited below using the R code +given in the example section. The spreadsheet is not included in the package +as its licence is not clear.

+ +
+ +

Examples

+ 

+## Not run: ------------------------------------
+#   # This is the code that was used to extract the data
+#   library(readxl)
+#   abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"
+#   JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")
+#   names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")
+#   drift_data_JKI <- list()
+# 
+#   for (n in 1:8) {
+#     drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2)
+#     drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) 
+#     dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]),
+#                                             crop = JKI_crops)
+#     drift_data_JKI[[n]] <- drift_data
+#   }
+#   save(drift_data_JKI, file = "data/drift_data_JKI.RData")
+## ---------------------------------------------
+
+# And this is the resulting data
+drift_data_JKI

+
[[1]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      2.77            NA            NA
+      3        NA         29.20         15.73
+      5      0.57         19.89          8.41
+      10     0.29         11.81          3.60
+      15     0.20          5.55          1.81
+      20     0.15          2.77          1.09
+      30     0.10          1.04          0.54
+      40     0.07          0.52          0.32
+      50     0.06          0.30          0.22
+
+[[2]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      2.38            NA            NA
+      3        NA         25.53         12.13
+      5      0.47         16.87          6.81
+      10     0.24          9.61          3.11
+      15     0.16          5.61          1.58
+      20     0.12          2.59          0.90
+      30     0.08          0.87          0.40
+      40     0.06          0.40          0.23
+      50     0.05          0.22          0.15
+
+[[3]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      2.01            NA            NA
+      3        NA         23.96         11.01
+      5      0.41         15.79          6.04
+      10     0.20          8.96          2.67
+      15     0.14          4.24          1.39
+      20     0.10          2.01          0.80
+      30     0.07          0.70          0.36
+      40     0.05          0.33          0.21
+      50     0.04          0.19          0.13
+
+[[4]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.85            NA            NA
+      3        NA         23.61         10.12
+      5      0.38         15.42          5.60
+      10     0.19          8.66          2.50
+      15     0.13          4.01          1.28
+      20     0.10          1.89          0.75
+      30     0.06          0.66          0.35
+      40     0.05          0.31          0.20
+      50     0.04          0.17          0.13
+
+[[5]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.75            NA            NA
+      3        NA         23.12          9.74
+      5      0.36         15.06          5.41
+      10     0.18          8.42          2.43
+      15     0.12          3.83          1.24
+      20     0.09          1.81          0.72
+      30     0.06          0.63          0.34
+      40     0.05          0.30          0.20
+      50     0.04          0.17          0.13
+
+[[6]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.64            NA            NA
+      3        NA         22.76          9.21
+      5      0.34         14.64          5.18
+      10     0.17          8.04          2.38
+      15     0.11          3.71          1.20
+      20     0.09          1.75          0.68
+      30     0.06          0.61          0.31
+      40     0.04          0.29          0.17
+      50     0.03          0.16          0.11
+
+[[7]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.61            NA            NA
+      3        NA         22.69          9.10
+      5      0.33         14.45          5.11
+      10     0.17          7.83          2.33
+      15     0.11          3.62          1.20
+      20     0.08          1.71          0.67
+      30     0.06          0.60          0.30
+      40     0.04          0.28          0.17
+      50     0.03          0.16          0.11
+
+[[8]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.52            NA            NA
+      3        NA         22.24          8.66
+      5      0.31         14.09          4.92
+      10     0.16          7.58          2.29
+      15     0.11          3.48          1.14
+      20     0.08          1.65          0.65
+      30     0.05          0.57          0.29
+      40     0.04          0.27          0.16
+      50     0.03          0.15          0.11
+
+
+
+
+ + + + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/endpoint.html b/docs/endpoint.html new file mode 100644 index 0000000..58696a9 --- /dev/null +++ b/docs/endpoint.html @@ -0,0 +1,158 @@ + + + + +endpoint. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Retrieve endpoint information from the chyaml field of a chent object

+ +
+
+

Usage

+ 
endpoint(chent, medium = "soil", type = c("degradation", "sorption"),
+  lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic",
+  "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean,
+  raw = FALSE, signif = 3)
+
+soil_DT50(chent, aggregator = geomean, signif = 3,
+  lab_field = "laboratory", value = "DT50ref", redox = "aerobic",
+  raw = FALSE)
+
+soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc",
+  raw = FALSE)
+
+soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
+
+soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc =
+  geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3),
+  raw = FALSE)
+ +

Arguments

+
+
chent
+
The chent object to get the information from
+
medium
+
The medium for which information is sought
+
type
+
The information type
+
lab_field
+
If not NA, do we want laboratory or field endpoints
+
redox
+
If not NA, are we looking for aerobic or anaerobic data
+
value
+
The name of the value we want. The list given in the +usage section is not exclusive
+
aggregator
+
The aggregator function. Can be mean, +geomean, or identity, for example.
+
raw
+
Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?
+
signif
+
How many significant digits do we want
+
values
+
The values to be returned
+
aggregators
+
A named vector of aggregator functions to be used
+
+ +
+

Value

+ +

+The result from applying the aggregator function to + the values converted to a numeric vector, rounded to the + given number of significant digits, or, if raw = TRUE, + the values as a character value, retaining any implicit + information on precision that may be present. +

+ +
+ +
+

Description

+ +

R6 class objects of class chent represent chemical entities +and can hold a list of information loaded from a chemical yaml file in their +chyaml field. Such information is extracted and optionally aggregated by +this function.

+ +
+ +
+

Details

+ +

The functions soil_* are functions to extract soil specific endpoints. +For the Freundlich exponent, the capital letter N is used in order to +facilitate dealing with such data in R. In pesticide fate modelling, this +exponent is often called 1/n.

+ +
+
+
+ + + + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/geomean.html b/docs/geomean.html new file mode 100644 index 0000000..3530c32 --- /dev/null +++ b/docs/geomean.html @@ -0,0 +1,121 @@ + + + + +geomean. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +

Calculate the geometric mean

+ +
+
+

Usage

+ 
geomean(x, na.rm = TRUE)
+ +

Arguments

+
+
x
+
Vector of numbers
+
na.rm
+
Should NA values be omitted?
+
+ +
+

Value

+ +

+The geometric mean +

+ +
+ +
+

Description

+ +

Based on some posts in a thread on Stackoverflow +http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in +This function checks for negative values, removes NA values per default and +returns 0 if at least one element of the vector is 0.

+ +
+ +

Examples

+ 
geomean(c(1, 3, 9))

+
[1] 3
+

+
geomean(c(1, 3, NA, 9))

+
[1] 3
+

+
## Not run: geomean(c(1, -3, 9)) # returns an error
+
+
+ + + + +

Author

+ +Johannes Ranke + + +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/img/glyphicons-halflings-white.png b/docs/img/glyphicons-halflings-white.png new file mode 100644 index 0000000..3bf6484 Binary files /dev/null and b/docs/img/glyphicons-halflings-white.png differ diff --git a/docs/img/glyphicons-halflings.png b/docs/img/glyphicons-halflings.png new file mode 100644 index 0000000..79bc568 Binary files /dev/null and b/docs/img/glyphicons-halflings.png differ diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 0000000..a82dcae --- /dev/null +++ b/docs/index.html @@ -0,0 +1,208 @@ + + + + +Home. pfm 0.3-8 + + + + + + + + + + + + + + + +
+
+
+ pfm 0.3-8 +
+ +
+
+
+
+ + +
+
+ +
+ +
+
+

pfm

+ +

The R package pfm provides some utilities for dealing with FOCUS pesticide fate modelling tools, +(currently only TOXSWA cwa and out files), made available under the GNU public license. +This means:

+ +
This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+details.
+
+You should have received a copy of the GNU General Public License along with
+this program. If not, see <http://www.gnu.org/licenses/>
+
+ +

Installation

+ +

You can install the package from github, e.g. +using the devtools package. Using quick = TRUE skips docs, +multiple-architecture builds, demos, and vignettes, to make installation as +fast and painless as possible.

+ +
library(devtools)
+install_github("jranke/pfm", subdir = "pkg", quick = TRUE)
+
+ +

Use

+ +

Analyse TOXSWA output

+ +

Read in and analyse a cwa file:

+ +
library(pfm, quietly = TRUE)
+
+ +
## 
+## Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) 
+## [GCC 4.9.2]
+
+ +
example_cwa <- read.TOXSWA_cwa("00003s_pa.cwa")
+plot(example_cwa)
+
+ +

+ +

Get events above thresholds of 20 and 100 µg/L, +and do a moving window analysis for windows of 7 days +and 21 days, print the results:

+ +
example_cwa$get_events(c(20, 100))
+example_cwa$moving_windows(c(7, 21))
+print(example_cwa)
+
+ +
## <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 
+##                datetime     t t_firstjan t_rel_to_max cwa_mug_per_L
+## 20  1978-10-01 00:00:00 0.000   273.0000      -55.333             0
+## 40  1978-10-01 01:00:00 0.042   273.0417      -55.291             0
+## 60  1978-10-01 02:00:00 0.083   273.0833      -55.250             0
+## 80  1978-10-01 03:00:00 0.125   273.1250      -55.208             0
+## 100 1978-10-01 04:00:00 0.167   273.1667      -55.166             0
+## 120 1978-10-01 05:00:00 0.208   273.2083      -55.125             0
+##     cwa_tot_mug_per_L
+## 20                  0
+## 40                  0
+## 60                  0
+## 80                  0
+## 100                 0
+## 120                 0
+## Moving window analysis
+##    window  max_TWAC max_AUC_h max_AUC_d
+## 1  7 days 2.3926551  401.9660  16.74859
+## 2 21 days 0.8369248  421.8101  17.57542
+## Event statistics for threshold 20 
+##   t_start  cwa_max duration pre_interval    AUC_h   AUC_d
+## 1  55.083 40.58401    0.417       55.083 365.7912 15.2413
+## Event statistics for threshold 100 
+## No events found
+
+ +

This can also be done with out files, the function reads +out files from current TOXSWA versions as well as cwa files +from old TOXSWA versions.

+ +

Calculate PEC soil

+ +

Simple PEC soil calculation for an application rate of 100 g/ha and +25% interception, assuming complete mixing into 5 cm and a soil bulk +density of 1.5 kg/L, output in mg/kg:

+ +
PEC_soil(100, interception = 0.25)
+
+ +
##      scenario
+## t_avg default
+##     0     0.1
+
+ +

Rautmann drift data

+ +

Some of the drift percentage data published by the JKI are included. To +see the data for one application:

+ +
drift_data_JKI[1]
+
+ +
## [[1]]
+##         crop
+## distance Ackerbau Obstbau frueh Obstbau spaet
+##       1      2.77            NA            NA
+##       3        NA         29.20         15.73
+##       5      0.57         19.89          8.41
+##       10     0.29         11.81          3.60
+##       15     0.20          5.55          1.81
+##       20     0.15          2.77          1.09
+##       30     0.10          1.04          0.54
+##       40     0.07          0.52          0.32
+##       50     0.06          0.30          0.22
+
+ +

PEC surface water due to drift

+ +

Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm +deep water body are obtained using

+ +
PEC_sw_drift(100, applications = 1)
+
+ +
##        1 m        5 m       10 m       20 m 
+## 0.92333333 0.19000000 0.09666667 0.05000000
+
+ +
+ +
+

Authors

+ +
+
+ + +
+ + \ No newline at end of file diff --git a/docs/js/bootstrap.js b/docs/js/bootstrap.js new file mode 100644 index 0000000..5d6e65b --- /dev/null +++ b/docs/js/bootstrap.js @@ -0,0 +1,1825 @@ +/* =================================================== + * bootstrap-transition.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#transitions + * =================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + $(function () { + + "use strict"; // jshint ;_; + + + /* CSS TRANSITION SUPPORT (http://www.modernizr.com/) + * ======================================================= */ + + $.support.transition = (function () { + + var transitionEnd = (function () { + + var el = document.createElement('bootstrap') + , transEndEventNames = { + 'WebkitTransition' : 'webkitTransitionEnd' + , 'MozTransition' : 'transitionend' + , 'OTransition' : 'oTransitionEnd' + , 'msTransition' : 'MSTransitionEnd' + , 'transition' : 'transitionend' + } + , name + + for (name in transEndEventNames){ + if (el.style[name] !== undefined) { + return transEndEventNames[name] + } + } + + }()) + + return transitionEnd && { + end: transitionEnd + } + + })() + + }) + +}(window.jQuery);/* ========================================================== + * bootstrap-alert.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#alerts + * ========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* ALERT CLASS DEFINITION + * ====================== */ + + var dismiss = '[data-dismiss="alert"]' + , Alert = function (el) { + $(el).on('click', dismiss, this.close) + } + + Alert.prototype.close = function (e) { + var $this = $(this) + , selector = $this.attr('data-target') + , $parent + + if (!selector) { + selector = $this.attr('href') + selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + $parent = $(selector) + + e && e.preventDefault() + + $parent.length || ($parent = $this.hasClass('alert') ? $this : $this.parent()) + + $parent.trigger(e = $.Event('close')) + + if (e.isDefaultPrevented()) return + + $parent.removeClass('in') + + function removeElement() { + $parent + .trigger('closed') + .remove() + } + + $.support.transition && $parent.hasClass('fade') ? + $parent.on($.support.transition.end, removeElement) : + removeElement() + } + + + /* ALERT PLUGIN DEFINITION + * ======================= */ + + $.fn.alert = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('alert') + if (!data) $this.data('alert', (data = new Alert(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + $.fn.alert.Constructor = Alert + + + /* ALERT DATA-API + * ============== */ + + $(function () { + $('body').on('click.alert.data-api', dismiss, Alert.prototype.close) + }) + +}(window.jQuery);/* ============================================================ + * bootstrap-button.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#buttons + * ============================================================ + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================ */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* BUTTON PUBLIC CLASS DEFINITION + * ============================== */ + + var Button = function (element, options) { + this.$element = $(element) + this.options = $.extend({}, $.fn.button.defaults, options) + } + + Button.prototype.setState = function (state) { + var d = 'disabled' + , $el = this.$element + , data = $el.data() + , val = $el.is('input') ? 'val' : 'html' + + state = state + 'Text' + data.resetText || $el.data('resetText', $el[val]()) + + $el[val](data[state] || this.options[state]) + + // push to event loop to allow forms to submit + setTimeout(function () { + state == 'loadingText' ? + $el.addClass(d).attr(d, d) : + $el.removeClass(d).removeAttr(d) + }, 0) + } + + Button.prototype.toggle = function () { + var $parent = this.$element.parent('[data-toggle="buttons-radio"]') + + $parent && $parent + .find('.active') + .removeClass('active') + + this.$element.toggleClass('active') + } + + + /* BUTTON PLUGIN DEFINITION + * ======================== */ + + $.fn.button = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('button') + , options = typeof option == 'object' && option + if (!data) $this.data('button', (data = new Button(this, options))) + if (option == 'toggle') data.toggle() + else if (option) data.setState(option) + }) + } + + $.fn.button.defaults = { + loadingText: 'loading...' + } + + $.fn.button.Constructor = Button + + + /* BUTTON DATA-API + * =============== */ + + $(function () { + $('body').on('click.button.data-api', '[data-toggle^=button]', function ( e ) { + var $btn = $(e.target) + if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn') + $btn.button('toggle') + }) + }) + +}(window.jQuery);/* ========================================================== + * bootstrap-carousel.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#carousel + * ========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* CAROUSEL CLASS DEFINITION + * ========================= */ + + var Carousel = function (element, options) { + this.$element = $(element) + this.options = options + this.options.slide && this.slide(this.options.slide) + this.options.pause == 'hover' && this.$element + .on('mouseenter', $.proxy(this.pause, this)) + .on('mouseleave', $.proxy(this.cycle, this)) + } + + Carousel.prototype = { + + cycle: function (e) { + if (!e) this.paused = false + this.options.interval + && !this.paused + && (this.interval = setInterval($.proxy(this.next, this), this.options.interval)) + return this + } + + , to: function (pos) { + var $active = this.$element.find('.active') + , children = $active.parent().children() + , activePos = children.index($active) + , that = this + + if (pos > (children.length - 1) || pos < 0) return + + if (this.sliding) { + return this.$element.one('slid', function () { + that.to(pos) + }) + } + + if (activePos == pos) { + return this.pause().cycle() + } + + return this.slide(pos > activePos ? 'next' : 'prev', $(children[pos])) + } + + , pause: function (e) { + if (!e) this.paused = true + clearInterval(this.interval) + this.interval = null + return this + } + + , next: function () { + if (this.sliding) return + return this.slide('next') + } + + , prev: function () { + if (this.sliding) return + return this.slide('prev') + } + + , slide: function (type, next) { + var $active = this.$element.find('.active') + , $next = next || $active[type]() + , isCycling = this.interval + , direction = type == 'next' ? 'left' : 'right' + , fallback = type == 'next' ? 'first' : 'last' + , that = this + , e = $.Event('slide') + + this.sliding = true + + isCycling && this.pause() + + $next = $next.length ? $next : this.$element.find('.item')[fallback]() + + if ($next.hasClass('active')) return + + if ($.support.transition && this.$element.hasClass('slide')) { + this.$element.trigger(e) + if (e.isDefaultPrevented()) return + $next.addClass(type) + $next[0].offsetWidth // force reflow + $active.addClass(direction) + $next.addClass(direction) + this.$element.one($.support.transition.end, function () { + $next.removeClass([type, direction].join(' ')).addClass('active') + $active.removeClass(['active', direction].join(' ')) + that.sliding = false + setTimeout(function () { that.$element.trigger('slid') }, 0) + }) + } else { + this.$element.trigger(e) + if (e.isDefaultPrevented()) return + $active.removeClass('active') + $next.addClass('active') + this.sliding = false + this.$element.trigger('slid') + } + + isCycling && this.cycle() + + return this + } + + } + + + /* CAROUSEL PLUGIN DEFINITION + * ========================== */ + + $.fn.carousel = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('carousel') + , options = $.extend({}, $.fn.carousel.defaults, typeof option == 'object' && option) + if (!data) $this.data('carousel', (data = new Carousel(this, options))) + if (typeof option == 'number') data.to(option) + else if (typeof option == 'string' || (option = options.slide)) data[option]() + else if (options.interval) data.cycle() + }) + } + + $.fn.carousel.defaults = { + interval: 5000 + , pause: 'hover' + } + + $.fn.carousel.Constructor = Carousel + + + /* CAROUSEL DATA-API + * ================= */ + + $(function () { + $('body').on('click.carousel.data-api', '[data-slide]', function ( e ) { + var $this = $(this), href + , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 + , options = !$target.data('modal') && $.extend({}, $target.data(), $this.data()) + $target.carousel(options) + e.preventDefault() + }) + }) + +}(window.jQuery);/* ============================================================= + * bootstrap-collapse.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#collapse + * ============================================================= + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================ */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* COLLAPSE PUBLIC CLASS DEFINITION + * ================================ */ + + var Collapse = function (element, options) { + this.$element = $(element) + this.options = $.extend({}, $.fn.collapse.defaults, options) + + if (this.options.parent) { + this.$parent = $(this.options.parent) + } + + this.options.toggle && this.toggle() + } + + Collapse.prototype = { + + constructor: Collapse + + , dimension: function () { + var hasWidth = this.$element.hasClass('width') + return hasWidth ? 'width' : 'height' + } + + , show: function () { + var dimension + , scroll + , actives + , hasData + + if (this.transitioning) return + + dimension = this.dimension() + scroll = $.camelCase(['scroll', dimension].join('-')) + actives = this.$parent && this.$parent.find('> .accordion-group > .in') + + if (actives && actives.length) { + hasData = actives.data('collapse') + if (hasData && hasData.transitioning) return + actives.collapse('hide') + hasData || actives.data('collapse', null) + } + + this.$element[dimension](0) + this.transition('addClass', $.Event('show'), 'shown') + this.$element[dimension](this.$element[0][scroll]) + } + + , hide: function () { + var dimension + if (this.transitioning) return + dimension = this.dimension() + this.reset(this.$element[dimension]()) + this.transition('removeClass', $.Event('hide'), 'hidden') + this.$element[dimension](0) + } + + , reset: function (size) { + var dimension = this.dimension() + + this.$element + .removeClass('collapse') + [dimension](size || 'auto') + [0].offsetWidth + + this.$element[size !== null ? 'addClass' : 'removeClass']('collapse') + + return this + } + + , transition: function (method, startEvent, completeEvent) { + var that = this + , complete = function () { + if (startEvent.type == 'show') that.reset() + that.transitioning = 0 + that.$element.trigger(completeEvent) + } + + this.$element.trigger(startEvent) + + if (startEvent.isDefaultPrevented()) return + + this.transitioning = 1 + + this.$element[method]('in') + + $.support.transition && this.$element.hasClass('collapse') ? + this.$element.one($.support.transition.end, complete) : + complete() + } + + , toggle: function () { + this[this.$element.hasClass('in') ? 'hide' : 'show']() + } + + } + + + /* COLLAPSIBLE PLUGIN DEFINITION + * ============================== */ + + $.fn.collapse = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('collapse') + , options = typeof option == 'object' && option + if (!data) $this.data('collapse', (data = new Collapse(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.collapse.defaults = { + toggle: true + } + + $.fn.collapse.Constructor = Collapse + + + /* COLLAPSIBLE DATA-API + * ==================== */ + + $(function () { + $('body').on('click.collapse.data-api', '[data-toggle=collapse]', function ( e ) { + var $this = $(this), href + , target = $this.attr('data-target') + || e.preventDefault() + || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7 + , option = $(target).data('collapse') ? 'toggle' : $this.data() + $(target).collapse(option) + }) + }) + +}(window.jQuery);/* ============================================================ + * bootstrap-dropdown.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#dropdowns + * ============================================================ + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================ */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* DROPDOWN CLASS DEFINITION + * ========================= */ + + var toggle = '[data-toggle="dropdown"]' + , Dropdown = function (element) { + var $el = $(element).on('click.dropdown.data-api', this.toggle) + $('html').on('click.dropdown.data-api', function () { + $el.parent().removeClass('open') + }) + } + + Dropdown.prototype = { + + constructor: Dropdown + + , toggle: function (e) { + var $this = $(this) + , $parent + , selector + , isActive + + if ($this.is('.disabled, :disabled')) return + + selector = $this.attr('data-target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + $parent = $(selector) + $parent.length || ($parent = $this.parent()) + + isActive = $parent.hasClass('open') + + clearMenus() + + if (!isActive) $parent.toggleClass('open') + + return false + } + + } + + function clearMenus() { + $(toggle).parent().removeClass('open') + } + + + /* DROPDOWN PLUGIN DEFINITION + * ========================== */ + + $.fn.dropdown = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('dropdown') + if (!data) $this.data('dropdown', (data = new Dropdown(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + $.fn.dropdown.Constructor = Dropdown + + + /* APPLY TO STANDARD DROPDOWN ELEMENTS + * =================================== */ + + $(function () { + $('html').on('click.dropdown.data-api', clearMenus) + $('body') + .on('click.dropdown', '.dropdown form', function (e) { e.stopPropagation() }) + .on('click.dropdown.data-api', toggle, Dropdown.prototype.toggle) + }) + +}(window.jQuery);/* ========================================================= + * bootstrap-modal.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#modals + * ========================================================= + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================= */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* MODAL CLASS DEFINITION + * ====================== */ + + var Modal = function (content, options) { + this.options = options + this.$element = $(content) + .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this)) + } + + Modal.prototype = { + + constructor: Modal + + , toggle: function () { + return this[!this.isShown ? 'show' : 'hide']() + } + + , show: function () { + var that = this + , e = $.Event('show') + + this.$element.trigger(e) + + if (this.isShown || e.isDefaultPrevented()) return + + $('body').addClass('modal-open') + + this.isShown = true + + escape.call(this) + backdrop.call(this, function () { + var transition = $.support.transition && that.$element.hasClass('fade') + + if (!that.$element.parent().length) { + that.$element.appendTo(document.body) //don't move modals dom position + } + + that.$element + .show() + + if (transition) { + that.$element[0].offsetWidth // force reflow + } + + that.$element.addClass('in') + + transition ? + that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) : + that.$element.trigger('shown') + + }) + } + + , hide: function (e) { + e && e.preventDefault() + + var that = this + + e = $.Event('hide') + + this.$element.trigger(e) + + if (!this.isShown || e.isDefaultPrevented()) return + + this.isShown = false + + $('body').removeClass('modal-open') + + escape.call(this) + + this.$element.removeClass('in') + + $.support.transition && this.$element.hasClass('fade') ? + hideWithTransition.call(this) : + hideModal.call(this) + } + + } + + + /* MODAL PRIVATE METHODS + * ===================== */ + + function hideWithTransition() { + var that = this + , timeout = setTimeout(function () { + that.$element.off($.support.transition.end) + hideModal.call(that) + }, 500) + + this.$element.one($.support.transition.end, function () { + clearTimeout(timeout) + hideModal.call(that) + }) + } + + function hideModal(that) { + this.$element + .hide() + .trigger('hidden') + + backdrop.call(this) + } + + function backdrop(callback) { + var that = this + , animate = this.$element.hasClass('fade') ? 'fade' : '' + + if (this.isShown && this.options.backdrop) { + var doAnimate = $.support.transition && animate + + this.$backdrop = $('
') + .appendTo(document.body) + + if (this.options.backdrop != 'static') { + this.$backdrop.click($.proxy(this.hide, this)) + } + + if (doAnimate) this.$backdrop[0].offsetWidth // force reflow + + this.$backdrop.addClass('in') + + doAnimate ? + this.$backdrop.one($.support.transition.end, callback) : + callback() + + } else if (!this.isShown && this.$backdrop) { + this.$backdrop.removeClass('in') + + $.support.transition && this.$element.hasClass('fade')? + this.$backdrop.one($.support.transition.end, $.proxy(removeBackdrop, this)) : + removeBackdrop.call(this) + + } else if (callback) { + callback() + } + } + + function removeBackdrop() { + this.$backdrop.remove() + this.$backdrop = null + } + + function escape() { + var that = this + if (this.isShown && this.options.keyboard) { + $(document).on('keyup.dismiss.modal', function ( e ) { + e.which == 27 && that.hide() + }) + } else if (!this.isShown) { + $(document).off('keyup.dismiss.modal') + } + } + + + /* MODAL PLUGIN DEFINITION + * ======================= */ + + $.fn.modal = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('modal') + , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option) + if (!data) $this.data('modal', (data = new Modal(this, options))) + if (typeof option == 'string') data[option]() + else if (options.show) data.show() + }) + } + + $.fn.modal.defaults = { + backdrop: true + , keyboard: true + , show: true + } + + $.fn.modal.Constructor = Modal + + + /* MODAL DATA-API + * ============== */ + + $(function () { + $('body').on('click.modal.data-api', '[data-toggle="modal"]', function ( e ) { + var $this = $(this), href + , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 + , option = $target.data('modal') ? 'toggle' : $.extend({}, $target.data(), $this.data()) + + e.preventDefault() + $target.modal(option) + }) + }) + +}(window.jQuery);/* =========================================================== + * bootstrap-tooltip.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#tooltips + * Inspired by the original jQuery.tipsy by Jason Frame + * =========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* TOOLTIP PUBLIC CLASS DEFINITION + * =============================== */ + + var Tooltip = function (element, options) { + this.init('tooltip', element, options) + } + + Tooltip.prototype = { + + constructor: Tooltip + + , init: function (type, element, options) { + var eventIn + , eventOut + + this.type = type + this.$element = $(element) + this.options = this.getOptions(options) + this.enabled = true + + if (this.options.trigger != 'manual') { + eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus' + eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur' + this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this)) + this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this)) + } + + this.options.selector ? + (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : + this.fixTitle() + } + + , getOptions: function (options) { + options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data()) + + if (options.delay && typeof options.delay == 'number') { + options.delay = { + show: options.delay + , hide: options.delay + } + } + + return options + } + + , enter: function (e) { + var self = $(e.currentTarget)[this.type](this._options).data(this.type) + + if (!self.options.delay || !self.options.delay.show) return self.show() + + clearTimeout(this.timeout) + self.hoverState = 'in' + this.timeout = setTimeout(function() { + if (self.hoverState == 'in') self.show() + }, self.options.delay.show) + } + + , leave: function (e) { + var self = $(e.currentTarget)[this.type](this._options).data(this.type) + + if (this.timeout) clearTimeout(this.timeout) + if (!self.options.delay || !self.options.delay.hide) return self.hide() + + self.hoverState = 'out' + this.timeout = setTimeout(function() { + if (self.hoverState == 'out') self.hide() + }, self.options.delay.hide) + } + + , show: function () { + var $tip + , inside + , pos + , actualWidth + , actualHeight + , placement + , tp + + if (this.hasContent() && this.enabled) { + $tip = this.tip() + this.setContent() + + if (this.options.animation) { + $tip.addClass('fade') + } + + placement = typeof this.options.placement == 'function' ? + this.options.placement.call(this, $tip[0], this.$element[0]) : + this.options.placement + + inside = /in/.test(placement) + + $tip + .remove() + .css({ top: 0, left: 0, display: 'block' }) + .appendTo(inside ? this.$element : document.body) + + pos = this.getPosition(inside) + + actualWidth = $tip[0].offsetWidth + actualHeight = $tip[0].offsetHeight + + switch (inside ? placement.split(' ')[1] : placement) { + case 'bottom': + tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2} + break + case 'top': + tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2} + break + case 'left': + tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth} + break + case 'right': + tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width} + break + } + + $tip + .css(tp) + .addClass(placement) + .addClass('in') + } + } + + , isHTML: function(text) { + // html string detection logic adapted from jQuery + return typeof text != 'string' + || ( text.charAt(0) === "<" + && text.charAt( text.length - 1 ) === ">" + && text.length >= 3 + ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text) + } + + , setContent: function () { + var $tip = this.tip() + , title = this.getTitle() + + $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title) + $tip.removeClass('fade in top bottom left right') + } + + , hide: function () { + var that = this + , $tip = this.tip() + + $tip.removeClass('in') + + function removeWithAnimation() { + var timeout = setTimeout(function () { + $tip.off($.support.transition.end).remove() + }, 500) + + $tip.one($.support.transition.end, function () { + clearTimeout(timeout) + $tip.remove() + }) + } + + $.support.transition && this.$tip.hasClass('fade') ? + removeWithAnimation() : + $tip.remove() + } + + , fixTitle: function () { + var $e = this.$element + if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { + $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title') + } + } + + , hasContent: function () { + return this.getTitle() + } + + , getPosition: function (inside) { + return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), { + width: this.$element[0].offsetWidth + , height: this.$element[0].offsetHeight + }) + } + + , getTitle: function () { + var title + , $e = this.$element + , o = this.options + + title = $e.attr('data-original-title') + || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) + + return title + } + + , tip: function () { + return this.$tip = this.$tip || $(this.options.template) + } + + , validate: function () { + if (!this.$element[0].parentNode) { + this.hide() + this.$element = null + this.options = null + } + } + + , enable: function () { + this.enabled = true + } + + , disable: function () { + this.enabled = false + } + + , toggleEnabled: function () { + this.enabled = !this.enabled + } + + , toggle: function () { + this[this.tip().hasClass('in') ? 'hide' : 'show']() + } + + } + + + /* TOOLTIP PLUGIN DEFINITION + * ========================= */ + + $.fn.tooltip = function ( option ) { + return this.each(function () { + var $this = $(this) + , data = $this.data('tooltip') + , options = typeof option == 'object' && option + if (!data) $this.data('tooltip', (data = new Tooltip(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.tooltip.Constructor = Tooltip + + $.fn.tooltip.defaults = { + animation: true + , placement: 'top' + , selector: false + , template: '
' + , trigger: 'hover' + , title: '' + , delay: 0 + } + +}(window.jQuery); +/* =========================================================== + * bootstrap-popover.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#popovers + * =========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * =========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* POPOVER PUBLIC CLASS DEFINITION + * =============================== */ + + var Popover = function ( element, options ) { + this.init('popover', element, options) + } + + + /* NOTE: POPOVER EXTENDS BOOTSTRAP-TOOLTIP.js + ========================================== */ + + Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype, { + + constructor: Popover + + , setContent: function () { + var $tip = this.tip() + , title = this.getTitle() + , content = this.getContent() + + $tip.find('.popover-title')[this.isHTML(title) ? 'html' : 'text'](title) + $tip.find('.popover-content > *')[this.isHTML(content) ? 'html' : 'text'](content) + + $tip.removeClass('fade top bottom left right in') + } + + , hasContent: function () { + return this.getTitle() || this.getContent() + } + + , getContent: function () { + var content + , $e = this.$element + , o = this.options + + content = $e.attr('data-content') + || (typeof o.content == 'function' ? o.content.call($e[0]) : o.content) + + return content + } + + , tip: function () { + if (!this.$tip) { + this.$tip = $(this.options.template) + } + return this.$tip + } + + }) + + + /* POPOVER PLUGIN DEFINITION + * ======================= */ + + $.fn.popover = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('popover') + , options = typeof option == 'object' && option + if (!data) $this.data('popover', (data = new Popover(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.popover.Constructor = Popover + + $.fn.popover.defaults = $.extend({} , $.fn.tooltip.defaults, { + placement: 'right' + , content: '' + , template: '

' + }) + +}(window.jQuery);/* ============================================================= + * bootstrap-scrollspy.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#scrollspy + * ============================================================= + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* SCROLLSPY CLASS DEFINITION + * ========================== */ + + function ScrollSpy( element, options) { + var process = $.proxy(this.process, this) + , $element = $(element).is('body') ? $(window) : $(element) + , href + this.options = $.extend({}, $.fn.scrollspy.defaults, options) + this.$scrollElement = $element.on('scroll.scroll.data-api', process) + this.selector = (this.options.target + || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 + || '') + ' .nav li > a' + this.$body = $('body') + this.refresh() + this.process() + } + + ScrollSpy.prototype = { + + constructor: ScrollSpy + + , refresh: function () { + var self = this + , $targets + + this.offsets = $([]) + this.targets = $([]) + + $targets = this.$body + .find(this.selector) + .map(function () { + var $el = $(this) + , href = $el.data('target') || $el.attr('href') + , $href = /^#\w/.test(href) && $(href) + return ( $href + && href.length + && [[ $href.position().top, href ]] ) || null + }) + .sort(function (a, b) { return a[0] - b[0] }) + .each(function () { + self.offsets.push(this[0]) + self.targets.push(this[1]) + }) + } + + , process: function () { + var scrollTop = this.$scrollElement.scrollTop() + this.options.offset + , scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight + , maxScroll = scrollHeight - this.$scrollElement.height() + , offsets = this.offsets + , targets = this.targets + , activeTarget = this.activeTarget + , i + + if (scrollTop >= maxScroll) { + return activeTarget != (i = targets.last()[0]) + && this.activate ( i ) + } + + for (i = offsets.length; i--;) { + activeTarget != targets[i] + && scrollTop >= offsets[i] + && (!offsets[i + 1] || scrollTop <= offsets[i + 1]) + && this.activate( targets[i] ) + } + } + + , activate: function (target) { + var active + , selector + + this.activeTarget = target + + $(this.selector) + .parent('.active') + .removeClass('active') + + selector = this.selector + + '[data-target="' + target + '"],' + + this.selector + '[href="' + target + '"]' + + active = $(selector) + .parent('li') + .addClass('active') + + if (active.parent('.dropdown-menu')) { + active = active.closest('li.dropdown').addClass('active') + } + + active.trigger('activate') + } + + } + + + /* SCROLLSPY PLUGIN DEFINITION + * =========================== */ + + $.fn.scrollspy = function ( option ) { + return this.each(function () { + var $this = $(this) + , data = $this.data('scrollspy') + , options = typeof option == 'object' && option + if (!data) $this.data('scrollspy', (data = new ScrollSpy(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.scrollspy.Constructor = ScrollSpy + + $.fn.scrollspy.defaults = { + offset: 10 + } + + + /* SCROLLSPY DATA-API + * ================== */ + + $(function () { + $('[data-spy="scroll"]').each(function () { + var $spy = $(this) + $spy.scrollspy($spy.data()) + }) + }) + +}(window.jQuery);/* ======================================================== + * bootstrap-tab.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#tabs + * ======================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ======================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* TAB CLASS DEFINITION + * ==================== */ + + var Tab = function ( element ) { + this.element = $(element) + } + + Tab.prototype = { + + constructor: Tab + + , show: function () { + var $this = this.element + , $ul = $this.closest('ul:not(.dropdown-menu)') + , selector = $this.attr('data-target') + , previous + , $target + , e + + if (!selector) { + selector = $this.attr('href') + selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + if ( $this.parent('li').hasClass('active') ) return + + previous = $ul.find('.active a').last()[0] + + e = $.Event('show', { + relatedTarget: previous + }) + + $this.trigger(e) + + if (e.isDefaultPrevented()) return + + $target = $(selector) + + this.activate($this.parent('li'), $ul) + this.activate($target, $target.parent(), function () { + $this.trigger({ + type: 'shown' + , relatedTarget: previous + }) + }) + } + + , activate: function ( element, container, callback) { + var $active = container.find('> .active') + , transition = callback + && $.support.transition + && $active.hasClass('fade') + + function next() { + $active + .removeClass('active') + .find('> .dropdown-menu > .active') + .removeClass('active') + + element.addClass('active') + + if (transition) { + element[0].offsetWidth // reflow for transition + element.addClass('in') + } else { + element.removeClass('fade') + } + + if ( element.parent('.dropdown-menu') ) { + element.closest('li.dropdown').addClass('active') + } + + callback && callback() + } + + transition ? + $active.one($.support.transition.end, next) : + next() + + $active.removeClass('in') + } + } + + + /* TAB PLUGIN DEFINITION + * ===================== */ + + $.fn.tab = function ( option ) { + return this.each(function () { + var $this = $(this) + , data = $this.data('tab') + if (!data) $this.data('tab', (data = new Tab(this))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.tab.Constructor = Tab + + + /* TAB DATA-API + * ============ */ + + $(function () { + $('body').on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) { + e.preventDefault() + $(this).tab('show') + }) + }) + +}(window.jQuery);/* ============================================================= + * bootstrap-typeahead.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#typeahead + * ============================================================= + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================ */ + + +!function($){ + + "use strict"; // jshint ;_; + + + /* TYPEAHEAD PUBLIC CLASS DEFINITION + * ================================= */ + + var Typeahead = function (element, options) { + this.$element = $(element) + this.options = $.extend({}, $.fn.typeahead.defaults, options) + this.matcher = this.options.matcher || this.matcher + this.sorter = this.options.sorter || this.sorter + this.highlighter = this.options.highlighter || this.highlighter + this.updater = this.options.updater || this.updater + this.$menu = $(this.options.menu).appendTo('body') + this.source = this.options.source + this.shown = false + this.listen() + } + + Typeahead.prototype = { + + constructor: Typeahead + + , select: function () { + var val = this.$menu.find('.active').attr('data-value') + this.$element + .val(this.updater(val)) + .change() + return this.hide() + } + + , updater: function (item) { + return item + } + + , show: function () { + var pos = $.extend({}, this.$element.offset(), { + height: this.$element[0].offsetHeight + }) + + this.$menu.css({ + top: pos.top + pos.height + , left: pos.left + }) + + this.$menu.show() + this.shown = true + return this + } + + , hide: function () { + this.$menu.hide() + this.shown = false + return this + } + + , lookup: function (event) { + var that = this + , items + , q + + this.query = this.$element.val() + + if (!this.query) { + return this.shown ? this.hide() : this + } + + items = $.grep(this.source, function (item) { + return that.matcher(item) + }) + + items = this.sorter(items) + + if (!items.length) { + return this.shown ? this.hide() : this + } + + return this.render(items.slice(0, this.options.items)).show() + } + + , matcher: function (item) { + return ~item.toLowerCase().indexOf(this.query.toLowerCase()) + } + + , sorter: function (items) { + var beginswith = [] + , caseSensitive = [] + , caseInsensitive = [] + , item + + while (item = items.shift()) { + if 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(event) { + var active = this.$menu.find('.active').removeClass('active') + , prev = active.prev() + + if (!prev.length) { + prev = this.$menu.find('li').last() + } + + prev.addClass('active') + } + + , listen: function () { + this.$element + .on('blur', $.proxy(this.blur, this)) + .on('keypress', $.proxy(this.keypress, this)) + .on('keyup', $.proxy(this.keyup, this)) + + if ($.browser.webkit || $.browser.msie) { + this.$element.on('keydown', $.proxy(this.keypress, this)) + } + + this.$menu + .on('click', $.proxy(this.click, this)) + .on('mouseenter', 'li', $.proxy(this.mouseenter, this)) + } + + , keyup: function (e) { + switch(e.keyCode) { + case 40: // down arrow + case 38: // up arrow + break + + case 9: // tab + case 13: // enter + if (!this.shown) return + this.select() + break + + case 27: // escape + if (!this.shown) return + this.hide() + break + + default: + this.lookup() + } + + e.stopPropagation() + e.preventDefault() + } + + , keypress: function (e) { + if (!this.shown) return + + switch(e.keyCode) { + case 9: // tab + case 13: // enter + case 27: // escape + e.preventDefault() + break + + case 38: // up arrow + if (e.type != 'keydown') break + e.preventDefault() + this.prev() + break + + case 40: // down arrow + if (e.type != 'keydown') break + e.preventDefault() + this.next() + break + } + + e.stopPropagation() + } + + , blur: function (e) { + var that = this + setTimeout(function () { that.hide() }, 150) + } + + , click: function (e) { + e.stopPropagation() + e.preventDefault() + this.select() + } + + , mouseenter: function (e) { + this.$menu.find('.active').removeClass('active') + $(e.currentTarget).addClass('active') + } + + } + + + /* TYPEAHEAD PLUGIN DEFINITION + * =========================== */ + + $.fn.typeahead = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('typeahead') + , options = typeof option == 'object' && option + if (!data) $this.data('typeahead', (data = new Typeahead(this, 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      ',item:'
      • '},a.fn.typeahead.Constructor=b,a(function(){a("body").on("focus.typeahead.data-api",'[data-provide="typeahead"]',function(b){var c=a(this);if(c.data("typeahead"))return;b.preventDefault(),c.typeahead(c.data())})})}(window.jQuery); \ No newline at end of file diff --git a/docs/pfm_degradation.html b/docs/pfm_degradation.html new file mode 100644 index 0000000..38e9e2b --- /dev/null +++ b/docs/pfm_degradation.html @@ -0,0 +1,123 @@ + + + + +pfm_degradation. pfm 0.3-8 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-8 +
      + +
      +
      +
      +
      + + +
      +
      + +
      + +

      Calculate a time course of relative concentrations based on an mkinmod model

      + +
      +
      +

      Usage

      + 
      pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
+  log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by =
+  step_days))
      + +

      Arguments

      +
      +
      model
      +
      The degradation model to be used. Either a parent only model like +'SFO' or 'FOMC', or an mkinmod object
      +
      DT50
      +
      The half-life. This is only used when simple exponential decline +is calculated (SFO model).
      +
      parms
      +
      The parameters used for the degradation model
      +
      years
      +
      For how many years should the degradation be predicted?
      +
      step_days
      +
      What step size in days should the output have?
      +
      times
      +
      The output times
      +
      + +
      +

      Description

      + +

      Calculate a time course of relative concentrations based on an mkinmod model

      + +
      + +

      Examples

      + 
      head(pfm_degradation("SFO", DT50 = 10))
      
+
        time    parent
+1    0 1.0000000
+2    1 0.9330330
+3    2 0.8705506
+4    3 0.8122524
+5    4 0.7578583
+6    5 0.7071068
+
      +
      +
      + + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/docs/plot.TOXSWA_cwa-2.png b/docs/plot.TOXSWA_cwa-2.png new file mode 100644 index 0000000..764c7f4 Binary files /dev/null and b/docs/plot.TOXSWA_cwa-2.png differ diff --git a/docs/plot.TOXSWA_cwa.html b/docs/plot.TOXSWA_cwa.html new file mode 100644 index 0000000..87dae02 --- /dev/null +++ b/docs/plot.TOXSWA_cwa.html @@ -0,0 +1,124 @@ + + + + +plot.TOXSWA_cwa. pfm 0.3-8 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-8 +
      + +
      +
      +
      +
      + + +
      +
      + +
      + +

      Plot TOXSWA surface water concentrations

      + +
      +
      +

      Usage

      + 
      # S3 method for TOXSWA_cwa
+plot(x, time_column = c("datetime", "t", "t_firstjan",
+  "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE,
+  total = FALSE, LC_TIME = "C", ...)
      + +

      Arguments

      +
      +
      x
      +
      The TOXSWA_cwa object to be plotted.
      +
      time_column
      +
      What should be used for the time axis. If "t_firstjan" is chosen, +the time is given in days relative to the first of January in the first year.
      +
      xlab, ylab
      +
      Labels for x and y axis.
      +
      add
      +
      Should we add to an existing plot?
      +
      total
      +
      Should the total concentration in water be plotted, including substance sorbed +to suspended matter?
      +
      LC_TIME
      +
      Specification of the locale used to format dates
      +
      ...
      +
      Further arguments passed to plot if we are not adding to an existing plot
      +
      + +
      +

      Description

      + +

      Plot TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body.

      + +
      + +

      Examples

      + 
      H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                             package = "pfm"))
+plot(H_sw_D4_pond)
      
+
      +
      +
      + + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/docs/read.TOXSWA_cwa.html b/docs/read.TOXSWA_cwa.html new file mode 100644 index 0000000..cc34733 --- /dev/null +++ b/docs/read.TOXSWA_cwa.html @@ -0,0 +1,142 @@ + + + + +read.TOXSWA_cwa. pfm 0.3-8 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-8 +
      + +
      +
      +
      +
      + + +
      +
      + +
      + +

      Read TOXSWA surface water concentrations

      + +
      +
      +

      Usage

      + 
      read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last",
+  substance = "parent", total = FALSE, windows = NULL,
+  thresholds = NULL)
      + +

      Arguments

      +
      +
      filename
      +
      The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).
      +
      basedir
      +
      The path to the directory where the cwa file resides.
      +
      zipfile
      +
      Optional path to a zip file containing the cwa file.
      +
      segment
      +
      The segment for which the data should be read. Either "last", or +the segment number.
      +
      substance
      +
      For TOXSWA 4 .out files, the default value "parent" leads +to reading concentrations of the parent compound. Alternatively, the substance +of interested can be selected by its code name.
      +
      total
      +
      Set this to TRUE in order to read total concentrations as well. This is +only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa +files. For .cwa files, the total concentration is always read as well.
      +
      windows
      +
      Numeric vector of width of moving windows in days, for calculating +maximum time weighted average concentrations and areas under the curve.
      +
      thresholds
      +
      Numeric vector of threshold concentrations in µg/L for +generating event statistics.
      +
      + +
      +

      Value

      + +

      +An instance of an R6 object of class +TOXSWA_cwa. +

      + +
      + +
      +

      Description

      + +

      Read TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body. Per default, the data for the last +segment are imported. As TOXSWA 4 reports the values at the end of the hour +(ConLiqWatLayCur) in its summary file, we use this value as well instead +of the hourly averages (ConLiqWatLay).

      + +
      + +

      Examples

      + 
      H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                                       package = "pfm"))
      +
      +
      + + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/docs/reference.html b/docs/reference.html new file mode 100644 index 0000000..83e788a --- /dev/null +++ b/docs/reference.html @@ -0,0 +1,164 @@ + + + + +Function reference. pfm 0.3-8 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-8 +
      + +
      +
      +
      +
      + + +
      +
      + +
      + +
      +
      +

      Function reference

      + +

      Degradation

      +

      Functions related to degradation

      + + +
        + +
      • + pfm_degradation
        Calculate a time course of relative concentrations based on an mkinmod model
        • + +
      • + SFO_actual_twa
        Actual and maximum moving window time average concentrations for SFO kinetics
        • + +
      +

      Mobility

      +

      Indicators related to mobility

      + + +
        + +
      • + GUS(GUS.chent, GUS.numeric, print.GUS_result)
        Groundwater ubiquity score based on Gustafson (1989)
        • + +
      • + SSLRC_mobility_classification
        Determine the SSLRC mobility classification for a chemical substance from its Koc
        • + +
      +

      Soil

      +

      Predicted environmental concentrations in soil

      + + +
        + +
      • + PEC_soil
        Calculate predicted environmental concentrations in soil
        • + +
      • + soil_scenario_data_EFSA_2015
        Properties of the predefined scenarios from the EFSA guidance from 2015
        • + +
      +

      Surface water

      +

      Predicted environmental concentrations in surface water

      + + +
        + +
      • + PEC_sw_drift
        Calculate predicted environmental concentrations in surface water due to drift
        • + +
      • + PEC_sw_sed
        Calculate predicted environmental concentrations in sediment from surface +water concentrations
        • + +
      • + drift_data_JKI
        Deposition from spray drift expressed as percent of the applied dose as +published by the JKI
        • + +
      • + PEC_sw_drainage_UK
        Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method
        • + +
      • + TOXSWA_cwa
        R6 class for holding TOXSWA cwa concentration data and associated statistics
        • + +
      • + read.TOXSWA_cwa
        Read TOXSWA surface water concentrations
        • + +
      • + plot.TOXSWA_cwa
        Plot TOXSWA surface water concentrations
        • + +
      +

      Groundwater

      +

      Predicted environmental concentrations in groundwater

      + + + +

      Chemical entities

      +

      Work with input stored in chemical entites as R objects using the chent package

      + + +
        + +
      • + endpoint(soil_DT50, soil_Kfoc, soil_N, soil_sorption)
        Retrieve endpoint information from the chyaml field of a chent object
        • + +
      +

      General

      +

      Utilities that are generally useful

      + + +
        + +
      • + geomean
        Calculate the geometric mean
        • + +
      +
      +
      + + +
      + + \ No newline at end of file diff --git a/docs/soil_scenario_data_EFSA_2015.html b/docs/soil_scenario_data_EFSA_2015.html new file mode 100644 index 0000000..405e5b0 --- /dev/null +++ b/docs/soil_scenario_data_EFSA_2015.html @@ -0,0 +1,144 @@ + + + + +soil_scenario_data_EFSA_2015. pfm 0.3-8 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-8 +
      + +
      +
      +
      +
      + + +
      +
      + +
      + +

      Properties of the predefined scenarios from the EFSA guidance from 2015

      + +
      +
      + +
      +

      Format

      + +

      A data frame with one row for each scenario. Row names are the scenario codes, + e.g. CTN for the Northern scenario for the total concentration in soil. Columns are + mostly self-explanatory. rho is the dry bulk density of the top soil.

      + +
      + +
      +

      Source

      + +

      EFSA (European Food Safety Authority) (2015) +EFSA guidance document for predicting environmental concentrations +of active substances of plant protection products and transformation products of these +active substances in soil. EFSA Journal 13(4) 4093 +doi:10.2903/j.efsa.2015.4093

      + +
      + +
      +

      Description

      + +

      Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the +scenario and model adjustment factors from p. 15 and p. 17 are included.

      + +
      + +

      Examples

      + 
      ## Not run: ------------------------------------
+#   # This is the code that was used to define the data
+#   soil_scenario_data_EFSA_2015 <- data.frame(
+#     Zone = rep(c("North", "Central", "South"), 2),
+#     Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),
+#     T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),
+#     T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),
+#     Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),
+#     f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),
+#     theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),
+#     rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),
+#     f_sce = c(3, 2, 2, 2, 1.5, 1.5),
+#     f_mod = c(2, 2, 2, 4, 4, 4),
+#     stringsAsFactors = FALSE,
+#     row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")
+#   )
+#   save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')
+## ---------------------------------------------
+
+# And this is the resulting dataframe
+soil_scenario_data_EFSA_2015
      
+
             Zone        Country T_arit T_arr     Texture  f_om theta_fc  rho f_sce
+CTN   North        Estonia    4.7   7.0      Coarse 0.118    0.244 0.95   3.0
+CTC Central        Germany    8.0  10.1      Coarse 0.086    0.244 1.05   2.0
+CTS   South         France   11.0  12.3 Medium fine 0.048    0.385 1.22   2.0
+CLN   North        Denmark    8.2   9.8      Medium 0.023    0.347 1.39   2.0
+CLC Central Czech Republik    9.1  11.2      Medium 0.018    0.347 1.43   1.5
+CLS   South          Spain   12.8  14.7      Medium 0.011    0.347 1.51   1.5
+    f_mod
+CTN     2
+CTC     2
+CTS     2
+CLN     4
+CLC     4
+CLS     4
+
      +
      +
      + + + + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/extdata/FOCUS_GW_scenarios_2012.R b/inst/extdata/FOCUS_GW_scenarios_2012.R new file mode 100644 index 0000000..3715325 --- /dev/null +++ b/inst/extdata/FOCUS_GW_scenarios_2012.R @@ -0,0 +1,59 @@ +# FOCUS 2012 p. 46 ff +FOCUS_GW_scenarios_2012 = list() + +n_layers = c(7, 6, 6, 5, 5, 6, 4, 6, 6) +acronyms = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi") +FOCUS_GW_scenarios_2012$names = c("Ch\u00e2teadun", "Hamburg", "Jokioinen", + "Kremsm\u00fcnster", "Okehampton", + "Piacenza", "Porto", "Sevilla", "Thiva") + +names(FOCUS_GW_scenarios_2012$names) = acronyms +FOCUS_GW_scenarios_2012$soils <- data.frame( + location= rep(acronyms, times = n_layers), + horizon = c("Ap", "B1", "B2", "II C1", "II C1", "II C2", "M", + "Ap", "BvI", "BvII", "Bv/Cv", "Cv", "Cv", + "Ap", "Bs", "BC1", "BC2", "BC2", "Cg", + rep(NA, 5), + "A", "Bw1", "BC", "C", "C", + "Ap", "Ap", "Bw", "Bw", "2C", "2C", + rep(NA, 4), + rep(NA, 6), + "Ap1", "Ap2", "Bw", "Bw", "Ck1", "Ck1"), + number = unlist(sapply(n_layers, function(x) 1:x)), + pH_H2O = c(8.0, 8.1, 8.2, 8.5, 8.5, 8.5, 8.3, + 6.4, 5.6, 5.6, 5.7, 5.5, 5.5, + 6.2, 5.6, 5.4, 5.4, 5.4, 5.3, + 7.7, 7.0, 7.1, 7.1, 7.1, + 5.8, 6.3, 6.5, 6.6, 6.6, + 7, 7, 6.3, 6.3, 6.4, 6.4, + 4.9, 4.8, 4.8, 4.8, + 7.3, 7.3, 7.8, 8.1, 8.1, 8.2, + 7.7, 7.7, 7.8, 7.8, 7.8, 7.8), + perc_clay = c(30, 31, 25, 26, 26, 24, 31, + 7.2, 6.7, 0.9, 0, 0, 0, + 3.6, 1.8, 1.2, 1.7, 1.7, 1.9, + 14, 25, 27, 27, 27, + 18, 17, 14, 9, 9, + 15, 15, 7, 7, 0, 0, + 10, 8, 8, 8, + 14, 13, 15, 16, 16, 22, + 25.3, 25.3, 29.6, 31.9, 32.9, 32.9), + perc_oc = c(1.39, 0.93, 0.7, 0.3, 0.3, 0.27, 0.21, + 1.5, 1, 0.2, 0, 0, 0, + 4.06, 0.84, 0.36, 0.29, 0.29, 0.21, + 3.6, 1.0, 0.5, 0.5, 0.5, + 2.2, 0.7, 0.4, 0.1, 0.1, + 1.26, 1.26, 0.47, 0.47, 0, 0, + 1.42, 0.78, 0.78, 0.78, + 0.93, 0.93, 0.70, 0.58, 0.58, 0.49, + 0.74, 0.74, 0.57, 0.31, 0.18, 0.18), + rel_deg = c(1, 0.5, 0.5, 0.3, 0, 0, 0, + 1, 0.5, 0.3, 0.3, 0.3, 0, + 1, 0.5, 0.3, 0.3, 0, 0, + 1, 0.5, 0.5, 0.3, 0, + 1, 0.5, 0.3, 0.3, 0, + 1, 0.5, 0.5, 0.3, 0.3, 0, + 1, 0.5, 0.3, 0, + 1, 1, 0.5, 0.3, 0, 0, + 1, 0.5, 0.5, 0.3, 0.3, 0)) +save(FOCUS_GW_scenarios_2012, file = "../../data/FOCUS_GW_scenarios_2012.RData") diff --git a/inst/extdata/Tabelle der Abdrifteckwerte.xls b/inst/extdata/Tabelle der Abdrifteckwerte.xls new file mode 100644 index 0000000..3d28817 Binary files /dev/null and b/inst/extdata/Tabelle der Abdrifteckwerte.xls differ diff --git a/inst/staticdocs/index.r b/inst/staticdocs/index.r new file mode 100644 index 0000000..421071c --- /dev/null +++ b/inst/staticdocs/index.r @@ -0,0 +1,42 @@ +sd_section( + "Degradation", + "Functions related to degradation", + c("pfm_degradation", "SFO_actual_twa") +) +sd_section( + "Mobility", + "Indicators related to mobility", + c("GUS", "SSLRC_mobility_classification") +) +sd_section( + "Soil", + "Predicted environmental concentrations in soil", + c("PEC_soil", "soil_scenario_data_EFSA_2015") +) +sd_section( + "Surface water", + "Predicted environmental concentrations in surface water", + c( + "PEC_sw_drift", "PEC_sw_sed", + "drift_data_JKI", + "PEC_sw_drainage_UK", + "TOXSWA_cwa", + "read.TOXSWA_cwa", + "plot.TOXSWA_cwa" + ) +) +sd_section( + "Groundwater", + "Predicted environmental concentrations in groundwater", + c("FOCUS_GW_scenarios_2012") +) +sd_section( + "Chemical entities", + "Work with input stored in chemical entites as R objects using the chent package", + c("endpoint") +) +sd_section( + "General", + "Utilities that are generally useful", + c("geomean") +) diff --git a/inst/testdata/SwashProjects.zip b/inst/testdata/SwashProjects.zip new file mode 100644 index 0000000..5b9ff49 Binary files /dev/null and b/inst/testdata/SwashProjects.zip differ diff --git a/inst/web/FOCUS_GW_scenarios_2012.html b/inst/web/FOCUS_GW_scenarios_2012.html new file mode 100644 index 0000000..43ac090 --- /dev/null +++ b/inst/web/FOCUS_GW_scenarios_2012.html @@ -0,0 +1,154 @@ + + + + +FOCUS_GW_scenarios_2012. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      A very small subset of the FOCUS Groundwater scenario defitions

      + +
      +
      + +
      +

      Description

      + +

      Currently, only a small subset of the soil definitions are provided.

      + +
      + +
      +

      References

      + +

      FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. + FOrum for the Co-ordination of pesticde fate models and their USe. + http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf

      + +
      + +

      Examples

      + 
      FOCUS_GW_scenarios_2012
+
      
+
      $names
+           Cha            Ham            Jok            Kre            Oke 
+  "Châteaudun"      "Hamburg"    "Jokioinen" "Kremsmünster"   "Okehampton" 
+           Pia            Por            Sev            Thi 
+    "Piacenza"        "Porto"      "Sevilla"        "Thiva" 
+
+$soils
+   location horizon number pH_H2O perc_clay perc_oc rel_deg
+1       Cha      Ap      1    8.0      30.0    1.39     1.0
+2       Cha      B1      2    8.1      31.0    0.93     0.5
+3       Cha      B2      3    8.2      25.0    0.70     0.5
+4       Cha   II C1      4    8.5      26.0    0.30     0.3
+5       Cha   II C1      5    8.5      26.0    0.30     0.0
+6       Cha   II C2      6    8.5      24.0    0.27     0.0
+7       Cha       M      7    8.3      31.0    0.21     0.0
+8       Ham      Ap      1    6.4       7.2    1.50     1.0
+9       Ham     BvI      2    5.6       6.7    1.00     0.5
+10      Ham    BvII      3    5.6       0.9    0.20     0.3
+11      Ham   Bv/Cv      4    5.7       0.0    0.00     0.3
+12      Ham      Cv      5    5.5       0.0    0.00     0.3
+13      Ham      Cv      6    5.5       0.0    0.00     0.0
+14      Jok      Ap      1    6.2       3.6    4.06     1.0
+15      Jok      Bs      2    5.6       1.8    0.84     0.5
+16      Jok     BC1      3    5.4       1.2    0.36     0.3
+17      Jok     BC2      4    5.4       1.7    0.29     0.3
+18      Jok     BC2      5    5.4       1.7    0.29     0.0
+19      Jok      Cg      6    5.3       1.9    0.21     0.0
+20      Kre    <NA>      1    7.7      14.0    3.60     1.0
+21      Kre    <NA>      2    7.0      25.0    1.00     0.5
+22      Kre    <NA>      3    7.1      27.0    0.50     0.5
+23      Kre    <NA>      4    7.1      27.0    0.50     0.3
+24      Kre    <NA>      5    7.1      27.0    0.50     0.0
+25      Oke       A      1    5.8      18.0    2.20     1.0
+26      Oke     Bw1      2    6.3      17.0    0.70     0.5
+27      Oke      BC      3    6.5      14.0    0.40     0.3
+28      Oke       C      4    6.6       9.0    0.10     0.3
+29      Oke       C      5    6.6       9.0    0.10     0.0
+30      Pia      Ap      1    7.0      15.0    1.26     1.0
+31      Pia      Ap      2    7.0      15.0    1.26     0.5
+32      Pia      Bw      3    6.3       7.0    0.47     0.5
+33      Pia      Bw      4    6.3       7.0    0.47     0.3
+34      Pia      2C      5    6.4       0.0    0.00     0.3
+35      Pia      2C      6    6.4       0.0    0.00     0.0
+36      Por    <NA>      1    4.9      10.0    1.42     1.0
+37      Por    <NA>      2    4.8       8.0    0.78     0.5
+38      Por    <NA>      3    4.8       8.0    0.78     0.3
+39      Por    <NA>      4    4.8       8.0    0.78     0.0
+40      Sev    <NA>      1    7.3      14.0    0.93     1.0
+41      Sev    <NA>      2    7.3      13.0    0.93     1.0
+42      Sev    <NA>      3    7.8      15.0    0.70     0.5
+43      Sev    <NA>      4    8.1      16.0    0.58     0.3
+44      Sev    <NA>      5    8.1      16.0    0.58     0.0
+45      Sev    <NA>      6    8.2      22.0    0.49     0.0
+46      Thi     Ap1      1    7.7      25.3    0.74     1.0
+47      Thi     Ap2      2    7.7      25.3    0.74     0.5
+48      Thi      Bw      3    7.8      29.6    0.57     0.5
+49      Thi      Bw      4    7.8      31.9    0.31     0.3
+50      Thi     Ck1      5    7.8      32.9    0.18     0.3
+51      Thi     Ck1      6    7.8      32.9    0.18     0.0
+
+
      +
      +
      + + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/GUS.html b/inst/web/GUS.html new file mode 100644 index 0000000..a330be2 --- /dev/null +++ b/inst/web/GUS.html @@ -0,0 +1,160 @@ + + + + +GUS. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Groundwater ubiquity score based on Gustafson (1989)

      + +
      +
      +

      Usage

      + 
      GUS(...)
      
+
      "GUS"(DT50, Koc, ...)
      
+
      "GUS"(chent, degradation_value = "DT50ref", lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc", degradation_aggregator = geomean, sorption_aggregator = geomean, ...)
      
+
      "print"(x, ..., digits = 1)
      + +

      Arguments

      +
      +
      ...
      +
      Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.
      +
      DT50
      +
      Half-life of the chemical in soil. Should be a field +half-life according to Gustafson (1989). However, leaching to the sub-soil +can not completely be excluded in field dissipation experiments and Gustafson +did not refer to any normalisation procedure, but says the field study should +be conducted under use conditions.
      +
      Koc
      +
      The sorption constant normalised to organic carbon. Gustafson +does not mention the nonlinearity of the sorption constant commonly +found and usually described by Freundlich sorption, therefore it is +unclear at which reference concentration the Koc should be observed +(and if the reference concentration would be in soil or in porewater).
      +
      chent
      +
      If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.
      +
      degradation_value
      +
      Which of the available degradation values should +be used?
      +
      lab_field
      +
      Should laboratory or field half-lives be used? This +defaults to lab in this implementation, in order to avoid +double-accounting for mobility. If comparability with the original GUS +values given by Gustafson (1989) is desired, non-normalised first-order +field half-lives obtained under actual use conditions should be used.
      +
      redox
      +
      Aerobic or anaerobic degradation data
      +
      sorption_value
      +
      Which of the available sorption values should be used? +Defaults to Kfoc as this is what is generally available from the European +pesticide peer review process. These values generally use a reference +concentration of 1 mg/L in porewater, that means they would be expected to +be Koc values at a concentration of 1 mg/L in the water phase.
      +
      degradation_aggregator
      +
      Function for aggregating half-lives
      +
      sorption_aggregator
      +
      Function for aggregation Koc values
      +
      x
      +
      An object of class GUS_result to be printed
      +
      digits
      +
      The number of digits used in the print method
      +
      + +
      +

      Value

      + +

      +A list with the DT50 and Koc used as well as the resulting score + of class GUS_result +

      + +
      + +
      +

      Description

      + +

      The groundwater ubiquity score GUS is calculated according to +the following equation +$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$

      + +
      + +
      +

      References

      + +

      Gustafson, David I. (1989) Groundwater ubiquity score: a simple +method for assessing pesticide leachability. Environmental +toxicology and chemistry 8(4) 339–57.

      + +
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/PEC_soil.html b/inst/web/PEC_soil.html new file mode 100644 index 0000000..1304d19 --- /dev/null +++ b/inst/web/PEC_soil.html @@ -0,0 +1,228 @@ + + + + +PEC_soil. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Calculate predicted environmental concentrations in soil

      + +
      +
      +

      Usage

      + 
      PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA, n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default", "EFSA_2015"), porewater = FALSE)
      + +

      Arguments

      +
      +
      rate
      +
      Application rate in units specified below
      +
      rate_units
      +
      Defaults to g/ha
      +
      interception
      +
      The fraction of the application rate that does not reach the soil
      +
      mixing_depth
      +
      Mixing depth in cm
      +
      PEC_units
      +
      Requested units for the calculated PEC. Only mg/kg currently supported
      +
      PEC_pw_units
      +
      Only mg/L currently supported
      +
      interval
      +
      Period of the deeper mixing, defaults to 365, which is a year if +rate units are in days
      +
      n_periods
      +
      Number of periods to be considered for long term PEC calculations
      +
      tillage_depth
      +
      Periodic (see interval) deeper mixing in cm
      +
      chent
      +
      An optional chent object holding substance specific information. Can +also be a name for the substance as a character string
      +
      DT50
      +
      If specified, overrides soil DT50 endpoints from a chent object +If DT50 is not specified here and not available from the chent object, zero +degradation is assumed
      +
      Koc
      +
      If specified, overrides Koc endpoints from a chent object
      +
      Kom
      +
      Calculated from Koc by default, but can explicitly be specified +as Kom here
      +
      t_avg
      +
      Averaging times for time weighted average concentrations
      +
      scenarios
      +
      If this is 'default', the DT50 will be used without correction +and soil properties as specified in the REACH guidance (R.16, Table +R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", +the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when +'chents' is specified, the DegT50 with destination 'PECgw' will be used), +and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also +model and scenario adjustment factors from the EFSA guidance are used.
      +
      porewater
      +
      Should equilibrium porewater concentrations be estimated +based on Kom and the organic carbon fraction of the soil instead of total +soil concentrations? Based on equation (7) given in the PPR panel opinion +(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, +p. 13).
      +
      + +
      +

      Value

      + +

      +The predicted concentration in soil +

      + +
      + +
      +

      Description

      + +

      This is a basic calculation of a contaminant concentration in bulk soil +based on complete, instantaneous mixing. If an interval is given, an +attempt is made at calculating a long term maximum concentration using +the concepts layed out for example in the PPR panel opinion (EFSA 2012).

      + +
      + +
      +

      Details

      + +

      This assumes that the complete load to soil during the time specified by +'interval' (typically 365 days) is dosed at once. As in the PPR panel +opinion cited below (PPR panel 2012), only temperature correction using the +Arrhenius equation is performed.

      + +

      Total soil and porewater PEC values for the scenarios as defined in the EFSA +guidance (2015, p. 13) can easily be calculated.

      + +
      + +
      +

      Note

      + +

      If temperature information is available in the selected scenarios, as + e.g. in the EFSA scenarios, the DT50 for groundwater modelling + (destination 'PECgw') is taken from the chent object, otherwise the DT50 + with destination 'PECsoil'.

      + +
      + +
      +

      References

      + +

      EFSA Panel on Plant Protection Products and their Residues (2012) + Scientific Opinion on the science behind the guidance for scenario + selection and scenario parameterisation for predicting environmental + concentrations of plant protection products in soil. EFSA Journal + 10(2) 2562, doi:10.2903/j.efsa.2012.2562

      + +

      EFSA (European Food Safety Authority) (2015) EFSA guidance document for + predicting environmental concentrations of active substances of plant + protection products and transformation products of these active substances + in soil. EFSA Journal 13(4) 4093 + doi:10.2903/j.efsa.2015.4093

      + +
      + +

      Examples

      + 
      PEC_soil(100, interception = 0.25)
+
      
+
           scenario
+t_avg default
+    0     0.1
+
      
+
      
+# This is example 1 starting at p. 79 of the EFSA guidance (2015)
+PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
+               scenarios = "EFSA_2015")
+
      
+
           scenario
+t_avg      CTN      CTC      CTS
+   0  21.96827 11.53750 9.145259
+   21 21.78517 11.40701 9.017370
+
      
+
      PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21),
+               Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE)
+
      
+
           scenario
+t_avg       CLN       CLC       CLS
+   0  0.7589401 0.6674322 0.9147861
+   21 0.7506036 0.6590345 0.8987279
+
      
+
      
+# The following is from example 4 starting at p. 85 of the EFSA guidance (2015)
+# Metabolite M2
+# Calculate total and porewater soil concentrations for tier 1 scenarios
+# Relative molar mass is 100/300, formation fraction is 0.7 * 1
+results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
+                        scenarios = "EFSA_2015")
+results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21),
+                           Kom = 100, scenarios = "EFSA_2015", porewater = TRUE)
+
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/PEC_soil_product.html b/inst/web/PEC_soil_product.html new file mode 100644 index 0000000..9704de2 --- /dev/null +++ b/inst/web/PEC_soil_product.html @@ -0,0 +1,141 @@ + + + + +PEC_soil_product. pfm 0.2-4 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.2-4 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Calculate predicted environmental concentrations in soil for a product

      + +
      +
      +

      Usage

      + 
      PEC_soil_product(product, rate, rate_units = "L/ha", interception = 0, mixing_depth = 5, tillage_depth = 20, interval = 365, PEC_units = "mg/kg", scenarios = "EFSA_2015")
      + +

      Arguments

      +
      +
      product
      +
      An object of class pp
      +
      rate
      +
      Application rate in units specified below
      +
      rate_units
      +
      Defaults to g/ha
      +
      interception
      +
      The fraction of the application rate that does not reach the soil
      +
      mixing_depth
      +
      Mixing depth in cm
      +
      tillage_depth
      +
      Periodic (see interval) deeper mixing in cm
      +
      interval
      +
      Period of the deeper mixing, defaults to 365, which is a year if +rate units are in days
      +
      PEC_units
      +
      Requested units for the calculated PEC. Only mg/kg currently supported
      +
      + +
      +

      Source

      + +

      EFSA Panel on Plant Protection Products and their Residues (2012) +Scientific Opinion on the science behind the guidance for scenario selection +and scenario parameterisation for predicting environmental concentrations +of plant protection products in soil. EFSA Journal 10(2) 2562, +doi:10.2903/j.efsa.2012.2562

      + +

      EFSA (European Food Safety Authority) (2015) +EFSA guidance document for predicting environmental concentrations +of active substances of plant protection products and transformation products of these +active substances in soil. EFSA Journal 13(4) 4093 +doi:10.2903/j.efsa.2015.4093

      + +
      + +
      +

      Value

      + +

      +A data frame with compound names, and initial, background (plateau minimum) + and long term maximum predicted concentrations in soil +

      + +
      + +
      +

      Description

      + +

      Calculates long term accumulation PEC values. Assumes that the complete load to soil during the +time specified by 'interval' (typically 365 days) is dosed at once. As in the PPR panel opinion +cited below (PPR panel 2012), only temperature correction using the Arrhenius equation is performed. +By default, PEC values for the scenarios as defined in the EFSA guidance +(2015, p. 13) are calculated.

      + +
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/PEC_sw_drainage_UK.html b/inst/web/PEC_sw_drainage_UK.html new file mode 100644 index 0000000..bf97fea --- /dev/null +++ b/inst/web/PEC_sw_drainage_UK.html @@ -0,0 +1,124 @@ + + + + +PEC_sw_drainage_UK. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

      + +
      +
      +

      Usage

      + 
      PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL)
      + +

      Arguments

      +
      +
      rate
      +
      Application rate in g/ha
      +
      interception
      +
      The fraction of the application rate that does not reach the soil
      +
      Koc
      +
      The sorption coefficient normalised to organic carbon in L/kg
      +
      latest_application
      +
      Latest application date, formatted as e.g. "01 July"
      +
      soil_DT50
      +
      Soil degradation half-life, if SFO kinetics are to be used
      +
      model
      +
      The soil degradation model to be used. Either one of "FOMC", +"DFOP", "HS", or "IORE", or an mkinmod object
      +
      model_parms
      +
      A named numeric vector containing the model parameters
      +
      + +
      +

      Value

      + +

      +The predicted concentration in surface water in µg/L +

      + +
      + +
      +

      Description

      + +

      This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet +published on the CRC website

      + +
      + +

      Examples

      + 
      PEC_sw_drainage_UK(150, Koc = 100)
+
      
+
      [1] 8.076923
+
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/PEC_sw_drainage_UK_ini.html b/inst/web/PEC_sw_drainage_UK_ini.html new file mode 100644 index 0000000..0d55bd9 --- /dev/null +++ b/inst/web/PEC_sw_drainage_UK_ini.html @@ -0,0 +1,124 @@ + + + + +PEC_sw_drainage_UK_ini. pfm 0.2-4 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.2-4 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

      + +
      +
      +

      Usage

      + 
      PEC_sw_drainage_UK_ini(rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL)
      + +

      Arguments

      +
      +
      rate
      +
      Application rate in g/ha
      +
      interception
      +
      The fraction of the application rate that does not reach the soil
      +
      Koc
      +
      The sorption coefficient normalised to organic carbon in L/kg
      +
      latest_application
      +
      Latest application date, formatted as e.g. "01 July"
      +
      soil_DT50
      +
      Soil degradation half-life, if SFO kinetics are to be used
      +
      model
      +
      The degradation model to be used. Either one of "FOMC", "DFOP", +"HS", or "IORE", or an mkinmod object
      +
      model_parms
      +
      A named numeric vector containing the model parameters
      +
      + +
      +

      Value

      + +

      +The predicted concentration in surface water in µg/L +

      + +
      + +
      +

      Description

      + +

      This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet +published on the CRC website

      + +
      + +

      Examples

      + 
      PEC_sw_drainage_UK_ini(150, Koc = 100)
+
      
+
      [1] 8.076923
+
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/PEC_sw_drift.html b/inst/web/PEC_sw_drift.html new file mode 100644 index 0000000..5d4bb47 --- /dev/null +++ b/inst/web/PEC_sw_drift.html @@ -0,0 +1,130 @@ + + + + +PEC_sw_drift. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Calculate predicted environmental concentrations in surface water due to drift

      + +
      +
      +

      Usage

      + 
      PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
      + +

      Arguments

      +
      +
      rate
      +
      Application rate in units specified below
      +
      applications
      +
      Number of applications for selection of drift percentile
      +
      water_depth
      +
      Depth of the water body in cm
      +
      drift_percentages
      +
      Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.
      +
      drift_data
      +
      Source of drift percentage data
      +
      crop
      +
      Crop name (use German names for JKI data), defaults to "Ackerbau"
      +
      distances
      +
      The distances in m for which to get PEC values
      +
      rate_units
      +
      Defaults to g/ha
      +
      PEC_units
      +
      Requested units for the calculated PEC. Only µg/L currently supported
      +
      + +
      +

      Value

      + +

      +The predicted concentration in surface water +

      + +
      + +
      +

      Description

      + +

      This is a basic, vectorised form of a simple calculation of a contaminant +concentration in surface water based on complete, instantaneous mixing +with input via spray drift.

      + +
      + +

      Examples

      + 
      PEC_sw_drift(100)
+
      
+
             1 m        5 m       10 m       20 m 
+0.92333333 0.19000000 0.09666667 0.05000000 
+
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/PEC_sw_drift_ini.html b/inst/web/PEC_sw_drift_ini.html new file mode 100644 index 0000000..bc7eed5 --- /dev/null +++ b/inst/web/PEC_sw_drift_ini.html @@ -0,0 +1,127 @@ + + + + +PEC_sw_drift_ini. pfm 0.2-4 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.2-4 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Calculate initial predicted environmental concentrations in surface water due to drift

      + +
      +
      +

      Usage

      + 
      PEC_sw_drift_ini(rate, applications = 1, water_depth = 30, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
      + +

      Arguments

      +
      +
      rate
      +
      Application rate in units specified below
      +
      applications
      +
      Number of applications for selection of drift percentile
      +
      water_depth
      +
      Depth of the water body in cm
      +
      drift_data
      +
      Source of drift percentage data
      +
      crop
      +
      Crop name (use German names for JKI data), defaults to "Ackerbau"
      +
      distances
      +
      The distances in m for which to get PEC values
      +
      rate_units
      +
      Defaults to g/ha
      +
      PEC_units
      +
      Requested units for the calculated PEC. Only µg/L currently supported
      +
      + +
      +

      Value

      + +

      +The predicted concentration in surface water +

      + +
      + +
      +

      Description

      + +

      This is a basic, vectorised form of a simple calculation of a contaminant +concentration in surface water based on complete, instantaneous mixing +with input via spray drift.

      + +
      + +

      Examples

      + 
      PEC_sw_drift_ini(100)
+
      
+
             1 m        5 m       10 m       20 m 
+0.92333333 0.19000000 0.09666667 0.05000000 
+
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/PEC_sw_sed.html b/inst/web/PEC_sw_sed.html new file mode 100644 index 0000000..4eda1d7 --- /dev/null +++ b/inst/web/PEC_sw_sed.html @@ -0,0 +1,127 @@ + + + + +PEC_sw_sed. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Calculate predicted environmental concentrations in sediment from surface +water concentrations

      + +
      +
      +

      Usage

      + 
      PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage", sediment_depth = 5, water_depth = 30, sediment_density = 1.3, PEC_sed_units = c("µg/kg", "mg/kg"))
      + +

      Arguments

      +
      +
      PEC_sw
      +
      Numeric vector or matrix of surface water concentrations in µg/L for +which the corresponding sediment concentration is to be estimated
      +
      percentage
      +
      The percentage in sediment, used for the percentage method
      +
      method
      +
      The method used for the calculation
      +
      sediment_depth
      +
      Depth of the sediment layer
      +
      water_depth
      +
      Depth of the water body in cm
      +
      sediment_density
      +
      The density of the sediment in L/kg (equivalent to +g/cm3)
      +
      PEC_sed_units
      +
      The units of the estimated sediment PEC value
      +
      + +
      +

      Value

      + +

      +The predicted concentration in sediment +

      + +
      + +
      +

      Description

      + +

      The method 'percentage' is equivalent to what is used in the CRD spreadsheet +PEC calculator

      + +
      + +

      Examples

      + 
      PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50)
+
      
+
           1 m 
+2.130769 
+
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/SFO_actual_twa.html b/inst/web/SFO_actual_twa.html new file mode 100644 index 0000000..3ce9220 --- /dev/null +++ b/inst/web/SFO_actual_twa.html @@ -0,0 +1,123 @@ + + + + +SFO_actual_twa. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Actual and maximum moving window time average concentrations for SFO kinetics

      + +
      +
      +

      Usage

      + 
      SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))
      + +

      Arguments

      +
      +
      DT50
      +
      The half-life.
      +
      times
      +
      The output times, and window sizes for time weighted average concentrations
      +
      + +
      +

      Source

      + +

      FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, + 18 December 2014, p. 251

      + +
      + +
      +

      Description

      + +

      Actual and maximum moving window time average concentrations for SFO kinetics

      + +
      + +

      Examples

      + 
      SFO_actual_twa(10)
+
      
+
                actual       twa
+0   1.0000000000       NaN
+1   0.9330329915 0.9661297
+2   0.8705505633 0.9337803
+4   0.7578582833 0.8733416
+7   0.6155722067 0.7923030
+14  0.3789291416 0.6400113
+21  0.2332582479 0.5267498
+28  0.1435872944 0.4412651
+42  0.0544094102 0.3248093
+50  0.0312500000 0.2795222
+100 0.0009765625 0.1441286
+
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/SSLRC_mobility_classification.html b/inst/web/SSLRC_mobility_classification.html new file mode 100644 index 0000000..43d701e --- /dev/null +++ b/inst/web/SSLRC_mobility_classification.html @@ -0,0 +1,117 @@ + + + + +SSLRC_mobility_classification. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Determine the SSLRC mobility classification for a chemical substance from its Koc

      + +
      +
      +

      Usage

      + 
      SSLRC_mobility_classification(Koc)
      + +

      Arguments

      +
      +
      Koc
      +
      The sorption coefficient normalised to organic carbon in L/kg
      +
      + +
      +

      Value

      + +

      +A list containing the classification and the percentage of the + compound transported per 10 mm drain water +

      + +
      + +
      +

      Description

      + +

      This implements the method specified in the UK data requirements handbook and was +checked against the spreadsheet published on the CRC website

      + +
      + +

      Examples

      + 
      SSLRC_mobility_classification(100)
+
      
+
      $`Mobility classification`
+[1] "Moderately mobile"
+
+$`Percentage drained per mm of drain water`
+[1] 0.7
+
+
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/TOXSWA_cwa.html b/inst/web/TOXSWA_cwa.html new file mode 100644 index 0000000..0d8ae17 --- /dev/null +++ b/inst/web/TOXSWA_cwa.html @@ -0,0 +1,176 @@ + + + + +TOXSWA_cwa. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      R6 class for holding TOXSWA cwa concentration data and associated statistics

      + +
      +
      +

      Usage

      + 
      TOXSWA_cwa
      + +
      +

      Format

      + +

      An R6Class generator object.

      + +
      + +
      +

      Description

      + +

      An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +Usually, an instance of this class will be generated by read.TOXSWA_cwa.

      + +
      + +
      +

      Fields

      + +

      + +

      +
      filename
      Length one character vector.

      + +

      basedir
      Length one character vector.

      + +

      segment
      Length one integer, specifying for which segment the cwa data were read.

      + +

      cwas
      Dataframe holding the concentrations.

      + +

      events
      List of dataframes holding the event statistics for each threshold.

      + +

      windows
      Matrix of maximum time weighted average concentrations (TWAC_max) +and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) +for the requested moving window sizes in days.

      + +

      + +
      + +
      +

      Methods

      + +

      + +

      +
      get_events(threshold, total = FALSE)
      + Populate a datataframe with event information for the specified threshold value + in µg/L. If total = TRUE, the total concentration including the amount + adsorbed to suspended matter will be used. The resulting dataframe is stored in the + events field of the object. +

      + +

      moving_windows(windows, total = FALSE)
      + Add to the windows field described above. + Again, if total = TRUE, the total concentration including the amount + adsorbed to suspended matter will be used. +

      + +

      + +

      + +
      + +

      Examples

      + 
      H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
+                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                             package = "pfm"))
+H_sw_R1_stream$get_events(c(2, 10))
+H_sw_R1_stream$moving_windows(c(7, 21))
+print(H_sw_R1_stream)
+
      
+
      <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 
+               datetime     t t_firstjan t_rel_to_max cwa_mug_per_L
+20  1978-10-01 00:00:00 0.000   273.0000      -55.333             0
+40  1978-10-01 01:00:00 0.042   273.0417      -55.291             0
+60  1978-10-01 02:00:00 0.083   273.0833      -55.250             0
+80  1978-10-01 03:00:00 0.125   273.1250      -55.208             0
+100 1978-10-01 04:00:00 0.167   273.1667      -55.166             0
+120 1978-10-01 05:00:00 0.208   273.2083      -55.125             0
+    cwa_tot_mug_per_L
+20                  0
+40                  0
+60                  0
+80                  0
+100                 0
+120                 0
+Moving window analysis
+   window  max_TWAC max_AUC_h max_AUC_d
+1  7 days 2.3926551  401.9660  16.74859
+2 21 days 0.8369248  421.8101  17.57542
+Event statistics for threshold 2 
+  t_start   cwa_max duration pre_interval     AUC_h     AUC_d
+1  44.375  4.167238    0.208       44.375  17.77202  0.740501
+2  55.042 40.584010    0.583       10.459 398.21189 16.592162
+Event statistics for threshold 10 
+  t_start  cwa_max duration pre_interval   AUC_h    AUC_d
+1  55.083 40.58401    0.459       55.083 379.433 15.80971
+
      +
      +
      + + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/css/bootstrap-responsive.css b/inst/web/css/bootstrap-responsive.css new file mode 100644 index 0000000..06e55c0 --- /dev/null +++ b/inst/web/css/bootstrap-responsive.css @@ -0,0 +1,815 @@ +/*! + * Bootstrap Responsive v2.0.4 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + */ + +.clearfix { + *zoom: 1; +} + +.clearfix:before, +.clearfix:after { + display: table; + content: ""; +} + +.clearfix:after { + clear: both; +} + +.hide-text { + font: 0/0 a; + color: transparent; + text-shadow: none; + background-color: transparent; + border: 0; +} + +.input-block-level { + display: block; + width: 100%; + min-height: 28px; + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; +} + +.hidden { + display: none; + visibility: hidden; +} + +.visible-phone { + display: none !important; +} + +.visible-tablet { + display: none !important; +} + +.hidden-desktop { + display: none !important; +} + +@media (max-width: 767px) { + .visible-phone { + display: inherit !important; + } + .hidden-phone { + display: none !important; + } + .hidden-desktop { + display: inherit !important; + } + .visible-desktop { + display: none !important; + } +} + +@media (min-width: 768px) and (max-width: 979px) { + .visible-tablet { + display: inherit !important; + } + .hidden-tablet { + display: none !important; + } + .hidden-desktop { + display: inherit !important; + } + .visible-desktop { + display: none !important ; + } +} + +@media (max-width: 480px) { + .nav-collapse { + -webkit-transform: translate3d(0, 0, 0); + } + .page-header h1 small { + display: block; + line-height: 18px; + } + input[type="checkbox"], + input[type="radio"] { + border: 1px solid #ccc; + } + .form-horizontal .control-group > label { + float: none; + width: auto; + padding-top: 0; + text-align: left; + } + .form-horizontal .controls { + margin-left: 0; + } + .form-horizontal .control-list { + padding-top: 0; + } + .form-horizontal .form-actions { + padding-right: 10px; + padding-left: 10px; + } + .modal { + position: absolute; + top: 10px; + right: 10px; + left: 10px; + width: auto; + margin: 0; + } + .modal.fade.in { + top: auto; + } + .modal-header .close { + padding: 10px; + margin: -10px; + } + .carousel-caption { + position: static; + } +} + +@media (max-width: 767px) { + body { + padding-right: 20px; + padding-left: 20px; + } + .navbar-fixed-top, + .navbar-fixed-bottom { + margin-right: -20px; + margin-left: -20px; + } + .container-fluid { + padding: 0; + } + .dl-horizontal dt { + float: none; + width: auto; + clear: none; + text-align: left; + } + .dl-horizontal dd { + margin-left: 0; + } + .container { + width: auto; + } + .row-fluid { + width: 100%; + } + .row, + .thumbnails { + margin-left: 0; + } + [class*="span"], + .row-fluid [class*="span"] { + display: block; + float: none; + width: auto; + margin-left: 0; + } + .input-large, + .input-xlarge, + .input-xxlarge, + input[class*="span"], + select[class*="span"], + textarea[class*="span"], + .uneditable-input { + display: block; + width: 100%; + min-height: 28px; + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; + } + .input-prepend input, + .input-append input, + .input-prepend input[class*="span"], + .input-append input[class*="span"] { + display: inline-block; + width: auto; + } +} + +@media (min-width: 768px) and (max-width: 979px) { + .row { + margin-left: -20px; + *zoom: 1; + } + .row:before, + .row:after { + display: table; + content: ""; + } + .row:after { + clear: both; + } + [class*="span"] { + float: left; + margin-left: 20px; + } + .container, + .navbar-fixed-top .container, + .navbar-fixed-bottom .container { + width: 724px; + } + .span12 { + width: 724px; + } + .span11 { + width: 662px; + } + .span10 { + width: 600px; + } + .span9 { + width: 538px; + } + .span8 { + width: 476px; + } + .span7 { + width: 414px; + } + .span6 { + width: 352px; + } + .span5 { + width: 290px; + } + .span4 { + width: 228px; + } + .span3 { + width: 166px; + } + .span2 { + width: 104px; + } + .span1 { + width: 42px; + } + .offset12 { + margin-left: 764px; + } + .offset11 { + margin-left: 702px; + } + .offset10 { + margin-left: 640px; + } + .offset9 { + margin-left: 578px; + } + .offset8 { + margin-left: 516px; + } + .offset7 { + margin-left: 454px; + } + .offset6 { + margin-left: 392px; + } + .offset5 { + margin-left: 330px; + } + .offset4 { + margin-left: 268px; + } + .offset3 { + margin-left: 206px; + } + .offset2 { + margin-left: 144px; + } + .offset1 { + margin-left: 82px; + } + .row-fluid { + width: 100%; + *zoom: 1; + } + .row-fluid:before, + .row-fluid:after { + display: table; + content: ""; + } + .row-fluid:after { + clear: both; + } + .row-fluid [class*="span"] { + display: block; + float: left; + width: 100%; + min-height: 28px; + margin-left: 2.762430939%; + *margin-left: 2.709239449638298%; + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; + } + .row-fluid [class*="span"]:first-child { + margin-left: 0; + } + .row-fluid .span12 { + width: 99.999999993%; + *width: 99.9468085036383%; + } + .row-fluid .span11 { + width: 91.436464082%; + *width: 91.38327259263829%; + } + .row-fluid .span10 { + width: 82.87292817100001%; + *width: 82.8197366816383%; + } + .row-fluid .span9 { + width: 74.30939226%; + *width: 74.25620077063829%; + } + .row-fluid .span8 { + width: 65.74585634900001%; + *width: 65.6926648596383%; + } + .row-fluid .span7 { + width: 57.182320438000005%; + *width: 57.129128948638304%; + } + .row-fluid .span6 { + width: 48.618784527%; + *width: 48.5655930376383%; + } + .row-fluid .span5 { + width: 40.055248616%; + *width: 40.0020571266383%; + } + .row-fluid .span4 { + width: 31.491712705%; + *width: 31.4385212156383%; + } + .row-fluid .span3 { + width: 22.928176794%; + *width: 22.874985304638297%; + } + .row-fluid .span2 { + width: 14.364640883%; + *width: 14.311449393638298%; + } + .row-fluid .span1 { + width: 5.801104972%; + *width: 5.747913482638298%; + } + input, + textarea, + .uneditable-input { + margin-left: 0; + } + input.span12, + textarea.span12, + .uneditable-input.span12 { + width: 714px; + } + input.span11, + textarea.span11, + .uneditable-input.span11 { + width: 652px; + } + input.span10, + textarea.span10, + .uneditable-input.span10 { + width: 590px; + } + input.span9, + textarea.span9, + .uneditable-input.span9 { + width: 528px; + } + input.span8, + textarea.span8, + .uneditable-input.span8 { + width: 466px; + } + input.span7, + textarea.span7, + .uneditable-input.span7 { + width: 404px; + } + input.span6, + textarea.span6, + .uneditable-input.span6 { + width: 342px; + } + input.span5, + textarea.span5, + .uneditable-input.span5 { + width: 280px; + } + input.span4, + textarea.span4, + .uneditable-input.span4 { + width: 218px; + } + input.span3, + textarea.span3, + .uneditable-input.span3 { + width: 156px; + } + input.span2, + textarea.span2, + .uneditable-input.span2 { + width: 94px; + } + input.span1, + textarea.span1, + .uneditable-input.span1 { + width: 32px; + } +} + +@media (min-width: 1200px) { + .row { + margin-left: -30px; + *zoom: 1; + } + .row:before, + .row:after { + display: table; + content: ""; + } + .row:after { + clear: both; + } + [class*="span"] { + float: left; + margin-left: 30px; + } + .container, + .navbar-fixed-top .container, + .navbar-fixed-bottom .container { + width: 1170px; + } + .span12 { + width: 1170px; + } + .span11 { + width: 1070px; + } + .span10 { + width: 970px; + } + .span9 { + width: 870px; + } + .span8 { + width: 770px; + } + .span7 { + width: 670px; + } + .span6 { + width: 570px; + } + .span5 { + width: 470px; + } + .span4 { + width: 370px; + } + .span3 { + width: 270px; + } + .span2 { + width: 170px; + } + .span1 { + width: 70px; + } + .offset12 { + margin-left: 1230px; + } + .offset11 { + margin-left: 1130px; + } + .offset10 { + margin-left: 1030px; + } + .offset9 { + margin-left: 930px; + } + .offset8 { + margin-left: 830px; + } + .offset7 { + margin-left: 730px; + } + .offset6 { + margin-left: 630px; + } + .offset5 { + margin-left: 530px; + } + .offset4 { + margin-left: 430px; + } + .offset3 { + margin-left: 330px; + } + .offset2 { + margin-left: 230px; + } + .offset1 { + margin-left: 130px; + } + .row-fluid { + width: 100%; + *zoom: 1; + } + .row-fluid:before, + .row-fluid:after { + display: table; + content: ""; + } + .row-fluid:after { + clear: both; + } + .row-fluid [class*="span"] { + display: block; + float: left; + width: 100%; + min-height: 28px; + margin-left: 2.564102564%; + *margin-left: 2.510911074638298%; + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; + } + .row-fluid [class*="span"]:first-child { + margin-left: 0; + } + .row-fluid .span12 { + width: 100%; + *width: 99.94680851063829%; + } + .row-fluid .span11 { + width: 91.45299145300001%; + *width: 91.3997999636383%; + } + .row-fluid .span10 { + width: 82.905982906%; + *width: 82.8527914166383%; + } + .row-fluid .span9 { + width: 74.358974359%; + *width: 74.30578286963829%; + } + .row-fluid .span8 { + width: 65.81196581200001%; + *width: 65.7587743226383%; + } + .row-fluid .span7 { + width: 57.264957265%; + *width: 57.2117657756383%; + } + .row-fluid .span6 { + width: 48.717948718%; + *width: 48.6647572286383%; + } + .row-fluid .span5 { + width: 40.170940171000005%; + *width: 40.117748681638304%; + } + .row-fluid .span4 { + width: 31.623931624%; + *width: 31.5707401346383%; + } + .row-fluid .span3 { + width: 23.076923077%; + *width: 23.0237315876383%; + } + .row-fluid .span2 { + width: 14.529914530000001%; + *width: 14.4767230406383%; + } + .row-fluid .span1 { + width: 5.982905983%; + *width: 5.929714493638298%; + } + input, + textarea, + .uneditable-input { + margin-left: 0; + } + input.span12, + textarea.span12, + .uneditable-input.span12 { + width: 1160px; + } + input.span11, + textarea.span11, + .uneditable-input.span11 { + width: 1060px; + } + input.span10, + textarea.span10, + .uneditable-input.span10 { + width: 960px; + } + input.span9, + textarea.span9, + .uneditable-input.span9 { + width: 860px; + } + input.span8, + textarea.span8, + .uneditable-input.span8 { + width: 760px; + } + input.span7, + textarea.span7, + .uneditable-input.span7 { + width: 660px; + } + input.span6, + textarea.span6, + .uneditable-input.span6 { + width: 560px; + } + input.span5, + textarea.span5, + .uneditable-input.span5 { + width: 460px; + } + input.span4, + textarea.span4, + .uneditable-input.span4 { + width: 360px; + } + input.span3, + textarea.span3, + .uneditable-input.span3 { + width: 260px; + } + input.span2, + textarea.span2, + .uneditable-input.span2 { + width: 160px; + } + input.span1, + textarea.span1, + .uneditable-input.span1 { + width: 60px; + } + .thumbnails { + margin-left: -30px; + } + .thumbnails > li { + margin-left: 30px; + } + .row-fluid .thumbnails { + margin-left: 0; + } +} + +@media (max-width: 979px) { + body { + padding-top: 0; + } + .navbar-fixed-top, + .navbar-fixed-bottom { + position: static; + } + .navbar-fixed-top { + margin-bottom: 18px; + } + .navbar-fixed-bottom { + margin-top: 18px; + } + .navbar-fixed-top .navbar-inner, + .navbar-fixed-bottom .navbar-inner { + padding: 5px; + } + .navbar .container { + width: auto; + padding: 0; + } + .navbar .brand { + padding-right: 10px; + padding-left: 10px; + margin: 0 0 0 -5px; + } + .nav-collapse { + clear: both; + } + .nav-collapse .nav { + float: none; + margin: 0 0 9px; + } + .nav-collapse .nav > li { + float: none; + } + .nav-collapse .nav > li > a { + margin-bottom: 2px; + } + .nav-collapse .nav > .divider-vertical { + display: none; + } + .nav-collapse .nav .nav-header { + color: #999999; + text-shadow: none; + } + .nav-collapse .nav > li > a, + .nav-collapse .dropdown-menu a { + padding: 6px 15px; + font-weight: bold; + color: #999999; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + } + .nav-collapse .btn { + padding: 4px 10px 4px; + font-weight: normal; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + } + .nav-collapse .dropdown-menu li + li a { + margin-bottom: 2px; + } + .nav-collapse .nav > li > a:hover, + .nav-collapse .dropdown-menu a:hover { + background-color: #222222; + } + .nav-collapse.in .btn-group { + padding: 0; + margin-top: 5px; + } + .nav-collapse .dropdown-menu { + position: static; + top: auto; + left: auto; + display: block; + float: none; + max-width: none; + padding: 0; + margin: 0 15px; + background-color: transparent; + border: none; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; + -webkit-box-shadow: none; + -moz-box-shadow: none; + box-shadow: none; + } + .nav-collapse .dropdown-menu:before, + .nav-collapse .dropdown-menu:after { + display: none; + } + .nav-collapse .dropdown-menu .divider { + display: none; + } + .nav-collapse .navbar-form, + .nav-collapse .navbar-search { + float: none; + padding: 9px 15px; + margin: 9px 0; + border-top: 1px solid #222222; + border-bottom: 1px solid #222222; + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1); + -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1); + } + .navbar .nav-collapse .nav.pull-right { + float: none; + margin-left: 0; + } + .nav-collapse, + .nav-collapse.collapse { + height: 0; + overflow: hidden; + } + .navbar .btn-navbar { + display: block; + } + .navbar-static .navbar-inner { + padding-right: 10px; + padding-left: 10px; + } +} + +@media (min-width: 980px) { + .nav-collapse.collapse { + height: auto !important; + overflow: visible !important; + } +} diff --git a/inst/web/css/bootstrap-responsive.min.css b/inst/web/css/bootstrap-responsive.min.css new file mode 100644 index 0000000..1f55036 --- /dev/null +++ b/inst/web/css/bootstrap-responsive.min.css @@ -0,0 +1,9 @@ +/*! + * Bootstrap Responsive v2.0.4 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + */.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;content:""}.clearfix:after{clear:both}.hide-text{font:0/0 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font-size: 100%; + -webkit-text-size-adjust: 100%; + -ms-text-size-adjust: 100%; +} + +a:focus { + outline: thin dotted #333; + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} + +a:hover, +a:active { + outline: 0; +} + +sub, +sup { + position: relative; + font-size: 75%; + line-height: 0; + vertical-align: baseline; +} + +sup { + top: -0.5em; +} + +sub { + bottom: -0.25em; +} + +img { + max-width: 100%; + vertical-align: middle; + border: 0; + -ms-interpolation-mode: bicubic; +} + +#map_canvas img { + max-width: none; +} + +button, +input, +select, +textarea { + margin: 0; + font-size: 100%; + vertical-align: middle; +} + +button, +input { + *overflow: visible; + line-height: normal; +} + +button::-moz-focus-inner, +input::-moz-focus-inner { + padding: 0; + border: 0; +} + +button, +input[type="button"], +input[type="reset"], +input[type="submit"] { + cursor: pointer; + -webkit-appearance: button; +} + +input[type="search"] { + -webkit-box-sizing: content-box; + -moz-box-sizing: content-box; + box-sizing: content-box; + -webkit-appearance: textfield; +} + +input[type="search"]::-webkit-search-decoration, +input[type="search"]::-webkit-search-cancel-button { + -webkit-appearance: none; +} + +textarea { + overflow: auto; + vertical-align: top; +} + +.clearfix { + *zoom: 1; +} + +.clearfix:before, +.clearfix:after { + display: table; + content: ""; +} + +.clearfix:after { + clear: both; +} + +.hide-text { + font: 0/0 a; + color: transparent; + text-shadow: none; + background-color: transparent; + border: 0; +} + +.input-block-level { + display: block; + width: 100%; + min-height: 28px; + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; +} + +body { + margin: 0; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 13px; + line-height: 18px; + color: #333333; + background-color: #ffffff; +} + +a { + color: #0088cc; + text-decoration: none; +} + +a:hover { + color: #005580; + text-decoration: underline; +} + +.row { + margin-left: -20px; + *zoom: 1; +} + +.row:before, +.row:after { + display: table; + content: ""; +} + +.row:after { + clear: both; +} + +[class*="span"] { + float: left; + margin-left: 20px; +} + +.container, +.navbar-fixed-top .container, +.navbar-fixed-bottom .container { + width: 940px; +} + +.span12 { + width: 940px; +} + +.span11 { + width: 860px; +} + +.span10 { + width: 780px; +} + +.span9 { + width: 700px; +} + +.span8 { + width: 620px; +} + +.span7 { + width: 540px; +} + +.span6 { + width: 460px; +} + +.span5 { + width: 380px; +} + +.span4 { + width: 300px; +} + +.span3 { + width: 220px; +} + +.span2 { + width: 140px; +} + +.span1 { + width: 60px; +} + +.offset12 { + margin-left: 980px; +} + +.offset11 { + margin-left: 900px; +} + +.offset10 { + margin-left: 820px; +} + +.offset9 { + margin-left: 740px; +} + +.offset8 { + margin-left: 660px; +} + +.offset7 { + margin-left: 580px; +} + +.offset6 { + margin-left: 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+.container-fluid:after { + display: table; + content: ""; +} + +.container-fluid:after { + clear: both; +} + +p { + margin: 0 0 9px; +} + +p small { + font-size: 11px; + color: #999999; +} + +.lead { + margin-bottom: 18px; + font-size: 20px; + font-weight: 200; + line-height: 27px; +} + +h1, +h2, +h3, +h4, +h5, +h6 { + margin: 0; + font-family: inherit; + font-weight: bold; + color: inherit; + text-rendering: optimizelegibility; +} + +h1 small, +h2 small, +h3 small, +h4 small, +h5 small, +h6 small { + font-weight: normal; + color: #999999; +} + +h1 { + font-size: 30px; + line-height: 36px; +} + +h1 small { + font-size: 18px; +} + +h2 { + font-size: 24px; + line-height: 36px; +} + +h2 small { + font-size: 18px; +} + +h3 { + font-size: 18px; + line-height: 27px; +} + +h3 small { + font-size: 14px; +} + +h4, +h5, +h6 { + line-height: 18px; +} + +h4 { + font-size: 14px; +} + +h4 small { + font-size: 12px; +} + +h5 { + font-size: 12px; +} + +h6 { + font-size: 11px; + color: #999999; + text-transform: uppercase; +} + +.page-header { + padding-bottom: 17px; + margin: 18px 0; + border-bottom: 1px solid #eeeeee; +} + +.page-header h1 { + line-height: 1; +} + +ul, +ol { + padding: 0; + margin: 0 0 9px 25px; +} + +ul ul, +ul ol, +ol ol, +ol ul { + margin-bottom: 0; +} + +ul { + list-style: disc; +} + +ol { + list-style: decimal; +} + +li { + line-height: 18px; +} + +ul.unstyled, +ol.unstyled { + margin-left: 0; + list-style: none; +} + +dl { + margin-bottom: 18px; +} + +dt, +dd { + line-height: 18px; +} + +dt { + font-weight: bold; + line-height: 17px; +} + +dd { + margin-left: 9px; +} + +.dl-horizontal dt { + float: left; + width: 120px; + overflow: hidden; + clear: left; + text-align: right; + text-overflow: ellipsis; + white-space: nowrap; +} + +.dl-horizontal dd { + margin-left: 130px; +} + +hr { + margin: 18px 0; + border: 0; + border-top: 1px solid #eeeeee; + border-bottom: 1px solid #ffffff; +} + +strong { + font-weight: bold; +} + +em { + font-style: italic; +} + +.muted { + color: #999999; +} + +abbr[title] { + cursor: help; + border-bottom: 1px dotted #999999; +} + +abbr.initialism { + font-size: 90%; + text-transform: uppercase; +} + +blockquote { + padding: 0 0 0 15px; + margin: 0 0 18px; + border-left: 5px solid #eeeeee; +} + +blockquote p { + margin-bottom: 0; + font-size: 16px; + font-weight: 300; + line-height: 22.5px; +} + +blockquote small { + display: block; + line-height: 18px; + color: #999999; +} + +blockquote small:before { + content: '\2014 \00A0'; +} + +blockquote.pull-right { + float: right; + padding-right: 15px; + padding-left: 0; + border-right: 5px solid #eeeeee; + border-left: 0; +} + +blockquote.pull-right p, +blockquote.pull-right small { + text-align: right; +} + +q:before, +q:after, +blockquote:before, +blockquote:after { + content: ""; +} + +address { + display: block; + margin-bottom: 18px; + font-style: normal; + line-height: 18px; +} + +small { + font-size: 100%; +} + +cite { + font-style: normal; +} + +code, +pre { + padding: 0 3px 2px; + font-family: Menlo, Monaco, Consolas, "Courier New", monospace; + font-size: 12px; + color: #333333; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; +} + +code { + padding: 2px 4px; + color: #d14; + background-color: #f7f7f9; + border: 1px solid #e1e1e8; +} + +pre { + display: block; + padding: 8.5px; + margin: 0 0 9px; + font-size: 12.025px; + line-height: 18px; + word-break: break-all; + word-wrap: break-word; + white-space: pre; + white-space: pre-wrap; + background-color: #f5f5f5; + border: 1px solid #ccc; + border: 1px solid rgba(0, 0, 0, 0.15); + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +pre.prettyprint { + margin-bottom: 18px; +} + +pre code { + padding: 0; + color: inherit; + background-color: transparent; + border: 0; +} + +.pre-scrollable { + max-height: 340px; + overflow-y: scroll; +} + +form { + margin: 0 0 18px; +} + +fieldset { + padding: 0; + margin: 0; + border: 0; +} + +legend { + display: block; + width: 100%; + padding: 0; + margin-bottom: 27px; + font-size: 19.5px; + line-height: 36px; + color: #333333; + border: 0; + border-bottom: 1px solid #e5e5e5; +} + +legend small { + font-size: 13.5px; + color: #999999; +} + +label, +input, +button, +select, +textarea { + font-size: 13px; + font-weight: normal; + line-height: 18px; +} + +input, +button, +select, +textarea { + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; +} + +label { + display: block; + margin-bottom: 5px; +} + +select, +textarea, +input[type="text"], +input[type="password"], +input[type="datetime"], +input[type="datetime-local"], +input[type="date"], +input[type="month"], +input[type="time"], +input[type="week"], +input[type="number"], +input[type="email"], +input[type="url"], +input[type="search"], +input[type="tel"], +input[type="color"], +.uneditable-input { + display: inline-block; + height: 18px; + padding: 4px; + margin-bottom: 9px; + font-size: 13px; + line-height: 18px; + color: #555555; +} + +input, +textarea { + width: 210px; +} + +textarea { + height: auto; +} + +textarea, +input[type="text"], +input[type="password"], +input[type="datetime"], +input[type="datetime-local"], +input[type="date"], +input[type="month"], +input[type="time"], +input[type="week"], +input[type="number"], +input[type="email"], +input[type="url"], +input[type="search"], +input[type="tel"], +input[type="color"], +.uneditable-input { + background-color: #ffffff; + border: 1px solid #cccccc; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + -webkit-transition: border linear 0.2s, box-shadow linear 0.2s; + -moz-transition: border linear 0.2s, box-shadow linear 0.2s; + -ms-transition: border linear 0.2s, box-shadow linear 0.2s; + -o-transition: border linear 0.2s, box-shadow linear 0.2s; + transition: border linear 0.2s, box-shadow linear 0.2s; +} + +textarea:focus, +input[type="text"]:focus, +input[type="password"]:focus, +input[type="datetime"]:focus, +input[type="datetime-local"]:focus, +input[type="date"]:focus, +input[type="month"]:focus, +input[type="time"]:focus, +input[type="week"]:focus, +input[type="number"]:focus, +input[type="email"]:focus, +input[type="url"]:focus, +input[type="search"]:focus, +input[type="tel"]:focus, +input[type="color"]:focus, +.uneditable-input:focus { + border-color: rgba(82, 168, 236, 0.8); + outline: 0; + outline: thin dotted \9; + /* IE6-9 */ + + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6); + -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6); +} + +input[type="radio"], +input[type="checkbox"] { + margin: 3px 0; + *margin-top: 0; + /* IE7 */ + + line-height: normal; + cursor: pointer; +} + +input[type="submit"], +input[type="reset"], +input[type="button"], +input[type="radio"], +input[type="checkbox"] { + width: auto; +} + +.uneditable-textarea { + width: auto; + height: auto; +} + +select, +input[type="file"] { + height: 28px; + /* In IE7, the height of the select element cannot be changed by height, only font-size */ + + *margin-top: 4px; + /* For IE7, add top margin to align select with labels */ + + line-height: 28px; +} + +select { + width: 220px; + border: 1px solid #bbb; +} + +select[multiple], +select[size] { + height: auto; +} + +select:focus, +input[type="file"]:focus, +input[type="radio"]:focus, +input[type="checkbox"]:focus { + outline: thin dotted #333; + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} + +.radio, +.checkbox { + min-height: 18px; + padding-left: 18px; +} + +.radio input[type="radio"], +.checkbox input[type="checkbox"] { + float: left; + margin-left: -18px; +} + +.controls > .radio:first-child, +.controls > .checkbox:first-child { + padding-top: 5px; +} + +.radio.inline, +.checkbox.inline { + display: inline-block; + padding-top: 5px; + margin-bottom: 0; + vertical-align: middle; +} + +.radio.inline + .radio.inline, +.checkbox.inline + .checkbox.inline { + margin-left: 10px; +} + +.input-mini { + width: 60px; +} + +.input-small { + width: 90px; +} + +.input-medium { + width: 150px; +} + +.input-large { + width: 210px; +} + +.input-xlarge { + width: 270px; +} + +.input-xxlarge { + width: 530px; +} + +input[class*="span"], +select[class*="span"], +textarea[class*="span"], +.uneditable-input[class*="span"], +.row-fluid input[class*="span"], +.row-fluid select[class*="span"], +.row-fluid textarea[class*="span"], +.row-fluid .uneditable-input[class*="span"] { + float: none; + margin-left: 0; +} + +.input-append input[class*="span"], +.input-append .uneditable-input[class*="span"], +.input-prepend input[class*="span"], +.input-prepend .uneditable-input[class*="span"], +.row-fluid .input-prepend [class*="span"], +.row-fluid .input-append [class*="span"] { + display: inline-block; +} + +input, +textarea, +.uneditable-input { + margin-left: 0; +} + +input.span12, +textarea.span12, +.uneditable-input.span12 { + width: 930px; +} + +input.span11, +textarea.span11, +.uneditable-input.span11 { + width: 850px; +} + +input.span10, +textarea.span10, +.uneditable-input.span10 { + width: 770px; +} + +input.span9, +textarea.span9, +.uneditable-input.span9 { + width: 690px; +} + +input.span8, +textarea.span8, +.uneditable-input.span8 { + width: 610px; +} + +input.span7, +textarea.span7, +.uneditable-input.span7 { + width: 530px; +} + +input.span6, +textarea.span6, +.uneditable-input.span6 { + width: 450px; +} + +input.span5, +textarea.span5, +.uneditable-input.span5 { + width: 370px; +} + +input.span4, +textarea.span4, +.uneditable-input.span4 { + width: 290px; +} + +input.span3, +textarea.span3, +.uneditable-input.span3 { + width: 210px; +} + +input.span2, +textarea.span2, +.uneditable-input.span2 { + width: 130px; +} + +input.span1, +textarea.span1, +.uneditable-input.span1 { + width: 50px; +} + +input[disabled], +select[disabled], +textarea[disabled], +input[readonly], +select[readonly], +textarea[readonly] { + cursor: not-allowed; + background-color: #eeeeee; + border-color: #ddd; +} + +input[type="radio"][disabled], +input[type="checkbox"][disabled], +input[type="radio"][readonly], +input[type="checkbox"][readonly] { + background-color: transparent; +} + +.control-group.warning > label, +.control-group.warning .help-block, +.control-group.warning .help-inline { + color: #c09853; +} + +.control-group.warning .checkbox, +.control-group.warning .radio, +.control-group.warning input, +.control-group.warning select, +.control-group.warning textarea { + color: #c09853; + border-color: #c09853; +} + +.control-group.warning .checkbox:focus, +.control-group.warning .radio:focus, +.control-group.warning input:focus, +.control-group.warning select:focus, +.control-group.warning textarea:focus { + border-color: #a47e3c; + -webkit-box-shadow: 0 0 6px #dbc59e; + -moz-box-shadow: 0 0 6px #dbc59e; + box-shadow: 0 0 6px #dbc59e; +} + +.control-group.warning .input-prepend .add-on, +.control-group.warning .input-append .add-on { + color: #c09853; + background-color: #fcf8e3; + border-color: #c09853; +} + +.control-group.error > label, +.control-group.error .help-block, +.control-group.error .help-inline { + color: #b94a48; +} + +.control-group.error .checkbox, +.control-group.error .radio, +.control-group.error input, +.control-group.error select, +.control-group.error textarea { + color: #b94a48; + border-color: #b94a48; +} + +.control-group.error .checkbox:focus, +.control-group.error .radio:focus, +.control-group.error input:focus, +.control-group.error select:focus, +.control-group.error textarea:focus { + border-color: #953b39; + -webkit-box-shadow: 0 0 6px #d59392; + -moz-box-shadow: 0 0 6px #d59392; + box-shadow: 0 0 6px #d59392; +} + +.control-group.error .input-prepend .add-on, +.control-group.error .input-append .add-on { + color: #b94a48; + background-color: #f2dede; + border-color: #b94a48; +} + +.control-group.success > label, +.control-group.success .help-block, +.control-group.success .help-inline { + color: #468847; +} + +.control-group.success .checkbox, +.control-group.success .radio, +.control-group.success input, +.control-group.success select, +.control-group.success textarea { + color: #468847; + border-color: #468847; +} + +.control-group.success .checkbox:focus, +.control-group.success .radio:focus, +.control-group.success input:focus, +.control-group.success select:focus, +.control-group.success textarea:focus { + border-color: #356635; + -webkit-box-shadow: 0 0 6px #7aba7b; + -moz-box-shadow: 0 0 6px #7aba7b; + box-shadow: 0 0 6px #7aba7b; +} + +.control-group.success .input-prepend .add-on, +.control-group.success .input-append .add-on { + color: #468847; + background-color: #dff0d8; + border-color: #468847; +} + +input:focus:required:invalid, +textarea:focus:required:invalid, +select:focus:required:invalid { + color: #b94a48; + border-color: #ee5f5b; +} + +input:focus:required:invalid:focus, +textarea:focus:required:invalid:focus, +select:focus:required:invalid:focus { + border-color: #e9322d; + -webkit-box-shadow: 0 0 6px #f8b9b7; + -moz-box-shadow: 0 0 6px #f8b9b7; + box-shadow: 0 0 6px #f8b9b7; +} + +.form-actions { + padding: 17px 20px 18px; + margin-top: 18px; + margin-bottom: 18px; + background-color: #f5f5f5; + border-top: 1px solid #e5e5e5; + *zoom: 1; +} + +.form-actions:before, +.form-actions:after { + display: table; + content: ""; +} + +.form-actions:after { + clear: both; +} + +.uneditable-input { + overflow: hidden; + white-space: nowrap; + cursor: not-allowed; + background-color: #ffffff; + border-color: #eee; + -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.025); + -moz-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.025); + box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.025); +} + +:-moz-placeholder { + color: #999999; +} + +:-ms-input-placeholder { + color: #999999; +} + +::-webkit-input-placeholder { + color: #999999; +} + +.help-block, +.help-inline { + color: #555555; +} + +.help-block { + display: block; + margin-bottom: 9px; +} + +.help-inline { + display: inline-block; + *display: inline; + padding-left: 5px; + vertical-align: middle; + *zoom: 1; +} + +.input-prepend, +.input-append { + margin-bottom: 5px; +} + +.input-prepend input, +.input-append input, +.input-prepend select, +.input-append select, +.input-prepend .uneditable-input, +.input-append .uneditable-input { + position: relative; + margin-bottom: 0; + *margin-left: 0; + vertical-align: middle; + -webkit-border-radius: 0 3px 3px 0; + -moz-border-radius: 0 3px 3px 0; + border-radius: 0 3px 3px 0; +} + +.input-prepend input:focus, +.input-append input:focus, +.input-prepend select:focus, +.input-append select:focus, +.input-prepend .uneditable-input:focus, +.input-append .uneditable-input:focus { + z-index: 2; +} + +.input-prepend .uneditable-input, +.input-append .uneditable-input { + border-left-color: #ccc; +} + +.input-prepend .add-on, +.input-append .add-on { + display: inline-block; + width: auto; + height: 18px; + min-width: 16px; + padding: 4px 5px; + font-weight: normal; + line-height: 18px; + text-align: center; + text-shadow: 0 1px 0 #ffffff; + vertical-align: middle; + background-color: #eeeeee; + border: 1px solid #ccc; +} + +.input-prepend .add-on, +.input-append .add-on, +.input-prepend .btn, +.input-append .btn { + margin-left: -1px; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.input-prepend .active, +.input-append .active { + background-color: #a9dba9; + border-color: #46a546; +} + +.input-prepend .add-on, +.input-prepend .btn { + margin-right: -1px; +} + +.input-prepend .add-on:first-child, +.input-prepend .btn:first-child { + -webkit-border-radius: 3px 0 0 3px; + -moz-border-radius: 3px 0 0 3px; + border-radius: 3px 0 0 3px; +} + +.input-append input, +.input-append select, +.input-append .uneditable-input { + -webkit-border-radius: 3px 0 0 3px; + -moz-border-radius: 3px 0 0 3px; + border-radius: 3px 0 0 3px; +} + +.input-append .uneditable-input { + border-right-color: #ccc; + border-left-color: #eee; +} + +.input-append .add-on:last-child, +.input-append .btn:last-child { + -webkit-border-radius: 0 3px 3px 0; + -moz-border-radius: 0 3px 3px 0; + border-radius: 0 3px 3px 0; +} + +.input-prepend.input-append input, +.input-prepend.input-append select, +.input-prepend.input-append .uneditable-input { + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.input-prepend.input-append .add-on:first-child, +.input-prepend.input-append .btn:first-child { + margin-right: -1px; + -webkit-border-radius: 3px 0 0 3px; + -moz-border-radius: 3px 0 0 3px; + border-radius: 3px 0 0 3px; +} + +.input-prepend.input-append .add-on:last-child, +.input-prepend.input-append .btn:last-child { + margin-left: -1px; + -webkit-border-radius: 0 3px 3px 0; + -moz-border-radius: 0 3px 3px 0; + border-radius: 0 3px 3px 0; +} + +.search-query { + padding-right: 14px; + padding-right: 4px \9; + padding-left: 14px; + padding-left: 4px \9; + /* IE7-8 doesn't have border-radius, so don't indent the padding */ + + margin-bottom: 0; + -webkit-border-radius: 14px; + -moz-border-radius: 14px; + border-radius: 14px; +} + +.form-search input, +.form-inline input, +.form-horizontal input, +.form-search textarea, +.form-inline textarea, +.form-horizontal textarea, +.form-search select, +.form-inline select, +.form-horizontal select, +.form-search .help-inline, +.form-inline .help-inline, +.form-horizontal .help-inline, +.form-search .uneditable-input, +.form-inline .uneditable-input, +.form-horizontal .uneditable-input, +.form-search .input-prepend, +.form-inline .input-prepend, +.form-horizontal .input-prepend, +.form-search .input-append, +.form-inline .input-append, +.form-horizontal .input-append { + display: inline-block; + *display: inline; + margin-bottom: 0; + *zoom: 1; +} + +.form-search .hide, +.form-inline .hide, +.form-horizontal .hide { + display: none; +} + +.form-search label, +.form-inline label { + display: inline-block; +} + +.form-search .input-append, +.form-inline .input-append, +.form-search .input-prepend, +.form-inline .input-prepend { + margin-bottom: 0; +} + +.form-search .radio, +.form-search .checkbox, +.form-inline .radio, +.form-inline .checkbox { + padding-left: 0; + margin-bottom: 0; + vertical-align: middle; +} + +.form-search .radio input[type="radio"], +.form-search .checkbox input[type="checkbox"], +.form-inline .radio input[type="radio"], +.form-inline .checkbox input[type="checkbox"] { + float: left; + margin-right: 3px; + margin-left: 0; +} + +.control-group { + margin-bottom: 9px; +} + +legend + .control-group { + margin-top: 18px; + -webkit-margin-top-collapse: separate; +} + +.form-horizontal .control-group { + margin-bottom: 18px; + *zoom: 1; +} + +.form-horizontal .control-group:before, +.form-horizontal .control-group:after { + display: table; + content: ""; +} + +.form-horizontal .control-group:after { + clear: both; +} + +.form-horizontal .control-label { + float: left; + width: 140px; + padding-top: 5px; + text-align: right; +} + +.form-horizontal .controls { + *display: inline-block; + *padding-left: 20px; + margin-left: 160px; + *margin-left: 0; +} + +.form-horizontal .controls:first-child { + *padding-left: 160px; +} + +.form-horizontal .help-block { + margin-top: 9px; + margin-bottom: 0; +} + +.form-horizontal .form-actions { + padding-left: 160px; +} + +table { + max-width: 100%; + background-color: transparent; + border-collapse: collapse; + border-spacing: 0; +} + +.table { + width: 100%; + margin-bottom: 18px; +} + +.table th, +.table td { + padding: 8px; + line-height: 18px; + text-align: left; + vertical-align: top; + border-top: 1px solid #dddddd; +} + +.table th { + font-weight: bold; +} + +.table thead th { + vertical-align: bottom; +} + +.table caption + thead tr:first-child th, +.table caption + thead tr:first-child td, +.table colgroup + thead tr:first-child th, +.table colgroup + thead tr:first-child td, +.table thead:first-child tr:first-child th, +.table thead:first-child tr:first-child td { + border-top: 0; +} + +.table tbody + tbody { + border-top: 2px solid #dddddd; +} + +.table-condensed th, +.table-condensed td { + padding: 4px 5px; +} + +.table-bordered { + border: 1px solid #dddddd; + border-collapse: separate; + *border-collapse: collapsed; + border-left: 0; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.table-bordered th, +.table-bordered td { + border-left: 1px solid #dddddd; +} + +.table-bordered caption + thead tr:first-child th, +.table-bordered caption + tbody tr:first-child th, +.table-bordered caption + tbody tr:first-child td, +.table-bordered colgroup + thead tr:first-child th, +.table-bordered colgroup + tbody tr:first-child th, +.table-bordered colgroup + tbody tr:first-child td, +.table-bordered thead:first-child tr:first-child th, +.table-bordered tbody:first-child tr:first-child th, +.table-bordered tbody:first-child tr:first-child td { + border-top: 0; +} + +.table-bordered thead:first-child tr:first-child th:first-child, +.table-bordered tbody:first-child tr:first-child td:first-child { + -webkit-border-top-left-radius: 4px; + border-top-left-radius: 4px; + -moz-border-radius-topleft: 4px; +} + +.table-bordered thead:first-child tr:first-child th:last-child, +.table-bordered tbody:first-child tr:first-child td:last-child { + -webkit-border-top-right-radius: 4px; + border-top-right-radius: 4px; + -moz-border-radius-topright: 4px; +} + +.table-bordered thead:last-child tr:last-child th:first-child, +.table-bordered tbody:last-child tr:last-child td:first-child { + -webkit-border-radius: 0 0 0 4px; + -moz-border-radius: 0 0 0 4px; + border-radius: 0 0 0 4px; + -webkit-border-bottom-left-radius: 4px; + border-bottom-left-radius: 4px; + -moz-border-radius-bottomleft: 4px; +} + +.table-bordered thead:last-child tr:last-child th:last-child, +.table-bordered tbody:last-child tr:last-child td:last-child { + -webkit-border-bottom-right-radius: 4px; + border-bottom-right-radius: 4px; + -moz-border-radius-bottomright: 4px; +} + +.table-striped tbody tr:nth-child(odd) td, +.table-striped tbody tr:nth-child(odd) th { + background-color: #f9f9f9; +} + +.table tbody tr:hover td, +.table tbody tr:hover th { + background-color: #f5f5f5; +} + +table .span1 { + float: none; + width: 44px; + margin-left: 0; +} + +table .span2 { + float: none; + width: 124px; + margin-left: 0; +} + +table .span3 { + float: none; + width: 204px; + margin-left: 0; +} + +table .span4 { + float: none; + width: 284px; + margin-left: 0; +} + +table .span5 { + float: none; + width: 364px; + margin-left: 0; +} + +table .span6 { + float: none; + width: 444px; + margin-left: 0; +} + +table .span7 { + float: none; + width: 524px; + margin-left: 0; +} + +table .span8 { + float: none; + width: 604px; + margin-left: 0; +} + +table .span9 { + float: none; + width: 684px; + margin-left: 0; +} + +table .span10 { + float: none; + width: 764px; + margin-left: 0; +} + +table .span11 { + float: none; + width: 844px; + margin-left: 0; +} + +table .span12 { + float: none; + width: 924px; + margin-left: 0; +} + +table .span13 { + float: none; + width: 1004px; + margin-left: 0; +} + +table .span14 { + float: none; + width: 1084px; + margin-left: 0; +} + +table .span15 { + float: none; + width: 1164px; + margin-left: 0; +} + +table .span16 { + float: none; + width: 1244px; + margin-left: 0; +} + +table .span17 { + float: none; + width: 1324px; + margin-left: 0; +} + +table .span18 { + float: none; + width: 1404px; + margin-left: 0; +} + +table .span19 { + float: none; + width: 1484px; + margin-left: 0; +} + +table .span20 { + float: none; + width: 1564px; + margin-left: 0; +} + +table .span21 { + float: none; + width: 1644px; + margin-left: 0; +} + +table .span22 { + float: none; + width: 1724px; + margin-left: 0; +} + +table .span23 { + float: none; + width: 1804px; + margin-left: 0; +} + +table .span24 { + float: none; + width: 1884px; + margin-left: 0; +} + +[class^="icon-"], +[class*=" icon-"] { + display: inline-block; + width: 14px; + height: 14px; + *margin-right: .3em; + line-height: 14px; + vertical-align: text-top; + background-image: url("../img/glyphicons-halflings.png"); + background-position: 14px 14px; + background-repeat: no-repeat; +} + +[class^="icon-"]:last-child, +[class*=" icon-"]:last-child { + *margin-left: 0; +} + +.icon-white { + background-image: url("../img/glyphicons-halflings-white.png"); +} + +.icon-glass { + background-position: 0 0; +} + +.icon-music { + background-position: -24px 0; +} + +.icon-search { + background-position: -48px 0; +} + +.icon-envelope { + background-position: -72px 0; +} + +.icon-heart { + background-position: -96px 0; +} + +.icon-star { + background-position: -120px 0; +} + +.icon-star-empty { + background-position: -144px 0; +} + +.icon-user { + background-position: -168px 0; +} + +.icon-film { + background-position: -192px 0; +} + +.icon-th-large { + background-position: -216px 0; +} + +.icon-th { + background-position: -240px 0; +} + +.icon-th-list { + background-position: -264px 0; +} + +.icon-ok { + background-position: -288px 0; +} + +.icon-remove { + background-position: -312px 0; +} + +.icon-zoom-in { + background-position: -336px 0; +} + +.icon-zoom-out { + background-position: -360px 0; +} + +.icon-off { + background-position: -384px 0; +} + +.icon-signal { + background-position: -408px 0; +} + +.icon-cog { + background-position: -432px 0; +} + +.icon-trash { + background-position: -456px 0; +} + +.icon-home { + background-position: 0 -24px; +} + +.icon-file { + background-position: -24px -24px; +} + +.icon-time { + background-position: -48px -24px; +} + +.icon-road { + background-position: -72px -24px; +} + +.icon-download-alt { + background-position: -96px -24px; +} + +.icon-download { + background-position: -120px -24px; +} + +.icon-upload { + background-position: -144px -24px; +} + +.icon-inbox { + background-position: -168px -24px; +} + +.icon-play-circle { + background-position: -192px -24px; +} + +.icon-repeat { + background-position: -216px -24px; +} + +.icon-refresh { + background-position: -240px -24px; +} + +.icon-list-alt { + background-position: -264px -24px; +} + +.icon-lock { + background-position: -287px -24px; +} + +.icon-flag { + background-position: -312px -24px; +} + +.icon-headphones { + background-position: -336px -24px; +} + +.icon-volume-off { + background-position: -360px -24px; +} + +.icon-volume-down { + background-position: -384px -24px; +} + +.icon-volume-up { + background-position: -408px -24px; +} + +.icon-qrcode { + background-position: -432px -24px; +} + +.icon-barcode { + background-position: -456px -24px; +} + +.icon-tag { + background-position: 0 -48px; +} + +.icon-tags { + background-position: -25px -48px; +} + +.icon-book { + background-position: -48px -48px; +} + +.icon-bookmark { + background-position: -72px -48px; +} + +.icon-print { + background-position: -96px -48px; +} + +.icon-camera { + background-position: -120px -48px; +} + +.icon-font { + background-position: -144px -48px; +} + +.icon-bold { + background-position: -167px -48px; +} + +.icon-italic { + background-position: -192px -48px; +} + +.icon-text-height { + background-position: -216px -48px; +} + +.icon-text-width { + background-position: -240px -48px; +} + +.icon-align-left { + background-position: -264px -48px; +} + +.icon-align-center { + background-position: -288px -48px; +} + +.icon-align-right { + background-position: -312px -48px; +} + +.icon-align-justify { + background-position: -336px -48px; +} + +.icon-list { + background-position: -360px -48px; +} + +.icon-indent-left { + background-position: -384px -48px; +} + +.icon-indent-right { + background-position: -408px -48px; +} + +.icon-facetime-video { + background-position: -432px -48px; +} + +.icon-picture { + background-position: -456px -48px; +} + +.icon-pencil { + background-position: 0 -72px; +} + +.icon-map-marker { + background-position: -24px -72px; +} + +.icon-adjust { + background-position: -48px -72px; +} + +.icon-tint { + background-position: -72px -72px; +} + +.icon-edit { + background-position: -96px -72px; +} + +.icon-share { + background-position: -120px -72px; +} + +.icon-check { + background-position: -144px -72px; +} + +.icon-move { + background-position: -168px -72px; +} + +.icon-step-backward { + background-position: -192px -72px; +} + +.icon-fast-backward { + background-position: -216px -72px; +} + +.icon-backward { + background-position: -240px -72px; +} + +.icon-play { + background-position: -264px -72px; +} + +.icon-pause { + background-position: -288px -72px; +} + +.icon-stop { + background-position: -312px -72px; +} + +.icon-forward { + background-position: -336px -72px; +} + +.icon-fast-forward { + background-position: -360px -72px; +} + +.icon-step-forward { + background-position: -384px -72px; +} + +.icon-eject { + background-position: -408px -72px; +} + +.icon-chevron-left { + background-position: -432px -72px; +} + +.icon-chevron-right { + background-position: -456px -72px; +} + +.icon-plus-sign { + background-position: 0 -96px; +} + +.icon-minus-sign { + background-position: -24px -96px; +} + +.icon-remove-sign { + background-position: -48px -96px; +} + +.icon-ok-sign { + background-position: -72px -96px; +} + +.icon-question-sign { + background-position: -96px -96px; +} + +.icon-info-sign { + background-position: -120px -96px; +} + +.icon-screenshot { + background-position: -144px -96px; +} + +.icon-remove-circle { + background-position: -168px -96px; +} + +.icon-ok-circle { + background-position: -192px -96px; +} + +.icon-ban-circle { + background-position: -216px -96px; +} + +.icon-arrow-left { + background-position: -240px -96px; +} + +.icon-arrow-right { + background-position: -264px -96px; +} + +.icon-arrow-up { + background-position: -289px -96px; +} + +.icon-arrow-down { + background-position: -312px -96px; +} + +.icon-share-alt { + background-position: -336px -96px; +} + +.icon-resize-full { + background-position: -360px -96px; +} + +.icon-resize-small { + background-position: -384px -96px; +} + +.icon-plus { + background-position: -408px -96px; +} + +.icon-minus { + background-position: -433px -96px; +} + +.icon-asterisk { + background-position: -456px -96px; +} + +.icon-exclamation-sign { + background-position: 0 -120px; +} + +.icon-gift { + background-position: -24px -120px; +} + +.icon-leaf { + background-position: -48px -120px; +} + +.icon-fire { + background-position: -72px -120px; +} + +.icon-eye-open { + background-position: -96px -120px; +} + +.icon-eye-close { + background-position: -120px -120px; +} + +.icon-warning-sign { + background-position: -144px -120px; +} + +.icon-plane { + background-position: -168px -120px; +} + +.icon-calendar { + background-position: -192px -120px; +} + +.icon-random { + background-position: -216px -120px; +} + +.icon-comment { + background-position: -240px -120px; +} + +.icon-magnet { + background-position: -264px -120px; +} + +.icon-chevron-up { + background-position: -288px -120px; +} + +.icon-chevron-down { + background-position: -313px -119px; +} + +.icon-retweet { + background-position: -336px -120px; +} + +.icon-shopping-cart { + background-position: -360px -120px; +} + +.icon-folder-close { + background-position: -384px -120px; +} + +.icon-folder-open { + background-position: -408px -120px; +} + +.icon-resize-vertical { + background-position: -432px -119px; +} + +.icon-resize-horizontal { + background-position: -456px -118px; +} + +.icon-hdd { + background-position: 0 -144px; +} + +.icon-bullhorn { + background-position: -24px -144px; +} + +.icon-bell { + background-position: -48px -144px; +} + +.icon-certificate { + background-position: -72px -144px; +} + +.icon-thumbs-up { + background-position: -96px -144px; +} + +.icon-thumbs-down { + background-position: -120px -144px; +} + +.icon-hand-right { + background-position: -144px -144px; +} + +.icon-hand-left { + background-position: -168px -144px; +} + +.icon-hand-up { + background-position: -192px -144px; +} + +.icon-hand-down { + background-position: -216px -144px; +} + +.icon-circle-arrow-right { + background-position: -240px -144px; +} + +.icon-circle-arrow-left { + background-position: -264px -144px; +} + +.icon-circle-arrow-up { + background-position: -288px -144px; +} + +.icon-circle-arrow-down { + background-position: -312px -144px; +} + +.icon-globe { + background-position: -336px -144px; +} + +.icon-wrench { + background-position: -360px -144px; +} + +.icon-tasks { + background-position: -384px -144px; +} + +.icon-filter { + background-position: -408px -144px; +} + +.icon-briefcase { + background-position: -432px -144px; +} + +.icon-fullscreen { + background-position: -456px -144px; +} + +.dropup, +.dropdown { + position: relative; +} + +.dropdown-toggle { + *margin-bottom: -3px; +} + +.dropdown-toggle:active, +.open .dropdown-toggle { + outline: 0; +} + +.caret { + display: inline-block; + width: 0; + height: 0; + vertical-align: top; + border-top: 4px solid #000000; + border-right: 4px solid transparent; + border-left: 4px solid transparent; + content: ""; + opacity: 0.3; + filter: alpha(opacity=30); +} + +.dropdown .caret { + margin-top: 8px; + margin-left: 2px; +} + +.dropdown:hover .caret, +.open .caret { + opacity: 1; + filter: alpha(opacity=100); +} + +.dropdown-menu { + position: absolute; + top: 100%; + left: 0; + z-index: 1000; + display: none; + float: left; + min-width: 160px; + padding: 4px 0; + margin: 1px 0 0; + list-style: none; + background-color: #ffffff; + border: 1px solid #ccc; + border: 1px solid rgba(0, 0, 0, 0.2); + *border-right-width: 2px; + *border-bottom-width: 2px; + -webkit-border-radius: 5px; + -moz-border-radius: 5px; + border-radius: 5px; + -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); + -moz-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); + box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); + -webkit-background-clip: padding-box; + -moz-background-clip: padding; + background-clip: padding-box; +} + +.dropdown-menu.pull-right { + right: 0; + left: auto; +} + +.dropdown-menu .divider { + *width: 100%; + height: 1px; + margin: 8px 1px; + *margin: -5px 0 5px; + overflow: hidden; + background-color: #e5e5e5; + border-bottom: 1px solid #ffffff; +} + +.dropdown-menu a { + display: block; + padding: 3px 15px; + clear: both; + font-weight: normal; + line-height: 18px; + color: #333333; + white-space: nowrap; +} + +.dropdown-menu li > a:hover, +.dropdown-menu .active > a, +.dropdown-menu .active > a:hover { + color: #ffffff; + text-decoration: none; + background-color: #0088cc; +} + +.open { + *z-index: 1000; +} + +.open > .dropdown-menu { + display: block; +} + +.pull-right > .dropdown-menu { + right: 0; + left: auto; +} + +.dropup .caret, +.navbar-fixed-bottom .dropdown .caret { + border-top: 0; + border-bottom: 4px solid #000000; + content: "\2191"; +} + +.dropup .dropdown-menu, +.navbar-fixed-bottom .dropdown .dropdown-menu { + top: auto; + bottom: 100%; + margin-bottom: 1px; +} + +.typeahead { + margin-top: 2px; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.well { + min-height: 20px; + padding: 19px; + margin-bottom: 20px; + background-color: #f5f5f5; + border: 1px solid #eee; + border: 1px solid rgba(0, 0, 0, 0.05); + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05); +} + +.well blockquote { + border-color: #ddd; + border-color: rgba(0, 0, 0, 0.15); +} + +.well-large { + padding: 24px; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; +} + +.well-small { + padding: 9px; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; +} + +.fade { + opacity: 0; + -webkit-transition: opacity 0.15s linear; + -moz-transition: opacity 0.15s linear; + -ms-transition: opacity 0.15s linear; + -o-transition: opacity 0.15s linear; + transition: opacity 0.15s linear; +} + +.fade.in { + opacity: 1; +} + +.collapse { + position: relative; + height: 0; + overflow: hidden; + -webkit-transition: height 0.35s ease; + -moz-transition: height 0.35s ease; + -ms-transition: height 0.35s ease; + -o-transition: height 0.35s ease; + transition: height 0.35s ease; +} + +.collapse.in { + height: auto; +} + +.close { + float: right; + font-size: 20px; + font-weight: bold; + line-height: 18px; + color: #000000; + text-shadow: 0 1px 0 #ffffff; + opacity: 0.2; + filter: alpha(opacity=20); +} + +.close:hover { + color: #000000; + text-decoration: none; + cursor: pointer; + opacity: 0.4; + filter: alpha(opacity=40); +} + +button.close { + padding: 0; + cursor: pointer; + background: transparent; + border: 0; + -webkit-appearance: none; +} + +.btn { + display: inline-block; + *display: inline; + padding: 4px 10px 4px; + margin-bottom: 0; + *margin-left: .3em; + font-size: 13px; + line-height: 18px; + *line-height: 20px; + color: #333333; + text-align: center; + text-shadow: 0 1px 1px rgba(255, 255, 255, 0.75); + vertical-align: middle; + cursor: pointer; + background-color: #f5f5f5; + *background-color: #e6e6e6; + background-image: -ms-linear-gradient(top, #ffffff, #e6e6e6); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6)); + background-image: -webkit-linear-gradient(top, #ffffff, #e6e6e6); + background-image: -o-linear-gradient(top, #ffffff, #e6e6e6); + background-image: linear-gradient(top, #ffffff, #e6e6e6); + background-image: -moz-linear-gradient(top, #ffffff, #e6e6e6); + background-repeat: repeat-x; + border: 1px solid #cccccc; + *border: 0; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + border-color: #e6e6e6 #e6e6e6 #bfbfbf; + border-bottom-color: #b3b3b3; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); + *zoom: 1; + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.btn:hover, +.btn:active, +.btn.active, +.btn.disabled, +.btn[disabled] { + background-color: #e6e6e6; + *background-color: #d9d9d9; +} + +.btn:active, +.btn.active { + background-color: #cccccc \9; +} + +.btn:first-child { + *margin-left: 0; +} + +.btn:hover { + color: #333333; + text-decoration: none; + background-color: #e6e6e6; + *background-color: #d9d9d9; + /* Buttons in IE7 don't get borders, so darken on hover */ + + background-position: 0 -15px; + -webkit-transition: background-position 0.1s linear; + -moz-transition: background-position 0.1s linear; + -ms-transition: background-position 0.1s linear; + -o-transition: background-position 0.1s linear; + transition: background-position 0.1s linear; +} + +.btn:focus { + outline: thin dotted #333; + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} + +.btn.active, +.btn:active { + background-color: #e6e6e6; + background-color: #d9d9d9 \9; + background-image: none; + outline: 0; + -webkit-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.btn.disabled, +.btn[disabled] { + cursor: default; + background-color: #e6e6e6; + background-image: none; + opacity: 0.65; + filter: alpha(opacity=65); + -webkit-box-shadow: none; + -moz-box-shadow: none; + box-shadow: none; +} + +.btn-large { + padding: 9px 14px; + font-size: 15px; + line-height: normal; + -webkit-border-radius: 5px; + -moz-border-radius: 5px; + border-radius: 5px; +} + +.btn-large [class^="icon-"] { + margin-top: 1px; +} + +.btn-small { + padding: 5px 9px; + font-size: 11px; + line-height: 16px; +} + +.btn-small [class^="icon-"] { + margin-top: -1px; +} + +.btn-mini { + padding: 2px 6px; + font-size: 11px; + line-height: 14px; +} + +.btn-primary, +.btn-primary:hover, +.btn-warning, +.btn-warning:hover, +.btn-danger, +.btn-danger:hover, +.btn-success, +.btn-success:hover, +.btn-info, +.btn-info:hover, +.btn-inverse, +.btn-inverse:hover { + color: #ffffff; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25); +} + +.btn-primary.active, +.btn-warning.active, +.btn-danger.active, +.btn-success.active, +.btn-info.active, +.btn-inverse.active { + color: rgba(255, 255, 255, 0.75); +} + +.btn { + border-color: #ccc; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); +} + +.btn-primary { + background-color: #0074cc; + *background-color: #0055cc; + background-image: -ms-linear-gradient(top, #0088cc, #0055cc); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0055cc)); + background-image: -webkit-linear-gradient(top, #0088cc, #0055cc); + background-image: -o-linear-gradient(top, #0088cc, #0055cc); + background-image: -moz-linear-gradient(top, #0088cc, #0055cc); + background-image: linear-gradient(top, #0088cc, #0055cc); + background-repeat: repeat-x; + border-color: #0055cc #0055cc #003580; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#0088cc', endColorstr='#0055cc', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-primary:hover, +.btn-primary:active, +.btn-primary.active, +.btn-primary.disabled, +.btn-primary[disabled] { + background-color: #0055cc; + *background-color: #004ab3; +} + +.btn-primary:active, +.btn-primary.active { + background-color: #004099 \9; +} + +.btn-warning { + background-color: #faa732; + *background-color: #f89406; + background-image: -ms-linear-gradient(top, #fbb450, #f89406); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406)); + background-image: -webkit-linear-gradient(top, #fbb450, #f89406); + background-image: -o-linear-gradient(top, #fbb450, #f89406); + background-image: -moz-linear-gradient(top, #fbb450, #f89406); + background-image: linear-gradient(top, #fbb450, #f89406); + background-repeat: repeat-x; + border-color: #f89406 #f89406 #ad6704; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-warning:hover, +.btn-warning:active, +.btn-warning.active, +.btn-warning.disabled, +.btn-warning[disabled] { + background-color: #f89406; + *background-color: #df8505; +} + +.btn-warning:active, +.btn-warning.active { + background-color: #c67605 \9; +} + +.btn-danger { + background-color: #da4f49; + *background-color: #bd362f; + background-image: -ms-linear-gradient(top, #ee5f5b, #bd362f); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#bd362f)); + background-image: -webkit-linear-gradient(top, #ee5f5b, #bd362f); + background-image: -o-linear-gradient(top, #ee5f5b, #bd362f); + background-image: -moz-linear-gradient(top, #ee5f5b, #bd362f); + background-image: linear-gradient(top, #ee5f5b, #bd362f); + background-repeat: repeat-x; + border-color: #bd362f #bd362f #802420; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#bd362f', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-danger:hover, +.btn-danger:active, +.btn-danger.active, +.btn-danger.disabled, +.btn-danger[disabled] { + background-color: #bd362f; + *background-color: #a9302a; +} + +.btn-danger:active, +.btn-danger.active { + background-color: #942a25 \9; +} + +.btn-success { + background-color: #5bb75b; + *background-color: #51a351; + background-image: -ms-linear-gradient(top, #62c462, #51a351); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#51a351)); + background-image: -webkit-linear-gradient(top, #62c462, #51a351); + background-image: -o-linear-gradient(top, #62c462, #51a351); + background-image: -moz-linear-gradient(top, #62c462, #51a351); + background-image: linear-gradient(top, #62c462, #51a351); + background-repeat: repeat-x; + border-color: #51a351 #51a351 #387038; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#62c462', endColorstr='#51a351', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-success:hover, +.btn-success:active, +.btn-success.active, +.btn-success.disabled, +.btn-success[disabled] { + background-color: #51a351; + *background-color: #499249; +} + +.btn-success:active, +.btn-success.active { + background-color: #408140 \9; +} + +.btn-info { + background-color: #49afcd; + *background-color: #2f96b4; + background-image: -ms-linear-gradient(top, #5bc0de, #2f96b4); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#2f96b4)); + background-image: -webkit-linear-gradient(top, #5bc0de, #2f96b4); + background-image: -o-linear-gradient(top, #5bc0de, #2f96b4); + background-image: -moz-linear-gradient(top, #5bc0de, #2f96b4); + background-image: linear-gradient(top, #5bc0de, #2f96b4); + background-repeat: repeat-x; + border-color: #2f96b4 #2f96b4 #1f6377; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#5bc0de', endColorstr='#2f96b4', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-info:hover, +.btn-info:active, +.btn-info.active, +.btn-info.disabled, +.btn-info[disabled] { + background-color: #2f96b4; + *background-color: #2a85a0; +} + +.btn-info:active, +.btn-info.active { + background-color: #24748c \9; +} + +.btn-inverse { + background-color: #414141; + *background-color: #222222; + background-image: -ms-linear-gradient(top, #555555, #222222); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#555555), to(#222222)); + background-image: -webkit-linear-gradient(top, #555555, #222222); + background-image: -o-linear-gradient(top, #555555, #222222); + background-image: -moz-linear-gradient(top, #555555, #222222); + background-image: linear-gradient(top, #555555, #222222); + background-repeat: repeat-x; + border-color: #222222 #222222 #000000; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#555555', endColorstr='#222222', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); +} + +.btn-inverse:hover, +.btn-inverse:active, +.btn-inverse.active, +.btn-inverse.disabled, +.btn-inverse[disabled] { + background-color: #222222; + *background-color: #151515; +} + +.btn-inverse:active, +.btn-inverse.active { + background-color: #080808 \9; +} + +button.btn, +input[type="submit"].btn { + *padding-top: 2px; + *padding-bottom: 2px; +} + +button.btn::-moz-focus-inner, +input[type="submit"].btn::-moz-focus-inner { + padding: 0; + border: 0; +} + +button.btn.btn-large, +input[type="submit"].btn.btn-large { + *padding-top: 7px; + *padding-bottom: 7px; +} + +button.btn.btn-small, +input[type="submit"].btn.btn-small { + *padding-top: 3px; + *padding-bottom: 3px; +} + +button.btn.btn-mini, +input[type="submit"].btn.btn-mini { + *padding-top: 1px; + *padding-bottom: 1px; +} + +.btn-group { + position: relative; + *margin-left: .3em; + *zoom: 1; +} + +.btn-group:before, +.btn-group:after { + display: table; + content: ""; +} + +.btn-group:after { + clear: both; +} + +.btn-group:first-child { + *margin-left: 0; +} + +.btn-group + .btn-group { + margin-left: 5px; +} + +.btn-toolbar { + margin-top: 9px; + margin-bottom: 9px; +} + +.btn-toolbar .btn-group { + display: inline-block; + *display: inline; + /* IE7 inline-block hack */ + + *zoom: 1; +} + +.btn-group > .btn { + position: relative; + float: left; + margin-left: -1px; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.btn-group > .btn:first-child { + margin-left: 0; + -webkit-border-bottom-left-radius: 4px; + border-bottom-left-radius: 4px; + -webkit-border-top-left-radius: 4px; + border-top-left-radius: 4px; + -moz-border-radius-bottomleft: 4px; + -moz-border-radius-topleft: 4px; +} + +.btn-group > .btn:last-child, +.btn-group > .dropdown-toggle { + -webkit-border-top-right-radius: 4px; + border-top-right-radius: 4px; + -webkit-border-bottom-right-radius: 4px; + border-bottom-right-radius: 4px; + -moz-border-radius-topright: 4px; + -moz-border-radius-bottomright: 4px; +} + +.btn-group > .btn.large:first-child { + margin-left: 0; + -webkit-border-bottom-left-radius: 6px; + border-bottom-left-radius: 6px; + -webkit-border-top-left-radius: 6px; + border-top-left-radius: 6px; + -moz-border-radius-bottomleft: 6px; + -moz-border-radius-topleft: 6px; +} + +.btn-group > .btn.large:last-child, +.btn-group > .large.dropdown-toggle { + -webkit-border-top-right-radius: 6px; + border-top-right-radius: 6px; + -webkit-border-bottom-right-radius: 6px; + border-bottom-right-radius: 6px; + -moz-border-radius-topright: 6px; + -moz-border-radius-bottomright: 6px; +} + +.btn-group > .btn:hover, +.btn-group > .btn:focus, +.btn-group > .btn:active, +.btn-group > .btn.active { + z-index: 2; +} + +.btn-group .dropdown-toggle:active, +.btn-group.open .dropdown-toggle { + outline: 0; +} + +.btn-group > .dropdown-toggle { + *padding-top: 4px; + padding-right: 8px; + *padding-bottom: 4px; + padding-left: 8px; + -webkit-box-shadow: inset 1px 0 0 rgba(255, 255, 255, 0.125), inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 1px 0 0 rgba(255, 255, 255, 0.125), inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: inset 1px 0 0 rgba(255, 255, 255, 0.125), inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.btn-group > .btn-mini.dropdown-toggle { + padding-right: 5px; + padding-left: 5px; +} + +.btn-group > .btn-small.dropdown-toggle { + *padding-top: 4px; + *padding-bottom: 4px; +} + +.btn-group > .btn-large.dropdown-toggle { + padding-right: 12px; + padding-left: 12px; +} + +.btn-group.open .dropdown-toggle { + background-image: none; + -webkit-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.btn-group.open .btn.dropdown-toggle { + background-color: #e6e6e6; +} + +.btn-group.open .btn-primary.dropdown-toggle { + background-color: #0055cc; +} + +.btn-group.open .btn-warning.dropdown-toggle { + background-color: #f89406; +} + +.btn-group.open .btn-danger.dropdown-toggle { + background-color: #bd362f; +} + +.btn-group.open .btn-success.dropdown-toggle { + background-color: #51a351; +} + +.btn-group.open .btn-info.dropdown-toggle { + background-color: #2f96b4; +} + +.btn-group.open .btn-inverse.dropdown-toggle { + background-color: #222222; +} + +.btn .caret { + margin-top: 7px; + margin-left: 0; +} + +.btn:hover .caret, +.open.btn-group .caret { + opacity: 1; + filter: alpha(opacity=100); +} + +.btn-mini .caret { + margin-top: 5px; +} + +.btn-small .caret { + margin-top: 6px; +} + +.btn-large .caret { + margin-top: 6px; + border-top-width: 5px; + border-right-width: 5px; + border-left-width: 5px; +} + +.dropup .btn-large .caret { + border-top: 0; + border-bottom: 5px solid #000000; +} + +.btn-primary .caret, +.btn-warning .caret, +.btn-danger .caret, +.btn-info .caret, +.btn-success .caret, +.btn-inverse .caret { + border-top-color: #ffffff; + border-bottom-color: #ffffff; + opacity: 0.75; + filter: alpha(opacity=75); +} + +.alert { + padding: 8px 35px 8px 14px; + margin-bottom: 18px; + color: #c09853; + text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5); + background-color: #fcf8e3; + border: 1px solid #fbeed5; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.alert-heading { + color: inherit; +} + +.alert .close { + position: relative; + top: -2px; + right: -21px; + line-height: 18px; +} + +.alert-success { + color: #468847; + background-color: #dff0d8; + border-color: #d6e9c6; +} + +.alert-danger, +.alert-error { + color: #b94a48; + background-color: #f2dede; + border-color: #eed3d7; +} + +.alert-info { + color: #3a87ad; + background-color: #d9edf7; + border-color: #bce8f1; +} + +.alert-block { + padding-top: 14px; + padding-bottom: 14px; +} + +.alert-block > p, +.alert-block > ul { + margin-bottom: 0; +} + +.alert-block p + p { + margin-top: 5px; +} + +.nav { + margin-bottom: 18px; + margin-left: 0; + list-style: none; +} + +.nav > li > a { + display: block; +} + +.nav > li > a:hover { + text-decoration: none; + background-color: #eeeeee; +} + +.nav > .pull-right { + float: right; +} + +.nav .nav-header { + display: block; + padding: 3px 15px; + font-size: 11px; + font-weight: bold; + line-height: 18px; + color: #999999; + text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5); + text-transform: uppercase; +} + +.nav li + .nav-header { + margin-top: 9px; +} + +.nav-list { + padding-right: 15px; + padding-left: 15px; + margin-bottom: 0; +} + +.nav-list > li > a, +.nav-list .nav-header { + margin-right: -15px; + margin-left: -15px; + text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5); +} + +.nav-list > li > a { + padding: 3px 15px; +} + +.nav-list > .active > a, +.nav-list > .active > a:hover { + color: #ffffff; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.2); + background-color: #0088cc; +} + +.nav-list [class^="icon-"] { + margin-right: 2px; +} + +.nav-list .divider { + *width: 100%; + height: 1px; + margin: 8px 1px; + *margin: -5px 0 5px; + overflow: hidden; + background-color: #e5e5e5; + border-bottom: 1px solid #ffffff; +} + +.nav-tabs, +.nav-pills { + *zoom: 1; +} + +.nav-tabs:before, +.nav-pills:before, +.nav-tabs:after, +.nav-pills:after { + display: table; + content: ""; +} + +.nav-tabs:after, +.nav-pills:after { + clear: both; +} + +.nav-tabs > li, +.nav-pills > li { + float: left; +} + +.nav-tabs > li > a, +.nav-pills > li > a { + padding-right: 12px; + padding-left: 12px; + margin-right: 2px; + line-height: 14px; +} + +.nav-tabs { + border-bottom: 1px solid #ddd; +} + +.nav-tabs > li { + margin-bottom: -1px; +} + +.nav-tabs > li > a { + padding-top: 8px; + padding-bottom: 8px; + line-height: 18px; + border: 1px solid transparent; + -webkit-border-radius: 4px 4px 0 0; + -moz-border-radius: 4px 4px 0 0; + border-radius: 4px 4px 0 0; +} + +.nav-tabs > li > a:hover { + border-color: #eeeeee #eeeeee #dddddd; +} + +.nav-tabs > .active > a, +.nav-tabs > .active > a:hover { + color: #555555; + cursor: default; + background-color: #ffffff; + border: 1px solid #ddd; + border-bottom-color: transparent; +} + +.nav-pills > li > a { + padding-top: 8px; + padding-bottom: 8px; + margin-top: 2px; + margin-bottom: 2px; + -webkit-border-radius: 5px; + -moz-border-radius: 5px; + border-radius: 5px; +} + +.nav-pills > .active > a, +.nav-pills > .active > a:hover { + color: #ffffff; + background-color: #0088cc; +} + +.nav-stacked > li { + float: none; +} + +.nav-stacked > li > a { + margin-right: 0; +} + +.nav-tabs.nav-stacked { + border-bottom: 0; +} + +.nav-tabs.nav-stacked > li > a { + border: 1px solid #ddd; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.nav-tabs.nav-stacked > li:first-child > a { + -webkit-border-radius: 4px 4px 0 0; + -moz-border-radius: 4px 4px 0 0; + border-radius: 4px 4px 0 0; +} + +.nav-tabs.nav-stacked > li:last-child > a { + -webkit-border-radius: 0 0 4px 4px; + -moz-border-radius: 0 0 4px 4px; + border-radius: 0 0 4px 4px; +} + +.nav-tabs.nav-stacked > li > a:hover { + z-index: 2; + border-color: #ddd; +} + +.nav-pills.nav-stacked > li > a { + margin-bottom: 3px; +} + +.nav-pills.nav-stacked > li:last-child > a { + margin-bottom: 1px; +} + +.nav-tabs .dropdown-menu { + -webkit-border-radius: 0 0 5px 5px; + -moz-border-radius: 0 0 5px 5px; + border-radius: 0 0 5px 5px; +} + +.nav-pills .dropdown-menu { + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.nav-tabs .dropdown-toggle .caret, +.nav-pills .dropdown-toggle .caret { + margin-top: 6px; + border-top-color: #0088cc; + border-bottom-color: #0088cc; +} + +.nav-tabs .dropdown-toggle:hover .caret, +.nav-pills .dropdown-toggle:hover .caret { + border-top-color: #005580; + border-bottom-color: #005580; +} + +.nav-tabs .active .dropdown-toggle .caret, +.nav-pills .active .dropdown-toggle .caret { + border-top-color: #333333; + border-bottom-color: #333333; +} + +.nav > .dropdown.active > a:hover { + color: #000000; + cursor: pointer; +} + +.nav-tabs .open .dropdown-toggle, +.nav-pills .open .dropdown-toggle, +.nav > li.dropdown.open.active > a:hover { + color: #ffffff; + background-color: #999999; + border-color: #999999; +} + +.nav li.dropdown.open .caret, +.nav li.dropdown.open.active .caret, +.nav li.dropdown.open a:hover .caret { + border-top-color: #ffffff; + border-bottom-color: #ffffff; + opacity: 1; + filter: alpha(opacity=100); +} + +.tabs-stacked .open > a:hover { + border-color: #999999; +} + +.tabbable { + *zoom: 1; +} + +.tabbable:before, +.tabbable:after { + display: table; + content: ""; +} + +.tabbable:after { + clear: both; +} + +.tab-content { + overflow: auto; +} + +.tabs-below > .nav-tabs, +.tabs-right > .nav-tabs, +.tabs-left > .nav-tabs { + border-bottom: 0; +} + +.tab-content > .tab-pane, +.pill-content > .pill-pane { + display: none; +} + +.tab-content > .active, +.pill-content > .active { + display: block; +} + +.tabs-below > .nav-tabs { + border-top: 1px solid #ddd; +} + +.tabs-below > .nav-tabs > li { + margin-top: -1px; + margin-bottom: 0; +} + +.tabs-below > .nav-tabs > li > a { + -webkit-border-radius: 0 0 4px 4px; + -moz-border-radius: 0 0 4px 4px; + border-radius: 0 0 4px 4px; +} + +.tabs-below > .nav-tabs > li > a:hover { + border-top-color: #ddd; + border-bottom-color: transparent; +} + +.tabs-below > .nav-tabs > .active > a, +.tabs-below > .nav-tabs > .active > a:hover { + border-color: transparent #ddd #ddd #ddd; +} + +.tabs-left > .nav-tabs > li, +.tabs-right > .nav-tabs > li { + float: none; +} + +.tabs-left > .nav-tabs > li > a, +.tabs-right > .nav-tabs > li > a { + min-width: 74px; + margin-right: 0; + margin-bottom: 3px; +} + +.tabs-left > .nav-tabs { + float: left; + margin-right: 19px; + border-right: 1px solid #ddd; +} + +.tabs-left > .nav-tabs > li > a { + margin-right: -1px; + -webkit-border-radius: 4px 0 0 4px; + -moz-border-radius: 4px 0 0 4px; + border-radius: 4px 0 0 4px; +} + +.tabs-left > .nav-tabs > li > a:hover { + border-color: #eeeeee #dddddd #eeeeee #eeeeee; +} + +.tabs-left > .nav-tabs .active > a, +.tabs-left > .nav-tabs .active > a:hover { + border-color: #ddd transparent #ddd #ddd; + *border-right-color: #ffffff; +} + +.tabs-right > .nav-tabs { + float: right; + margin-left: 19px; + border-left: 1px solid #ddd; +} + +.tabs-right > .nav-tabs > li > a { + margin-left: -1px; + -webkit-border-radius: 0 4px 4px 0; + -moz-border-radius: 0 4px 4px 0; + border-radius: 0 4px 4px 0; +} + +.tabs-right > .nav-tabs > li > a:hover { + border-color: #eeeeee #eeeeee #eeeeee #dddddd; +} + +.tabs-right > .nav-tabs .active > a, +.tabs-right > .nav-tabs .active > a:hover { + border-color: #ddd #ddd #ddd transparent; + *border-left-color: #ffffff; +} + +.navbar { + *position: relative; + *z-index: 2; + margin-bottom: 18px; + overflow: visible; +} + +.navbar-inner { + min-height: 40px; + padding-right: 20px; + padding-left: 20px; + background-color: #2c2c2c; + background-image: -moz-linear-gradient(top, #333333, #222222); + background-image: -ms-linear-gradient(top, #333333, #222222); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#222222)); + background-image: -webkit-linear-gradient(top, #333333, #222222); + background-image: -o-linear-gradient(top, #333333, #222222); + background-image: linear-gradient(top, #333333, #222222); + background-repeat: repeat-x; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#333333', endColorstr='#222222', GradientType=0); + -webkit-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.25), inset 0 -1px 0 rgba(0, 0, 0, 0.1); + -moz-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.25), inset 0 -1px 0 rgba(0, 0, 0, 0.1); + box-shadow: 0 1px 3px rgba(0, 0, 0, 0.25), inset 0 -1px 0 rgba(0, 0, 0, 0.1); +} + +.navbar .container { + width: auto; +} + +.nav-collapse.collapse { + height: auto; +} + +.navbar { + color: #999999; +} + +.navbar .brand:hover { + text-decoration: none; +} + +.navbar .brand { + display: block; + float: left; + padding: 8px 20px 12px; + margin-left: -20px; + font-size: 20px; + font-weight: 200; + line-height: 1; + color: #999999; +} + +.navbar .navbar-text { + margin-bottom: 0; + line-height: 40px; +} + +.navbar .navbar-link { + color: #999999; +} + +.navbar .navbar-link:hover { + color: #ffffff; +} + +.navbar .btn, +.navbar .btn-group { + margin-top: 5px; +} + +.navbar .btn-group .btn { + margin: 0; +} + +.navbar-form { + margin-bottom: 0; + *zoom: 1; +} + +.navbar-form:before, +.navbar-form:after { + display: table; + content: ""; +} + +.navbar-form:after { + clear: both; +} + +.navbar-form input, +.navbar-form select, +.navbar-form .radio, +.navbar-form .checkbox { + margin-top: 5px; +} + +.navbar-form input, +.navbar-form select { + display: inline-block; + margin-bottom: 0; +} + +.navbar-form input[type="image"], +.navbar-form input[type="checkbox"], +.navbar-form input[type="radio"] { + margin-top: 3px; +} + +.navbar-form .input-append, +.navbar-form .input-prepend { + margin-top: 6px; + white-space: nowrap; +} + +.navbar-form .input-append input, +.navbar-form .input-prepend input { + margin-top: 0; +} + +.navbar-search { + position: relative; + float: left; + margin-top: 6px; + margin-bottom: 0; +} + +.navbar-search .search-query { + padding: 4px 9px; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 13px; + font-weight: normal; + line-height: 1; + color: #ffffff; + background-color: #626262; + border: 1px solid #151515; + -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1), 0 1px 0 rgba(255, 255, 255, 0.15); + -moz-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1), 0 1px 0 rgba(255, 255, 255, 0.15); + box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1), 0 1px 0 rgba(255, 255, 255, 0.15); + -webkit-transition: none; + -moz-transition: none; + -ms-transition: none; + -o-transition: none; + transition: none; +} + +.navbar-search .search-query:-moz-placeholder { + color: #cccccc; +} + +.navbar-search .search-query:-ms-input-placeholder { + color: #cccccc; +} + +.navbar-search .search-query::-webkit-input-placeholder { + color: #cccccc; +} + +.navbar-search .search-query:focus, +.navbar-search .search-query.focused { + padding: 5px 10px; + color: #333333; + text-shadow: 0 1px 0 #ffffff; + background-color: #ffffff; + border: 0; + outline: 0; + -webkit-box-shadow: 0 0 3px rgba(0, 0, 0, 0.15); + -moz-box-shadow: 0 0 3px rgba(0, 0, 0, 0.15); + box-shadow: 0 0 3px rgba(0, 0, 0, 0.15); +} + +.navbar-fixed-top, +.navbar-fixed-bottom { + position: fixed; + right: 0; + left: 0; + z-index: 1030; + margin-bottom: 0; +} + +.navbar-fixed-top .navbar-inner, +.navbar-fixed-bottom .navbar-inner { + padding-right: 0; + padding-left: 0; + -webkit-border-radius: 0; + -moz-border-radius: 0; + border-radius: 0; +} + +.navbar-fixed-top .container, +.navbar-fixed-bottom .container { + width: 940px; +} + +.navbar-fixed-top { + top: 0; +} + +.navbar-fixed-bottom { + bottom: 0; +} + +.navbar .nav { + position: relative; + left: 0; + display: block; + float: left; + margin: 0 10px 0 0; +} + +.navbar .nav.pull-right { + float: right; +} + +.navbar .nav > li { + display: block; + float: left; +} + +.navbar .nav > li > a { + float: none; + padding: 9px 10px 11px; + line-height: 19px; + color: #999999; + text-decoration: none; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25); +} + +.navbar .btn { + display: inline-block; + padding: 4px 10px 4px; + margin: 5px 5px 6px; + line-height: 18px; +} + +.navbar .btn-group { + padding: 5px 5px 6px; + margin: 0; +} + +.navbar .nav > li > a:hover { + color: #ffffff; + text-decoration: none; + background-color: transparent; +} + +.navbar .nav .active > a, +.navbar .nav .active > a:hover { + color: #ffffff; + text-decoration: none; + background-color: #222222; +} + +.navbar .divider-vertical { + width: 1px; + height: 40px; + margin: 0 9px; + overflow: hidden; + background-color: #222222; + border-right: 1px solid #333333; +} + +.navbar .nav.pull-right { + margin-right: 0; + margin-left: 10px; +} + +.navbar .btn-navbar { + display: none; + float: right; + padding: 7px 10px; + margin-right: 5px; + margin-left: 5px; + background-color: #2c2c2c; + *background-color: #222222; + background-image: -ms-linear-gradient(top, #333333, #222222); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#222222)); + background-image: -webkit-linear-gradient(top, #333333, #222222); + background-image: -o-linear-gradient(top, #333333, #222222); + background-image: linear-gradient(top, #333333, #222222); + background-image: -moz-linear-gradient(top, #333333, #222222); + background-repeat: repeat-x; + border-color: #222222 #222222 #000000; + border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25); + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#333333', endColorstr='#222222', GradientType=0); + filter: progid:dximagetransform.microsoft.gradient(enabled=false); + -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.075); + -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.075); + box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.075); +} + +.navbar .btn-navbar:hover, +.navbar .btn-navbar:active, +.navbar .btn-navbar.active, +.navbar .btn-navbar.disabled, +.navbar .btn-navbar[disabled] { + background-color: #222222; + *background-color: #151515; +} + +.navbar .btn-navbar:active, +.navbar .btn-navbar.active { + background-color: #080808 \9; +} + +.navbar .btn-navbar .icon-bar { + display: block; + width: 18px; + height: 2px; + background-color: #f5f5f5; + -webkit-border-radius: 1px; + -moz-border-radius: 1px; + border-radius: 1px; + -webkit-box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25); + -moz-box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25); + box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25); +} + +.btn-navbar .icon-bar + .icon-bar { + margin-top: 3px; +} + +.navbar .dropdown-menu:before { + position: absolute; + top: -7px; + left: 9px; + display: inline-block; + border-right: 7px solid transparent; + border-bottom: 7px solid #ccc; + border-left: 7px solid transparent; + border-bottom-color: rgba(0, 0, 0, 0.2); + content: ''; +} + +.navbar .dropdown-menu:after { + position: absolute; + top: -6px; + left: 10px; + display: inline-block; + border-right: 6px solid transparent; + border-bottom: 6px solid #ffffff; + border-left: 6px solid transparent; + content: ''; +} + +.navbar-fixed-bottom .dropdown-menu:before { + top: auto; + bottom: -7px; + border-top: 7px solid #ccc; + border-bottom: 0; + border-top-color: rgba(0, 0, 0, 0.2); +} + +.navbar-fixed-bottom .dropdown-menu:after { + top: auto; + bottom: -6px; + border-top: 6px solid #ffffff; + border-bottom: 0; +} + +.navbar .nav li.dropdown .dropdown-toggle .caret, +.navbar .nav li.dropdown.open .caret { + border-top-color: #ffffff; + border-bottom-color: #ffffff; +} + +.navbar .nav li.dropdown.active .caret { + opacity: 1; + filter: alpha(opacity=100); +} + +.navbar .nav li.dropdown.open > .dropdown-toggle, +.navbar .nav li.dropdown.active > .dropdown-toggle, +.navbar .nav li.dropdown.open.active > .dropdown-toggle { + background-color: transparent; +} + +.navbar .nav li.dropdown.active > .dropdown-toggle:hover { + color: #ffffff; +} + +.navbar .pull-right .dropdown-menu, +.navbar .dropdown-menu.pull-right { + right: 0; + left: auto; +} + +.navbar .pull-right .dropdown-menu:before, +.navbar .dropdown-menu.pull-right:before { + right: 12px; + left: auto; +} + +.navbar .pull-right .dropdown-menu:after, +.navbar .dropdown-menu.pull-right:after { + right: 13px; + left: auto; +} + +.breadcrumb { + padding: 7px 14px; + margin: 0 0 18px; + list-style: none; + background-color: #fbfbfb; + background-image: -moz-linear-gradient(top, #ffffff, #f5f5f5); + background-image: -ms-linear-gradient(top, #ffffff, #f5f5f5); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#f5f5f5)); + background-image: -webkit-linear-gradient(top, #ffffff, #f5f5f5); + background-image: -o-linear-gradient(top, #ffffff, #f5f5f5); + background-image: linear-gradient(top, #ffffff, #f5f5f5); + background-repeat: repeat-x; + border: 1px solid #ddd; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#ffffff', endColorstr='#f5f5f5', GradientType=0); + -webkit-box-shadow: inset 0 1px 0 #ffffff; + -moz-box-shadow: inset 0 1px 0 #ffffff; + box-shadow: inset 0 1px 0 #ffffff; +} + +.breadcrumb li { + display: inline-block; + *display: inline; + text-shadow: 0 1px 0 #ffffff; + *zoom: 1; +} + +.breadcrumb .divider { + padding: 0 5px; + color: #999999; +} + +.breadcrumb .active a { + color: #333333; +} + +.pagination { + height: 36px; + margin: 18px 0; +} + +.pagination ul { + display: inline-block; + *display: inline; + margin-bottom: 0; + margin-left: 0; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; + *zoom: 1; + -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05); + -moz-box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05); + box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05); +} + +.pagination li { + display: inline; +} + +.pagination a { + float: left; + padding: 0 14px; + line-height: 34px; + text-decoration: none; + border: 1px solid #ddd; + border-left-width: 0; +} + +.pagination a:hover, +.pagination .active a { + background-color: #f5f5f5; +} + +.pagination .active a { + color: #999999; + cursor: default; +} + +.pagination .disabled span, +.pagination .disabled a, +.pagination .disabled a:hover { + color: #999999; + cursor: default; + background-color: transparent; +} + +.pagination li:first-child a { + border-left-width: 1px; + -webkit-border-radius: 3px 0 0 3px; + -moz-border-radius: 3px 0 0 3px; + border-radius: 3px 0 0 3px; +} + +.pagination li:last-child a { + -webkit-border-radius: 0 3px 3px 0; + -moz-border-radius: 0 3px 3px 0; + border-radius: 0 3px 3px 0; +} + +.pagination-centered { + text-align: center; +} + +.pagination-right { + text-align: right; +} + +.pager { + margin-bottom: 18px; + margin-left: 0; + text-align: center; + list-style: none; + *zoom: 1; +} + +.pager:before, +.pager:after { + display: table; + content: ""; +} + +.pager:after { + clear: both; +} + +.pager li { + display: inline; +} + +.pager a { + display: inline-block; + padding: 5px 14px; + background-color: #fff; + border: 1px solid #ddd; + -webkit-border-radius: 15px; + -moz-border-radius: 15px; + border-radius: 15px; +} + +.pager a:hover { + text-decoration: none; + background-color: #f5f5f5; +} + +.pager .next a { + float: right; +} + +.pager .previous a { + float: left; +} + +.pager .disabled a, +.pager .disabled a:hover { + color: #999999; + cursor: default; + background-color: #fff; +} + +.modal-open .dropdown-menu { + z-index: 2050; +} + +.modal-open .dropdown.open { + *z-index: 2050; +} + +.modal-open .popover { + z-index: 2060; +} + +.modal-open .tooltip { + z-index: 2070; +} + +.modal-backdrop { + position: fixed; + top: 0; + right: 0; + bottom: 0; + left: 0; + z-index: 1040; + background-color: #000000; +} + +.modal-backdrop.fade { + opacity: 0; +} + +.modal-backdrop, +.modal-backdrop.fade.in { + opacity: 0.8; + filter: alpha(opacity=80); +} + +.modal { + position: fixed; + top: 50%; + left: 50%; + z-index: 1050; + width: 560px; + margin: -250px 0 0 -280px; + overflow: auto; + background-color: #ffffff; + border: 1px solid #999; + border: 1px solid rgba(0, 0, 0, 0.3); + *border: 1px solid #999; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; +} + +.modal.fade { + top: -25%; + -webkit-transition: opacity 0.3s linear, top 0.3s ease-out; + -moz-transition: opacity 0.3s linear, top 0.3s ease-out; + -ms-transition: opacity 0.3s linear, top 0.3s ease-out; + -o-transition: opacity 0.3s linear, top 0.3s ease-out; + transition: opacity 0.3s linear, top 0.3s ease-out; +} + +.modal.fade.in { + top: 50%; +} + +.modal-header { + padding: 9px 15px; + border-bottom: 1px solid #eee; +} + +.modal-header .close { + margin-top: 2px; +} + +.modal-body { + max-height: 400px; + padding: 15px; + overflow-y: auto; +} + +.modal-form { + margin-bottom: 0; +} + +.modal-footer { + padding: 14px 15px 15px; + margin-bottom: 0; + text-align: right; + background-color: #f5f5f5; + border-top: 1px solid #ddd; + -webkit-border-radius: 0 0 6px 6px; + -moz-border-radius: 0 0 6px 6px; + border-radius: 0 0 6px 6px; + *zoom: 1; + -webkit-box-shadow: inset 0 1px 0 #ffffff; + -moz-box-shadow: inset 0 1px 0 #ffffff; + box-shadow: inset 0 1px 0 #ffffff; +} + +.modal-footer:before, +.modal-footer:after { + display: table; + content: ""; +} + +.modal-footer:after { + clear: both; +} + +.modal-footer .btn + .btn { + margin-bottom: 0; + margin-left: 5px; +} + +.modal-footer .btn-group .btn + .btn { + margin-left: -1px; +} + +.tooltip { + position: absolute; + z-index: 1020; + display: block; + padding: 5px; + font-size: 11px; + opacity: 0; + filter: alpha(opacity=0); + visibility: visible; +} + +.tooltip.in { + opacity: 0.8; + filter: alpha(opacity=80); +} + +.tooltip.top { + margin-top: -2px; +} + +.tooltip.right { + margin-left: 2px; +} + +.tooltip.bottom { + margin-top: 2px; +} + +.tooltip.left { + margin-left: -2px; +} + +.tooltip.top .tooltip-arrow { + bottom: 0; + left: 50%; + margin-left: -5px; + border-top: 5px solid #000000; + border-right: 5px solid transparent; + border-left: 5px solid transparent; +} + +.tooltip.left .tooltip-arrow { + top: 50%; + right: 0; + margin-top: -5px; + border-top: 5px solid transparent; + border-bottom: 5px solid transparent; + border-left: 5px solid #000000; +} + +.tooltip.bottom .tooltip-arrow { + top: 0; + left: 50%; + margin-left: -5px; + border-right: 5px solid transparent; + border-bottom: 5px solid #000000; + border-left: 5px solid transparent; +} + +.tooltip.right .tooltip-arrow { + top: 50%; + left: 0; + margin-top: -5px; + border-top: 5px solid transparent; + border-right: 5px solid #000000; + border-bottom: 5px solid transparent; +} + +.tooltip-inner { + max-width: 200px; + padding: 3px 8px; + color: #ffffff; + text-align: center; + text-decoration: none; + background-color: #000000; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; +} + +.tooltip-arrow { + position: absolute; + width: 0; + height: 0; +} + +.popover { + position: absolute; + top: 0; + left: 0; + z-index: 1010; + display: none; + padding: 5px; +} + +.popover.top { + margin-top: -5px; +} + +.popover.right { + margin-left: 5px; +} + +.popover.bottom { + margin-top: 5px; +} + +.popover.left { + margin-left: -5px; +} + +.popover.top .arrow { + bottom: 0; + left: 50%; + margin-left: -5px; + border-top: 5px solid #000000; + border-right: 5px solid transparent; + border-left: 5px solid transparent; +} + +.popover.right .arrow { + top: 50%; + left: 0; + margin-top: -5px; + border-top: 5px solid transparent; + border-right: 5px solid #000000; + border-bottom: 5px solid transparent; +} + +.popover.bottom .arrow { + top: 0; + left: 50%; + margin-left: -5px; + border-right: 5px solid transparent; + border-bottom: 5px solid #000000; + border-left: 5px solid transparent; +} + +.popover.left .arrow { + top: 50%; + right: 0; + margin-top: -5px; + border-top: 5px solid transparent; + border-bottom: 5px solid transparent; + border-left: 5px solid #000000; +} + +.popover .arrow { + position: absolute; + width: 0; + height: 0; +} + +.popover-inner { + width: 280px; + padding: 3px; + overflow: hidden; + background: #000000; + background: rgba(0, 0, 0, 0.8); + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); +} + +.popover-title { + padding: 9px 15px; + line-height: 1; + background-color: #f5f5f5; + border-bottom: 1px solid #eee; + -webkit-border-radius: 3px 3px 0 0; + -moz-border-radius: 3px 3px 0 0; + border-radius: 3px 3px 0 0; +} + +.popover-content { + padding: 14px; + background-color: #ffffff; + -webkit-border-radius: 0 0 3px 3px; + -moz-border-radius: 0 0 3px 3px; + border-radius: 0 0 3px 3px; + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; +} + +.popover-content p, +.popover-content ul, +.popover-content ol { + margin-bottom: 0; +} + +.thumbnails { + margin-left: -20px; + list-style: none; + *zoom: 1; +} + +.thumbnails:before, +.thumbnails:after { + display: table; + content: ""; +} + +.thumbnails:after { + clear: both; +} + +.row-fluid .thumbnails { + margin-left: 0; +} + +.thumbnails > li { + float: left; + margin-bottom: 18px; + margin-left: 20px; +} + +.thumbnail { + display: block; + padding: 4px; + line-height: 1; + border: 1px solid #ddd; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + -webkit-box-shadow: 0 1px 1px rgba(0, 0, 0, 0.075); + -moz-box-shadow: 0 1px 1px rgba(0, 0, 0, 0.075); + box-shadow: 0 1px 1px rgba(0, 0, 0, 0.075); +} + +a.thumbnail:hover { + border-color: #0088cc; + -webkit-box-shadow: 0 1px 4px rgba(0, 105, 214, 0.25); + -moz-box-shadow: 0 1px 4px rgba(0, 105, 214, 0.25); + box-shadow: 0 1px 4px rgba(0, 105, 214, 0.25); +} + +.thumbnail > img { + display: block; + max-width: 100%; + margin-right: auto; + margin-left: auto; +} + +.thumbnail .caption { + padding: 9px; +} + +.label, +.badge { + font-size: 10.998px; + font-weight: bold; + line-height: 14px; + color: #ffffff; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25); + white-space: nowrap; + vertical-align: baseline; + background-color: #999999; +} + +.label { + padding: 1px 4px 2px; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + border-radius: 3px; +} + +.badge { + padding: 1px 9px 2px; + -webkit-border-radius: 9px; + -moz-border-radius: 9px; + border-radius: 9px; +} + +a.label:hover, +a.badge:hover { + color: #ffffff; + text-decoration: none; + cursor: pointer; +} + +.label-important, +.badge-important { + background-color: #b94a48; +} + +.label-important[href], +.badge-important[href] { + background-color: #953b39; +} + +.label-warning, +.badge-warning { + background-color: #f89406; +} + +.label-warning[href], +.badge-warning[href] { + background-color: #c67605; +} + +.label-success, +.badge-success { + background-color: #468847; +} + +.label-success[href], +.badge-success[href] { + background-color: #356635; +} + +.label-info, +.badge-info { + background-color: #3a87ad; +} + +.label-info[href], +.badge-info[href] { + background-color: #2d6987; +} + +.label-inverse, +.badge-inverse { + background-color: #333333; +} + +.label-inverse[href], +.badge-inverse[href] { + background-color: #1a1a1a; +} + +@-webkit-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} + +@-moz-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} + +@-ms-keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} + +@-o-keyframes progress-bar-stripes { + from { + background-position: 0 0; + } + to { + background-position: 40px 0; + } +} + +@keyframes progress-bar-stripes { + from { + background-position: 40px 0; + } + to { + background-position: 0 0; + } +} + +.progress { + height: 18px; + margin-bottom: 18px; + overflow: hidden; + background-color: #f7f7f7; + background-image: -moz-linear-gradient(top, #f5f5f5, #f9f9f9); + background-image: -ms-linear-gradient(top, #f5f5f5, #f9f9f9); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9)); + background-image: -webkit-linear-gradient(top, #f5f5f5, #f9f9f9); + background-image: -o-linear-gradient(top, #f5f5f5, #f9f9f9); + background-image: linear-gradient(top, #f5f5f5, #f9f9f9); + background-repeat: repeat-x; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + border-radius: 4px; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#f5f5f5', endColorstr='#f9f9f9', GradientType=0); + -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1); + -moz-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1); + box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1); +} + +.progress .bar { + width: 0; + height: 18px; + font-size: 12px; + color: #ffffff; + text-align: center; + text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25); + background-color: #0e90d2; + background-image: -moz-linear-gradient(top, #149bdf, #0480be); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be)); + background-image: -webkit-linear-gradient(top, #149bdf, #0480be); + background-image: -o-linear-gradient(top, #149bdf, #0480be); + background-image: linear-gradient(top, #149bdf, #0480be); + background-image: -ms-linear-gradient(top, #149bdf, #0480be); + background-repeat: repeat-x; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#149bdf', endColorstr='#0480be', GradientType=0); + -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15); + -moz-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15); + box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15); + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + -ms-box-sizing: border-box; + box-sizing: border-box; + -webkit-transition: width 0.6s ease; + -moz-transition: width 0.6s ease; + -ms-transition: width 0.6s ease; + -o-transition: width 0.6s ease; + transition: width 0.6s ease; +} + +.progress-striped .bar { + background-color: #149bdf; + background-image: -o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent)); + background-image: linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + -webkit-background-size: 40px 40px; + -moz-background-size: 40px 40px; + -o-background-size: 40px 40px; + background-size: 40px 40px; +} + +.progress.active .bar { + -webkit-animation: progress-bar-stripes 2s linear infinite; + -moz-animation: progress-bar-stripes 2s linear infinite; + -ms-animation: progress-bar-stripes 2s linear infinite; + -o-animation: progress-bar-stripes 2s linear infinite; + animation: progress-bar-stripes 2s linear infinite; +} + +.progress-danger .bar { + background-color: #dd514c; + background-image: -moz-linear-gradient(top, #ee5f5b, #c43c35); + background-image: -ms-linear-gradient(top, #ee5f5b, #c43c35); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35)); + background-image: -webkit-linear-gradient(top, #ee5f5b, #c43c35); + background-image: -o-linear-gradient(top, #ee5f5b, #c43c35); + background-image: linear-gradient(top, #ee5f5b, #c43c35); + background-repeat: repeat-x; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0); +} + +.progress-danger.progress-striped .bar { + background-color: #ee5f5b; + background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent)); + background-image: -webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); +} + +.progress-success .bar { + background-color: #5eb95e; + background-image: -moz-linear-gradient(top, #62c462, #57a957); + background-image: -ms-linear-gradient(top, #62c462, #57a957); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957)); + background-image: -webkit-linear-gradient(top, #62c462, #57a957); + background-image: -o-linear-gradient(top, #62c462, #57a957); + background-image: linear-gradient(top, #62c462, #57a957); + background-repeat: repeat-x; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0); +} + +.progress-success.progress-striped .bar { + background-color: #62c462; + background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent)); + background-image: -webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); +} + +.progress-info .bar { + background-color: #4bb1cf; + background-image: -moz-linear-gradient(top, #5bc0de, #339bb9); + background-image: -ms-linear-gradient(top, #5bc0de, #339bb9); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9)); + background-image: -webkit-linear-gradient(top, #5bc0de, #339bb9); + background-image: -o-linear-gradient(top, #5bc0de, #339bb9); + background-image: linear-gradient(top, #5bc0de, #339bb9); + background-repeat: repeat-x; + filter: progid:dximagetransform.microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0); +} + +.progress-info.progress-striped .bar { + background-color: #5bc0de; + background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent)); + background-image: -webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); + background-image: linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent); +} + +.progress-warning .bar { + background-color: #faa732; + background-image: -moz-linear-gradient(top, #fbb450, #f89406); + background-image: -ms-linear-gradient(top, #fbb450, #f89406); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406)); + background-image: 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+.accordion-heading .accordion-toggle { + display: block; + padding: 8px 15px; +} + +.accordion-toggle { + cursor: pointer; +} + +.accordion-inner { + padding: 9px 15px; + border-top: 1px solid #e5e5e5; +} + +.carousel { + position: relative; + margin-bottom: 18px; + line-height: 1; +} + +.carousel-inner { + position: relative; + width: 100%; + overflow: hidden; +} + +.carousel .item { + position: relative; + display: none; + -webkit-transition: 0.6s ease-in-out left; + -moz-transition: 0.6s ease-in-out left; + -ms-transition: 0.6s ease-in-out left; + -o-transition: 0.6s ease-in-out left; + transition: 0.6s ease-in-out left; +} + +.carousel .item > img { + display: block; + line-height: 1; +} + +.carousel .active, +.carousel .next, +.carousel .prev { + display: block; +} + +.carousel .active { + left: 0; +} + +.carousel .next, +.carousel .prev { + position: absolute; + top: 0; + width: 100%; +} + +.carousel .next { + left: 100%; +} + +.carousel .prev { + left: -100%; +} + +.carousel .next.left, +.carousel .prev.right { + left: 0; +} + +.carousel .active.left { + left: -100%; +} + +.carousel .active.right { + left: 100%; +} + +.carousel-control { + position: absolute; + top: 40%; + left: 15px; + width: 40px; + height: 40px; + margin-top: -20px; + font-size: 60px; + font-weight: 100; + line-height: 30px; + color: #ffffff; + text-align: center; + background: #222222; + border: 3px solid #ffffff; + -webkit-border-radius: 23px; + -moz-border-radius: 23px; + border-radius: 23px; + opacity: 0.5; + filter: alpha(opacity=50); +} + +.carousel-control.right { + right: 15px; + left: auto; +} + +.carousel-control:hover { + color: #ffffff; + text-decoration: none; + opacity: 0.9; + filter: alpha(opacity=90); +} + +.carousel-caption { + position: absolute; + right: 0; + bottom: 0; + left: 0; + padding: 10px 15px 5px; + background: #333333; + background: rgba(0, 0, 0, 0.75); +} + +.carousel-caption h4, +.carousel-caption p { + color: #ffffff; +} + +.hero-unit { + padding: 60px; + margin-bottom: 30px; + background-color: #eeeeee; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; +} + +.hero-unit h1 { + margin-bottom: 0; + font-size: 60px; + line-height: 1; + letter-spacing: -1px; + color: inherit; +} + +.hero-unit p { + font-size: 18px; + font-weight: 200; + line-height: 27px; + color: inherit; +} + +.pull-right { + float: right; +} + +.pull-left { + float: left; +} + +.hide { + display: none; +} + +.show { + display: block; +} + +.invisible { + visibility: hidden; +} diff --git a/inst/web/css/bootstrap.min.css b/inst/web/css/bootstrap.min.css new file mode 100644 index 0000000..b74b454 --- /dev/null +++ b/inst/web/css/bootstrap.min.css @@ -0,0 +1,9 @@ +/*! + * Bootstrap v2.0.4 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + 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#fff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:.5;filter:alpha(opacity=50)}.carousel-control.right{right:15px;left:auto}.carousel-control:hover{color:#fff;text-decoration:none;opacity:.9;filter:alpha(opacity=90)}.carousel-caption{position:absolute;right:0;bottom:0;left:0;padding:10px 15px 5px;background:#333;background:rgba(0,0,0,0.75)}.carousel-caption h4,.carousel-caption p{color:#fff}.hero-unit{padding:60px;margin-bottom:30px;background-color:#eee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;letter-spacing:-1px;color:inherit}.hero-unit p{font-size:18px;font-weight:200;line-height:27px;color:inherit}.pull-right{float:right}.pull-left{float:left}.hide{display:none}.show{display:block}.invisible{visibility:hidden} diff --git a/inst/web/css/highlight.css b/inst/web/css/highlight.css new file mode 100644 index 0000000..4b85237 --- /dev/null +++ b/inst/web/css/highlight.css @@ -0,0 +1,28 @@ +/* Syntax highlighting ---------------------------------------------------- */ + +pre .input { + border-left: 3px solid #ccc; + padding-left: 0.5em; +} +pre .output { + background-color: #eee; +} + +.number {color:rgb(21,20,181);} +.functioncall {color:#264D66 ;} +.string {color:#375D81 ;} +.keyword {font-weight:bolder ;color:black;} +.argument {color:#264D66 ;} +.comment {color: #333;} +.formalargs {color: #264D66;} +.eqformalargs {color:#264D66;} +.slot {font-style:italic;} +.symbol {color:black ;} +.prompt {color:black ;} + +pre img { + background-color: #fff; + border: 1px solid #ccc; + display: block; + margin: 0.5em auto 0.5em auto; +} diff --git a/inst/web/css/staticdocs.css b/inst/web/css/staticdocs.css new file mode 100644 index 0000000..9fee28b --- /dev/null +++ b/inst/web/css/staticdocs.css @@ -0,0 +1,18 @@ +h2 {padding-top: 20px} + +.icon img { + float: right; + border: 1px solid #ccc; +} +.index .internal {display: none;} +ul.index li {margin-bottom: 0.5em; clear: both;} + +footer { + margin-top: 45px; + padding: 35px 0 36px; + border-top: 1px solid #e5e5e5; +} +footer p { + margin-bottom: 0; + color: #555; +} diff --git a/inst/web/drift_data_JKI.html b/inst/web/drift_data_JKI.html new file mode 100644 index 0000000..c3471c9 --- /dev/null +++ b/inst/web/drift_data_JKI.html @@ -0,0 +1,239 @@ + + + + +drift_data_JKI. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Deposition from spray drift expressed as percent of the applied dose as +published by the JKI

      + +
      +
      + +
      +

      Format

      + +

      A list currently containing matrices with spray drift percentage +data for field crops (Ackerbau), and Pome/stone fruit, early and late +(Obstbau frueh, spaet).

      + +
      + +
      +

      Source

      + +

      JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved +from +http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html +on 2015-06-11

      + +
      + +
      +

      Description

      + +

      Deposition from spray drift expressed as percent of the applied dose as +published by the German Julius-Kühn Institute (JKI).

      + +
      + +
      +

      Details

      + +

      The data were extracted from the spreadsheet cited below using the R code +given in the example section. The spreadsheet is not included in the package +as its licence is not clear.

      + +
      + +

      Examples

      + 
      
+## Not run: 
+#   # This is the code that was used to extract the data
+#   library(readxl)
+#   abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"
+#   JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")
+#   names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")
+#   drift_data_JKI <- list()
+# 
+#   for (n in 1:8) {
+#     drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2)
+#     drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) 
+#     dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]),
+#                                             crop = JKI_crops)
+#     drift_data_JKI[[n]] <- drift_data
+#   }
+#   save(drift_data_JKI, file = "data/drift_data_JKI.RData")
+# ## End(Not run)
+
+# And this is the resulting data
+drift_data_JKI
+
      
+
      [[1]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      2.77            NA            NA
+      3        NA         29.20         15.73
+      5      0.57         19.89          8.41
+      10     0.29         11.81          3.60
+      15     0.20          5.55          1.81
+      20     0.15          2.77          1.09
+      30     0.10          1.04          0.54
+      40     0.07          0.52          0.32
+      50     0.06          0.30          0.22
+
+[[2]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      2.38            NA            NA
+      3        NA         25.53         12.13
+      5      0.47         16.87          6.81
+      10     0.24          9.61          3.11
+      15     0.16          5.61          1.58
+      20     0.12          2.59          0.90
+      30     0.08          0.87          0.40
+      40     0.06          0.40          0.23
+      50     0.05          0.22          0.15
+
+[[3]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      2.01            NA            NA
+      3        NA         23.96         11.01
+      5      0.41         15.79          6.04
+      10     0.20          8.96          2.67
+      15     0.14          4.24          1.39
+      20     0.10          2.01          0.80
+      30     0.07          0.70          0.36
+      40     0.05          0.33          0.21
+      50     0.04          0.19          0.13
+
+[[4]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.85            NA            NA
+      3        NA         23.61         10.12
+      5      0.38         15.42          5.60
+      10     0.19          8.66          2.50
+      15     0.13          4.01          1.28
+      20     0.10          1.89          0.75
+      30     0.06          0.66          0.35
+      40     0.05          0.31          0.20
+      50     0.04          0.17          0.13
+
+[[5]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.75            NA            NA
+      3        NA         23.12          9.74
+      5      0.36         15.06          5.41
+      10     0.18          8.42          2.43
+      15     0.12          3.83          1.24
+      20     0.09          1.81          0.72
+      30     0.06          0.63          0.34
+      40     0.05          0.30          0.20
+      50     0.04          0.17          0.13
+
+[[6]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.64            NA            NA
+      3        NA         22.76          9.21
+      5      0.34         14.64          5.18
+      10     0.17          8.04          2.38
+      15     0.11          3.71          1.20
+      20     0.09          1.75          0.68
+      30     0.06          0.61          0.31
+      40     0.04          0.29          0.17
+      50     0.03          0.16          0.11
+
+[[7]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.61            NA            NA
+      3        NA         22.69          9.10
+      5      0.33         14.45          5.11
+      10     0.17          7.83          2.33
+      15     0.11          3.62          1.20
+      20     0.08          1.71          0.67
+      30     0.06          0.60          0.30
+      40     0.04          0.28          0.17
+      50     0.03          0.16          0.11
+
+[[8]]
+        crop
+distance Ackerbau Obstbau frueh Obstbau spaet
+      1      1.52            NA            NA
+      3        NA         22.24          8.66
+      5      0.31         14.09          4.92
+      10     0.16          7.58          2.29
+      15     0.11          3.48          1.14
+      20     0.08          1.65          0.65
+      30     0.05          0.57          0.29
+      40     0.04          0.27          0.16
+      50     0.03          0.15          0.11
+
+
      +
      +
      + + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/endpoint.html b/inst/web/endpoint.html new file mode 100644 index 0000000..521f7f4 --- /dev/null +++ b/inst/web/endpoint.html @@ -0,0 +1,142 @@ + + + + +endpoint. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Retrieve endpoint information from the chyaml field of a chent object

      + +
      +
      +

      Usage

      + 
      endpoint(chent, medium = "soil", type = c("degradation", "sorption"), lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, raw = FALSE, signif = 3)
      
+
      soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)
      
+
      soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)
      
+
      soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
      
+
      soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE)
      + +

      Arguments

      +
      +
      chent
      +
      The chent object to get the information from
      +
      medium
      +
      The medium for which information is sought
      +
      type
      +
      The information type
      +
      lab_field
      +
      If not NA, do we want laboratory or field endpoints
      +
      redox
      +
      If not NA, are we looking for aerobic or anaerobic data
      +
      value
      +
      The name of the value we want. The list given in the +usage section is not exclusive
      +
      aggregator
      +
      The aggregator function. Can be mean, +geomean, or identity, for example.
      +
      raw
      +
      Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?
      +
      signif
      +
      How many significant digits do we want
      +
      values
      +
      The values to be returned
      +
      aggregators
      +
      A named vector of aggregator functions to be used
      +
      + +
      +

      Value

      + +

      +The result from applying the aggregator function to + the values converted to a numeric vector, rounded to the + given number of significant digits, or, if raw = TRUE, + the values as a character value, retaining any implicit + information on precision that may be present. +

      + +
      + +
      +

      Description

      + +

      R6 class objects of class chent represent chemical entities +and can hold a list of information loaded from a chemical yaml file in their +chyaml field. Such information is extracted and optionally aggregated by +this function.

      + +
      + +
      +

      Details

      + +

      The functions soil_* are functions to extract soil specific endpoints. +For the Freundlich exponent, the capital letter N is used in order to +facilitate dealing with such data in R. In pesticide fate modelling, this +exponent is often called 1/n.

      + +
      +
      +
      + + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/geomean.html b/inst/web/geomean.html new file mode 100644 index 0000000..672e9b5 --- /dev/null +++ b/inst/web/geomean.html @@ -0,0 +1,121 @@ + + + + +geomean. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +

      Calculate the geometric mean

      + +
      +
      +

      Usage

      + 
      geomean(x, na.rm = TRUE)
      + +

      Arguments

      +
      +
      x
      +
      Vector of numbers
      +
      na.rm
      +
      Should NA values be omitted?
      +
      + +
      +

      Value

      + +

      +The geometric mean +

      + +
      + +
      +

      Description

      + +

      Based on some posts in a thread on Stackoverflow +http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in +This function checks for negative values, removes NA values per default and +returns 0 if at least one element of the vector is 0.

      + +
      + +

      Examples

      + 
      geomean(c(1, 3, 9))
+
      
+
      [1] 3
+
      
+
      geomean(c(1, 3, NA, 9))
+
      
+
      [1] 3
+
      
+
      ## Not run: geomean(c(1, -3, 9)) # returns an error
+
      +
      +
      + + + +

      Author

      + +Johannes Ranke + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/img/glyphicons-halflings-white.png b/inst/web/img/glyphicons-halflings-white.png new file mode 100644 index 0000000..3bf6484 Binary files /dev/null and b/inst/web/img/glyphicons-halflings-white.png differ diff --git a/inst/web/img/glyphicons-halflings.png b/inst/web/img/glyphicons-halflings.png new file mode 100644 index 0000000..79bc568 Binary files /dev/null and b/inst/web/img/glyphicons-halflings.png differ diff --git a/inst/web/index.html b/inst/web/index.html new file mode 100644 index 0000000..54f0f35 --- /dev/null +++ b/inst/web/index.html @@ -0,0 +1,182 @@ + + + + +Index. pfm 0.3-7 + + + + + + + + + + + + + + + +
      +
      +
      + pfm 0.3-7 +
      + +
      +
      +
      +
      + +
      +
      + +
      + +
      +
      + Utilities for simple calculations of predicted environmental +concentrations (PECs) and for dealing with data from some FOCUS pesticide +fate modelling software packages. + +

      Help topics

      + +

      Degradation

      +

      Functions related to degradation

      + + +
        + +
      • + pfm_degradation
        Calculate a time course of relative concentrations based on an mkinmod model
        • + +
      • + SFO_actual_twa
        Actual and maximum moving window time average concentrations for SFO kinetics
        • + +
      +

      Mobility

      +

      Indicators related to mobility

      + + +
        + +
      • + GUS(GUS.chent, GUS.numeric, print.GUS_result)
        Groundwater ubiquity score based on Gustafson (1989)
        • + +
      • + SSLRC_mobility_classification
        Determine the SSLRC mobility classification for a chemical substance from its Koc
        • + +
      +

      Soil

      +

      Predicted environmental concentrations in soil

      + + +
        + +
      • + PEC_soil
        Calculate predicted environmental concentrations in soil
        • + +
      • + soil_scenario_data_EFSA_2015
        Properties of the predefined scenarios from the EFSA guidance from 2015
        • + +
      +

      Surface water

      +

      Predicted environmental concentrations in surface water

      + + +
        + +
      • + PEC_sw_drift
        Calculate predicted environmental concentrations in surface water due to drift
        • + +
      • + PEC_sw_sed
        Calculate predicted environmental concentrations in sediment from surface +
        • + +
      • + drift_data_JKI
        Deposition from spray drift expressed as percent of the applied dose as +
        • + +
      • + PEC_sw_drainage_UK
        Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method
        • + +
      • + TOXSWA_cwa
        R6 class for holding TOXSWA cwa concentration data and associated statistics
        • + +
      • + read.TOXSWA_cwa
        Read TOXSWA surface water concentrations
        • + +
      • + plot.TOXSWA_cwa
        Plot TOXSWA surface water concentrations
        • + +
      +

      Groundwater

      +

      Predicted environmental concentrations in groundwater

      + + + +

      Chemical entities

      +

      Work with input stored in chemical entites as R objects using the chent package

      + + +
        + +
      • + endpoint(soil_DT50, soil_Kfoc, soil_N, soil_sorption)
        Retrieve endpoint information from the chyaml field of a chent object
        • + +
      +

      General

      +

      Utilities that are generally useful

      + + +
        + +
      • + geomean
        Calculate the geometric mean
        • + +
      +
      + +
      + +

      Dependencies

      +
        +
      • Depends: R6, mkin
        • +
      • Imports: graphics, chents, readr, methods
        • +
      • Suggests: testthat
        • + +
      +

      Authors

      + + +
      +
      + + +
      + + \ No newline at end of file diff --git a/inst/web/js/bootstrap.js b/inst/web/js/bootstrap.js new file mode 100644 index 0000000..5d6e65b --- /dev/null +++ b/inst/web/js/bootstrap.js @@ -0,0 +1,1825 @@ +/* =================================================== + * bootstrap-transition.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#transitions + * =================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + $(function () { + + "use strict"; // jshint ;_; + + + /* CSS TRANSITION SUPPORT (http://www.modernizr.com/) + * ======================================================= */ + + $.support.transition = (function () { + + var transitionEnd = (function () { + + var el = document.createElement('bootstrap') + , transEndEventNames = { + 'WebkitTransition' : 'webkitTransitionEnd' + , 'MozTransition' : 'transitionend' + , 'OTransition' : 'oTransitionEnd' + , 'msTransition' : 'MSTransitionEnd' + , 'transition' : 'transitionend' + } + , name + + for (name in transEndEventNames){ + if (el.style[name] !== undefined) { + return transEndEventNames[name] + } + } + + }()) + + return transitionEnd && { + end: transitionEnd + } + + })() + + }) + +}(window.jQuery);/* ========================================================== + * bootstrap-alert.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#alerts + * ========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* ALERT CLASS DEFINITION + * ====================== */ + + var dismiss = '[data-dismiss="alert"]' + , Alert = function (el) { + $(el).on('click', dismiss, this.close) + } + + Alert.prototype.close = function (e) { + var $this = $(this) + , selector = $this.attr('data-target') + , $parent + + if (!selector) { + selector = $this.attr('href') + selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + $parent = $(selector) + + e && e.preventDefault() + + $parent.length || ($parent = $this.hasClass('alert') ? $this : $this.parent()) + + $parent.trigger(e = $.Event('close')) + + if (e.isDefaultPrevented()) return + + $parent.removeClass('in') + + function removeElement() { + $parent + .trigger('closed') + .remove() + } + + $.support.transition && $parent.hasClass('fade') ? + $parent.on($.support.transition.end, removeElement) : + removeElement() + } + + + /* ALERT PLUGIN DEFINITION + * ======================= */ + + $.fn.alert = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('alert') + if (!data) $this.data('alert', (data = new Alert(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + $.fn.alert.Constructor = Alert + + + /* ALERT DATA-API + * ============== */ + + $(function () { + $('body').on('click.alert.data-api', dismiss, Alert.prototype.close) + }) + +}(window.jQuery);/* ============================================================ + * bootstrap-button.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#buttons + * ============================================================ + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================ */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* BUTTON PUBLIC CLASS DEFINITION + * ============================== */ + + var Button = function (element, options) { + this.$element = $(element) + this.options = $.extend({}, $.fn.button.defaults, options) + } + + Button.prototype.setState = function (state) { + var d = 'disabled' + , $el = this.$element + , data = $el.data() + , val = $el.is('input') ? 'val' : 'html' + + state = state + 'Text' + data.resetText || $el.data('resetText', $el[val]()) + + $el[val](data[state] || this.options[state]) + + // push to event loop to allow forms to submit + setTimeout(function () { + state == 'loadingText' ? + $el.addClass(d).attr(d, d) : + $el.removeClass(d).removeAttr(d) + }, 0) + } + + Button.prototype.toggle = function () { + var $parent = this.$element.parent('[data-toggle="buttons-radio"]') + + $parent && $parent + .find('.active') + .removeClass('active') + + this.$element.toggleClass('active') + } + + + /* BUTTON PLUGIN DEFINITION + * ======================== */ + + $.fn.button = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('button') + , options = typeof option == 'object' && option + if (!data) $this.data('button', (data = new Button(this, options))) + if (option == 'toggle') data.toggle() + else if (option) data.setState(option) + }) + } + + $.fn.button.defaults = { + loadingText: 'loading...' + } + + $.fn.button.Constructor = Button + + + /* BUTTON DATA-API + * =============== */ + + $(function () { + $('body').on('click.button.data-api', '[data-toggle^=button]', function ( e ) { + var $btn = $(e.target) + if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn') + $btn.button('toggle') + }) + }) + +}(window.jQuery);/* ========================================================== + * bootstrap-carousel.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#carousel + * ========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* CAROUSEL CLASS DEFINITION + * ========================= */ + + var Carousel = function (element, options) { + this.$element = $(element) + this.options = options + this.options.slide && this.slide(this.options.slide) + this.options.pause == 'hover' && this.$element + .on('mouseenter', $.proxy(this.pause, this)) + .on('mouseleave', $.proxy(this.cycle, this)) + } + + Carousel.prototype = { + + cycle: function (e) { + if (!e) this.paused = false + this.options.interval + && !this.paused + && (this.interval = setInterval($.proxy(this.next, this), this.options.interval)) + return this + } + + , to: function (pos) { + var $active = this.$element.find('.active') + , children = $active.parent().children() + , activePos = children.index($active) + , that = this + + if (pos > (children.length - 1) || pos < 0) return + + if (this.sliding) { + return this.$element.one('slid', function () { + that.to(pos) + }) + } + + if (activePos == pos) { + return this.pause().cycle() + } + + return this.slide(pos > activePos ? 'next' : 'prev', $(children[pos])) + } + + , pause: function (e) { + if (!e) this.paused = true + clearInterval(this.interval) + this.interval = null + return this + } + + , next: function () { + if (this.sliding) return + return this.slide('next') + } + + , prev: function () { + if (this.sliding) return + return this.slide('prev') + } + + , slide: function (type, next) { + var $active = this.$element.find('.active') + , $next = next || $active[type]() + , isCycling = this.interval + , direction = type == 'next' ? 'left' : 'right' + , fallback = type == 'next' ? 'first' : 'last' + , that = this + , e = $.Event('slide') + + this.sliding = true + + isCycling && this.pause() + + $next = $next.length ? $next : this.$element.find('.item')[fallback]() + + if ($next.hasClass('active')) return + + if ($.support.transition && this.$element.hasClass('slide')) { + this.$element.trigger(e) + if (e.isDefaultPrevented()) return + $next.addClass(type) + $next[0].offsetWidth // force reflow + $active.addClass(direction) + $next.addClass(direction) + this.$element.one($.support.transition.end, function () { + $next.removeClass([type, direction].join(' ')).addClass('active') + $active.removeClass(['active', direction].join(' ')) + that.sliding = false + setTimeout(function () { that.$element.trigger('slid') }, 0) + }) + } else { + this.$element.trigger(e) + if (e.isDefaultPrevented()) return + $active.removeClass('active') + $next.addClass('active') + this.sliding = false + this.$element.trigger('slid') + } + + isCycling && this.cycle() + + return this + } + + } + + + /* CAROUSEL PLUGIN DEFINITION + * ========================== */ + + $.fn.carousel = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('carousel') + , options = $.extend({}, $.fn.carousel.defaults, typeof option == 'object' && option) + if (!data) $this.data('carousel', (data = new Carousel(this, options))) + if (typeof option == 'number') data.to(option) + else if (typeof option == 'string' || (option = options.slide)) data[option]() + else if (options.interval) data.cycle() + }) + } + + $.fn.carousel.defaults = { + interval: 5000 + , pause: 'hover' + } + + $.fn.carousel.Constructor = Carousel + + + /* CAROUSEL DATA-API + * ================= */ + + $(function () { + $('body').on('click.carousel.data-api', '[data-slide]', function ( e ) { + var $this = $(this), href + , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 + , options = !$target.data('modal') && $.extend({}, $target.data(), $this.data()) + $target.carousel(options) + e.preventDefault() + }) + }) + +}(window.jQuery);/* ============================================================= + * bootstrap-collapse.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#collapse + * ============================================================= + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================ */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* COLLAPSE PUBLIC CLASS DEFINITION + * ================================ */ + + var Collapse = function (element, options) { + this.$element = $(element) + this.options = $.extend({}, $.fn.collapse.defaults, options) + + if (this.options.parent) { + this.$parent = $(this.options.parent) + } + + this.options.toggle && this.toggle() + } + + Collapse.prototype = { + + constructor: Collapse + + , dimension: function () { + var hasWidth = this.$element.hasClass('width') + return hasWidth ? 'width' : 'height' + } + + , show: function () { + var dimension + , scroll + , actives + , hasData + + if (this.transitioning) return + + dimension = this.dimension() + scroll = $.camelCase(['scroll', dimension].join('-')) + actives = this.$parent && this.$parent.find('> .accordion-group > .in') + + if (actives && actives.length) { + hasData = actives.data('collapse') + if (hasData && hasData.transitioning) return + actives.collapse('hide') + hasData || actives.data('collapse', null) + } + + this.$element[dimension](0) + this.transition('addClass', $.Event('show'), 'shown') + this.$element[dimension](this.$element[0][scroll]) + } + + , hide: function () { + var dimension + if (this.transitioning) return + dimension = this.dimension() + this.reset(this.$element[dimension]()) + this.transition('removeClass', $.Event('hide'), 'hidden') + this.$element[dimension](0) + } + + , reset: function (size) { + var dimension = this.dimension() + + this.$element + .removeClass('collapse') + [dimension](size || 'auto') + [0].offsetWidth + + this.$element[size !== null ? 'addClass' : 'removeClass']('collapse') + + return this + } + + , transition: function (method, startEvent, completeEvent) { + var that = this + , complete = function () { + if (startEvent.type == 'show') that.reset() + that.transitioning = 0 + that.$element.trigger(completeEvent) + } + + this.$element.trigger(startEvent) + + if (startEvent.isDefaultPrevented()) return + + this.transitioning = 1 + + this.$element[method]('in') + + $.support.transition && this.$element.hasClass('collapse') ? + this.$element.one($.support.transition.end, complete) : + complete() + } + + , toggle: function () { + this[this.$element.hasClass('in') ? 'hide' : 'show']() + } + + } + + + /* COLLAPSIBLE PLUGIN DEFINITION + * ============================== */ + + $.fn.collapse = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('collapse') + , options = typeof option == 'object' && option + if (!data) $this.data('collapse', (data = new Collapse(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.collapse.defaults = { + toggle: true + } + + $.fn.collapse.Constructor = Collapse + + + /* COLLAPSIBLE DATA-API + * ==================== */ + + $(function () { + $('body').on('click.collapse.data-api', '[data-toggle=collapse]', function ( e ) { + var $this = $(this), href + , target = $this.attr('data-target') + || e.preventDefault() + || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7 + , option = $(target).data('collapse') ? 'toggle' : $this.data() + $(target).collapse(option) + }) + }) + +}(window.jQuery);/* ============================================================ + * bootstrap-dropdown.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#dropdowns + * ============================================================ + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================ */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* DROPDOWN CLASS DEFINITION + * ========================= */ + + var toggle = '[data-toggle="dropdown"]' + , Dropdown = function (element) { + var $el = $(element).on('click.dropdown.data-api', this.toggle) + $('html').on('click.dropdown.data-api', function () { + $el.parent().removeClass('open') + }) + } + + Dropdown.prototype = { + + constructor: Dropdown + + , toggle: function (e) { + var $this = $(this) + , $parent + , selector + , isActive + + if ($this.is('.disabled, :disabled')) return + + selector = $this.attr('data-target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + $parent = $(selector) + $parent.length || ($parent = $this.parent()) + + isActive = $parent.hasClass('open') + + clearMenus() + + if (!isActive) $parent.toggleClass('open') + + return false + } + + } + + function clearMenus() { + $(toggle).parent().removeClass('open') + } + + + /* DROPDOWN PLUGIN DEFINITION + * ========================== */ + + $.fn.dropdown = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('dropdown') + if (!data) $this.data('dropdown', (data = new Dropdown(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + $.fn.dropdown.Constructor = Dropdown + + + /* APPLY TO STANDARD DROPDOWN ELEMENTS + * =================================== */ + + $(function () { + $('html').on('click.dropdown.data-api', clearMenus) + $('body') + .on('click.dropdown', '.dropdown form', function (e) { e.stopPropagation() }) + .on('click.dropdown.data-api', toggle, Dropdown.prototype.toggle) + }) + +}(window.jQuery);/* ========================================================= + * bootstrap-modal.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#modals + * ========================================================= + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================= */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* MODAL CLASS DEFINITION + * ====================== */ + + var Modal = function (content, options) { + this.options = options + this.$element = $(content) + .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this)) + } + + Modal.prototype = { + + constructor: Modal + + , toggle: function () { + return this[!this.isShown ? 'show' : 'hide']() + } + + , show: function () { + var that = this + , e = $.Event('show') + + this.$element.trigger(e) + + if (this.isShown || e.isDefaultPrevented()) return + + $('body').addClass('modal-open') + + this.isShown = true + + escape.call(this) + backdrop.call(this, function () { + var transition = $.support.transition && that.$element.hasClass('fade') + + if (!that.$element.parent().length) { + that.$element.appendTo(document.body) //don't move modals dom position + } + + that.$element + .show() + + if (transition) { + that.$element[0].offsetWidth // force reflow + } + + that.$element.addClass('in') + + transition ? + that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) : + that.$element.trigger('shown') + + }) + } + + , hide: function (e) { + e && e.preventDefault() + + var that = this + + e = $.Event('hide') + + this.$element.trigger(e) + + if (!this.isShown || e.isDefaultPrevented()) return + + this.isShown = false + + $('body').removeClass('modal-open') + + escape.call(this) + + this.$element.removeClass('in') + + $.support.transition && this.$element.hasClass('fade') ? + hideWithTransition.call(this) : + hideModal.call(this) + } + + } + + + /* MODAL PRIVATE METHODS + * ===================== */ + + function hideWithTransition() { + var that = this + , timeout = setTimeout(function () { + that.$element.off($.support.transition.end) + hideModal.call(that) + }, 500) + + this.$element.one($.support.transition.end, function () { + clearTimeout(timeout) + hideModal.call(that) + }) + } + + function hideModal(that) { + this.$element + .hide() + .trigger('hidden') + + backdrop.call(this) + } + + function backdrop(callback) { + var that = this + , animate = this.$element.hasClass('fade') ? 'fade' : '' + + if (this.isShown && this.options.backdrop) { + var doAnimate = $.support.transition && animate + + this.$backdrop = $('
      ') + .appendTo(document.body) + + if (this.options.backdrop != 'static') { + this.$backdrop.click($.proxy(this.hide, this)) + } + + if (doAnimate) this.$backdrop[0].offsetWidth // force reflow + + this.$backdrop.addClass('in') + + doAnimate ? + this.$backdrop.one($.support.transition.end, callback) : + callback() + + } else if (!this.isShown && this.$backdrop) { + this.$backdrop.removeClass('in') + + $.support.transition && this.$element.hasClass('fade')? + this.$backdrop.one($.support.transition.end, $.proxy(removeBackdrop, this)) : + removeBackdrop.call(this) + + } else if (callback) { + callback() + } + } + + function removeBackdrop() { + this.$backdrop.remove() + this.$backdrop = null + } + + function escape() { + var that = this + if (this.isShown && this.options.keyboard) { + $(document).on('keyup.dismiss.modal', function ( e ) { + e.which == 27 && that.hide() + }) + } else if (!this.isShown) { + $(document).off('keyup.dismiss.modal') + } + } + + + /* MODAL PLUGIN DEFINITION + * ======================= */ + + $.fn.modal = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('modal') + , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option) + if (!data) $this.data('modal', (data = new Modal(this, options))) + if (typeof option == 'string') data[option]() + else if (options.show) data.show() + }) + } + + $.fn.modal.defaults = { + backdrop: true + , keyboard: true + , show: true + } + + $.fn.modal.Constructor = Modal + + + /* MODAL DATA-API + * ============== */ + + $(function () { + $('body').on('click.modal.data-api', '[data-toggle="modal"]', function ( e ) { + var $this = $(this), href + , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 + , option = $target.data('modal') ? 'toggle' : $.extend({}, $target.data(), $this.data()) + + e.preventDefault() + $target.modal(option) + }) + }) + +}(window.jQuery);/* =========================================================== + * bootstrap-tooltip.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#tooltips + * Inspired by the original jQuery.tipsy by Jason Frame + * =========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* TOOLTIP PUBLIC CLASS DEFINITION + * =============================== */ + + var Tooltip = function (element, options) { + this.init('tooltip', element, options) + } + + Tooltip.prototype = { + + constructor: Tooltip + + , init: function (type, element, options) { + var eventIn + , eventOut + + this.type = type + this.$element = $(element) + this.options = this.getOptions(options) + this.enabled = true + + if (this.options.trigger != 'manual') { + eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus' + eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur' + this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this)) + this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this)) + } + + this.options.selector ? + (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : + this.fixTitle() + } + + , getOptions: function (options) { + options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data()) + + if (options.delay && typeof options.delay == 'number') { + options.delay = { + show: options.delay + , hide: options.delay + } + } + + return options + } + + , enter: function (e) { + var self = $(e.currentTarget)[this.type](this._options).data(this.type) + + if (!self.options.delay || !self.options.delay.show) return self.show() + + clearTimeout(this.timeout) + self.hoverState = 'in' + this.timeout = setTimeout(function() { + if (self.hoverState == 'in') self.show() + }, self.options.delay.show) + } + + , leave: function (e) { + var self = $(e.currentTarget)[this.type](this._options).data(this.type) + + if (this.timeout) clearTimeout(this.timeout) + if (!self.options.delay || !self.options.delay.hide) return self.hide() + + self.hoverState = 'out' + this.timeout = setTimeout(function() { + if (self.hoverState == 'out') self.hide() + }, self.options.delay.hide) + } + + , show: function () { + var $tip + , inside + , pos + , actualWidth + , actualHeight + , placement + , tp + + if (this.hasContent() && this.enabled) { + $tip = this.tip() + this.setContent() + + if (this.options.animation) { + $tip.addClass('fade') + } + + placement = typeof this.options.placement == 'function' ? + this.options.placement.call(this, $tip[0], this.$element[0]) : + this.options.placement + + inside = /in/.test(placement) + + $tip + .remove() + .css({ top: 0, left: 0, display: 'block' }) + .appendTo(inside ? this.$element : document.body) + + pos = this.getPosition(inside) + + actualWidth = $tip[0].offsetWidth + actualHeight = $tip[0].offsetHeight + + switch (inside ? placement.split(' ')[1] : placement) { + case 'bottom': + tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2} + break + case 'top': + tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2} + break + case 'left': + tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth} + break + case 'right': + tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width} + break + } + + $tip + .css(tp) + .addClass(placement) + .addClass('in') + } + } + + , isHTML: function(text) { + // html string detection logic adapted from jQuery + return typeof text != 'string' + || ( text.charAt(0) === "<" + && text.charAt( text.length - 1 ) === ">" + && text.length >= 3 + ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text) + } + + , setContent: function () { + var $tip = this.tip() + , title = this.getTitle() + + $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title) + $tip.removeClass('fade in top bottom left right') + } + + , hide: function () { + var that = this + , $tip = this.tip() + + $tip.removeClass('in') + + function removeWithAnimation() { + var timeout = setTimeout(function () { + $tip.off($.support.transition.end).remove() + }, 500) + + $tip.one($.support.transition.end, function () { + clearTimeout(timeout) + $tip.remove() + }) + } + + $.support.transition && this.$tip.hasClass('fade') ? + removeWithAnimation() : + $tip.remove() + } + + , fixTitle: function () { + var $e = this.$element + if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { + $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title') + } + } + + , hasContent: function () { + return this.getTitle() + } + + , getPosition: function (inside) { + return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), { + width: this.$element[0].offsetWidth + , height: this.$element[0].offsetHeight + }) + } + + , getTitle: function () { + var title + , $e = this.$element + , o = this.options + + title = $e.attr('data-original-title') + || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) + + return title + } + + , tip: function () { + return this.$tip = this.$tip || $(this.options.template) + } + + , validate: function () { + if (!this.$element[0].parentNode) { + this.hide() + this.$element = null + this.options = null + } + } + + , enable: function () { + this.enabled = true + } + + , disable: function () { + this.enabled = false + } + + , toggleEnabled: function () { + this.enabled = !this.enabled + } + + , toggle: function () { + this[this.tip().hasClass('in') ? 'hide' : 'show']() + } + + } + + + /* TOOLTIP PLUGIN DEFINITION + * ========================= */ + + $.fn.tooltip = function ( option ) { + return this.each(function () { + var $this = $(this) + , data = $this.data('tooltip') + , options = typeof option == 'object' && option + if (!data) $this.data('tooltip', (data = new Tooltip(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.tooltip.Constructor = Tooltip + + $.fn.tooltip.defaults = { + animation: true + , placement: 'top' + , selector: false + , template: '
      ' + , trigger: 'hover' + , title: '' + , delay: 0 + } + +}(window.jQuery); +/* =========================================================== + * bootstrap-popover.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#popovers + * =========================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * =========================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* POPOVER PUBLIC CLASS DEFINITION + * =============================== */ + + var Popover = function ( element, options ) { + this.init('popover', element, options) + } + + + /* NOTE: POPOVER EXTENDS BOOTSTRAP-TOOLTIP.js + ========================================== */ + + Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype, { + + constructor: Popover + + , setContent: function () { + var $tip = this.tip() + , title = this.getTitle() + , content = this.getContent() + + $tip.find('.popover-title')[this.isHTML(title) ? 'html' : 'text'](title) + $tip.find('.popover-content > *')[this.isHTML(content) ? 'html' : 'text'](content) + + $tip.removeClass('fade top bottom left right in') + } + + , hasContent: function () { + return this.getTitle() || this.getContent() + } + + , getContent: function () { + var content + , $e = this.$element + , o = this.options + + content = $e.attr('data-content') + || (typeof o.content == 'function' ? o.content.call($e[0]) : o.content) + + return content + } + + , tip: function () { + if (!this.$tip) { + this.$tip = $(this.options.template) + } + return this.$tip + } + + }) + + + /* POPOVER PLUGIN DEFINITION + * ======================= */ + + $.fn.popover = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('popover') + , options = typeof option == 'object' && option + if (!data) $this.data('popover', (data = new Popover(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.popover.Constructor = Popover + + $.fn.popover.defaults = $.extend({} , $.fn.tooltip.defaults, { + placement: 'right' + , content: '' + , template: '

      ' + }) + +}(window.jQuery);/* ============================================================= + * bootstrap-scrollspy.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#scrollspy + * ============================================================= + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* SCROLLSPY CLASS DEFINITION + * ========================== */ + + function ScrollSpy( element, options) { + var process = $.proxy(this.process, this) + , $element = $(element).is('body') ? $(window) : $(element) + , href + this.options = $.extend({}, $.fn.scrollspy.defaults, options) + this.$scrollElement = $element.on('scroll.scroll.data-api', process) + this.selector = (this.options.target + || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 + || '') + ' .nav li > a' + this.$body = $('body') + this.refresh() + this.process() + } + + ScrollSpy.prototype = { + + constructor: ScrollSpy + + , refresh: function () { + var self = this + , $targets + + this.offsets = $([]) + this.targets = $([]) + + $targets = this.$body + .find(this.selector) + .map(function () { + var $el = $(this) + , href = $el.data('target') || $el.attr('href') + , $href = /^#\w/.test(href) && $(href) + return ( $href + && href.length + && [[ $href.position().top, href ]] ) || null + }) + .sort(function (a, b) { return a[0] - b[0] }) + .each(function () { + self.offsets.push(this[0]) + self.targets.push(this[1]) + }) + } + + , process: function () { + var scrollTop = this.$scrollElement.scrollTop() + this.options.offset + , scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight + , maxScroll = scrollHeight - this.$scrollElement.height() + , offsets = this.offsets + , targets = this.targets + , activeTarget = this.activeTarget + , i + + if (scrollTop >= maxScroll) { + return activeTarget != (i = targets.last()[0]) + && this.activate ( i ) + } + + for (i = offsets.length; i--;) { + activeTarget != targets[i] + && scrollTop >= offsets[i] + && (!offsets[i + 1] || scrollTop <= offsets[i + 1]) + && this.activate( targets[i] ) + } + } + + , activate: function (target) { + var active + , selector + + this.activeTarget = target + + $(this.selector) + .parent('.active') + .removeClass('active') + + selector = this.selector + + '[data-target="' + target + '"],' + + this.selector + '[href="' + target + '"]' + + active = $(selector) + .parent('li') + .addClass('active') + + if (active.parent('.dropdown-menu')) { + active = active.closest('li.dropdown').addClass('active') + } + + active.trigger('activate') + } + + } + + + /* SCROLLSPY PLUGIN DEFINITION + * =========================== */ + + $.fn.scrollspy = function ( option ) { + return this.each(function () { + var $this = $(this) + , data = $this.data('scrollspy') + , options = typeof option == 'object' && option + if (!data) $this.data('scrollspy', (data = new ScrollSpy(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.scrollspy.Constructor = ScrollSpy + + $.fn.scrollspy.defaults = { + offset: 10 + } + + + /* SCROLLSPY DATA-API + * ================== */ + + $(function () { + $('[data-spy="scroll"]').each(function () { + var $spy = $(this) + $spy.scrollspy($spy.data()) + }) + }) + +}(window.jQuery);/* ======================================================== + * bootstrap-tab.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#tabs + * ======================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ======================================================== */ + + +!function ($) { + + "use strict"; // jshint ;_; + + + /* TAB CLASS DEFINITION + * ==================== */ + + var Tab = function ( element ) { + this.element = $(element) + } + + Tab.prototype = { + + constructor: Tab + + , show: function () { + var $this = this.element + , $ul = $this.closest('ul:not(.dropdown-menu)') + , selector = $this.attr('data-target') + , previous + , $target + , e + + if (!selector) { + selector = $this.attr('href') + selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + if ( $this.parent('li').hasClass('active') ) return + + previous = $ul.find('.active a').last()[0] + + e = $.Event('show', { + relatedTarget: previous + }) + + $this.trigger(e) + + if (e.isDefaultPrevented()) return + + $target = $(selector) + + this.activate($this.parent('li'), $ul) + this.activate($target, $target.parent(), function () { + $this.trigger({ + type: 'shown' + , relatedTarget: previous + }) + }) + } + + , activate: function ( element, container, callback) { + var $active = container.find('> .active') + , transition = callback + && $.support.transition + && $active.hasClass('fade') + + function next() { + $active + .removeClass('active') + .find('> .dropdown-menu > .active') + .removeClass('active') + + element.addClass('active') + + if (transition) { + element[0].offsetWidth // reflow for transition + element.addClass('in') + } else { + element.removeClass('fade') + } + + if ( element.parent('.dropdown-menu') ) { + element.closest('li.dropdown').addClass('active') + } + + callback && callback() + } + + transition ? + $active.one($.support.transition.end, next) : + next() + + $active.removeClass('in') + } + } + + + /* TAB PLUGIN DEFINITION + * ===================== */ + + $.fn.tab = function ( option ) { + return this.each(function () { + var $this = $(this) + , data = $this.data('tab') + if (!data) $this.data('tab', (data = new Tab(this))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.tab.Constructor = Tab + + + /* TAB DATA-API + * ============ */ + + $(function () { + $('body').on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) { + e.preventDefault() + $(this).tab('show') + }) + }) + +}(window.jQuery);/* ============================================================= + * bootstrap-typeahead.js v2.0.4 + * http://twitter.github.com/bootstrap/javascript.html#typeahead + * ============================================================= + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ============================================================ */ + + +!function($){ + + "use strict"; // jshint ;_; + + + /* TYPEAHEAD PUBLIC CLASS DEFINITION + * ================================= */ + + var Typeahead = function (element, options) { + this.$element = $(element) + this.options = $.extend({}, $.fn.typeahead.defaults, options) + this.matcher = this.options.matcher || this.matcher + this.sorter = this.options.sorter || this.sorter + this.highlighter = this.options.highlighter || this.highlighter + this.updater = this.options.updater || this.updater + this.$menu = $(this.options.menu).appendTo('body') + this.source = this.options.source + this.shown = false + this.listen() + } + + Typeahead.prototype = { + + constructor: Typeahead + + , select: function () { + var val = this.$menu.find('.active').attr('data-value') + this.$element + .val(this.updater(val)) + .change() + return this.hide() + } + + , updater: function (item) { + return item + } + + , show: function () { + var pos = $.extend({}, this.$element.offset(), { + height: this.$element[0].offsetHeight + }) + + this.$menu.css({ + top: pos.top + pos.height + , left: pos.left + }) + + this.$menu.show() + this.shown = true + return this + } + + , hide: function () { + this.$menu.hide() + this.shown = false + return this + } + + , lookup: function (event) { + var that = this + , items + , q + + this.query = this.$element.val() + + if (!this.query) { + return this.shown ? this.hide() : this + } + + items = $.grep(this.source, function (item) { + return that.matcher(item) + }) + + items = this.sorter(items) + + if (!items.length) { + return this.shown ? this.hide() : this + } + + return this.render(items.slice(0, this.options.items)).show() + } + + , matcher: function (item) { + return ~item.toLowerCase().indexOf(this.query.toLowerCase()) + } + + , sorter: function (items) { + var beginswith = [] + , caseSensitive = [] + , caseInsensitive = [] + , item + + while (item = items.shift()) { + if (!item.toLowerCase().indexOf(this.query.toLowerCase())) beginswith.push(item) + else if (~item.indexOf(this.query)) caseSensitive.push(item) + else caseInsensitive.push(item) + } + + return beginswith.concat(caseSensitive, caseInsensitive) + } + + , highlighter: function (item) { + var query = this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, '\\$&') + return item.replace(new RegExp('(' + query + ')', 'ig'), function ($1, match) { + return '' + match + '' + }) + } + + , render: function (items) { + var that = this + + items = $(items).map(function (i, item) { + i = $(that.options.item).attr('data-value', item) + i.find('a').html(that.highlighter(item)) + return i[0] + }) + + items.first().addClass('active') + this.$menu.html(items) + return this + } + + , next: function (event) { + var active = this.$menu.find('.active').removeClass('active') + , next = active.next() + + if (!next.length) { + next = $(this.$menu.find('li')[0]) + } + + next.addClass('active') + } + + , prev: function (event) { + var active = this.$menu.find('.active').removeClass('active') + , prev = active.prev() + + if (!prev.length) { + prev = this.$menu.find('li').last() + } + + prev.addClass('active') + } + + , listen: function () { + this.$element + .on('blur', $.proxy(this.blur, this)) + .on('keypress', $.proxy(this.keypress, this)) + .on('keyup', $.proxy(this.keyup, this)) + + if ($.browser.webkit || $.browser.msie) { + this.$element.on('keydown', $.proxy(this.keypress, this)) + } + + this.$menu + .on('click', $.proxy(this.click, this)) + .on('mouseenter', 'li', $.proxy(this.mouseenter, this)) + } + + , keyup: function (e) { + switch(e.keyCode) { + case 40: // down arrow + case 38: // up arrow + break + + case 9: // tab + case 13: // enter + if (!this.shown) return + this.select() + break + + case 27: // escape + if (!this.shown) return + this.hide() + break + + default: + this.lookup() + } + + e.stopPropagation() + e.preventDefault() + } + + , keypress: function (e) { + if (!this.shown) return + + switch(e.keyCode) { + case 9: // tab + case 13: // enter + case 27: // escape + e.preventDefault() + break + + case 38: // up arrow + if (e.type != 'keydown') break + e.preventDefault() + this.prev() + break + + case 40: // down arrow + if (e.type != 'keydown') break + e.preventDefault() + this.next() + break + } + + e.stopPropagation() + } + + , blur: function (e) { + var that = this + setTimeout(function () { that.hide() }, 150) + } + + , click: function (e) { + e.stopPropagation() + e.preventDefault() + this.select() + } + + , mouseenter: function (e) { + this.$menu.find('.active').removeClass('active') + $(e.currentTarget).addClass('active') + } + + } + + + /* TYPEAHEAD PLUGIN DEFINITION + * =========================== */ + + $.fn.typeahead = function (option) { + return this.each(function () { + var $this = $(this) + , data = $this.data('typeahead') + , options = typeof option == 'object' && option + if (!data) $this.data('typeahead', (data = new Typeahead(this, options))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.typeahead.defaults = { + source: [] + , items: 8 + , menu: '
        ' + , item: '
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13:if(!this.shown)return;this.select();break;case 27:if(!this.shown)return;this.hide();break;default:this.lookup()}a.stopPropagation(),a.preventDefault()},keypress:function(a){if(!this.shown)return;switch(a.keyCode){case 9:case 13:case 27:a.preventDefault();break;case 38:if(a.type!="keydown")break;a.preventDefault(),this.prev();break;case 40:if(a.type!="keydown")break;a.preventDefault(),this.next()}a.stopPropagation()},blur:function(a){var b=this;setTimeout(function(){b.hide()},150)},click:function(a){a.stopPropagation(),a.preventDefault(),this.select()},mouseenter:function(b){this.$menu.find(".active").removeClass("active"),a(b.currentTarget).addClass("active")}},a.fn.typeahead=function(c){return this.each(function(){var d=a(this),e=d.data("typeahead"),f=typeof c=="object"&&c;e||d.data("typeahead",e=new b(this,f)),typeof c=="string"&&e[c]()})},a.fn.typeahead.defaults={source:[],items:8,menu:'
          ',item:'
          • '},a.fn.typeahead.Constructor=b,a(function(){a("body").on("focus.typeahead.data-api",'[data-provide="typeahead"]',function(b){var c=a(this);if(c.data("typeahead"))return;b.preventDefault(),c.typeahead(c.data())})})}(window.jQuery); \ No newline at end of file diff --git a/inst/web/pfm_degradation.html b/inst/web/pfm_degradation.html new file mode 100644 index 0000000..fad64be --- /dev/null +++ b/inst/web/pfm_degradation.html @@ -0,0 +1,119 @@ + + + + +pfm_degradation. pfm 0.3-7 + + + + + + + + + + + + + + + +
          +
          +
          + pfm 0.3-7 +
          + +
          +
          +
          +
          + +
          +
          + +
          + +

          Calculate a time course of relative concentrations based on an mkinmod model

          + +
          +
          +

          Usage

          + 
          pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = step_days))
          + +

          Arguments

          +
          +
          model
          +
          The degradation model to be used. Either a parent only model like +'SFO' or 'FOMC', or an mkinmod object
          +
          DT50
          +
          The half-life. This is only used when simple exponential decline +is calculated (SFO model).
          +
          parms
          +
          The parameters used for the degradation model
          +
          years
          +
          For how many years should the degradation be predicted?
          +
          step_days
          +
          What step size in days should the output have?
          +
          times
          +
          The output times
          +
          + +
          +

          Description

          + +

          Calculate a time course of relative concentrations based on an mkinmod model

          + +
          + +

          Examples

          + 
          head(pfm_degradation("SFO", DT50 = 10))
+
          
+
            time    parent
+1    0 1.0000000
+2    1 0.9330330
+3    2 0.8705506
+4    3 0.8122524
+5    4 0.7578583
+6    5 0.7071068
+
          +
          +
          + + + +

          Author

          + +Johannes Ranke + + +
          +
          + + +
          + + \ No newline at end of file diff --git a/inst/web/plot.TOXSWA_cwa-2.png b/inst/web/plot.TOXSWA_cwa-2.png new file mode 100644 index 0000000..764c7f4 Binary files /dev/null and b/inst/web/plot.TOXSWA_cwa-2.png differ diff --git a/inst/web/plot.TOXSWA_cwa-4.png b/inst/web/plot.TOXSWA_cwa-4.png new file mode 100644 index 0000000..764c7f4 Binary files /dev/null and b/inst/web/plot.TOXSWA_cwa-4.png differ diff --git a/inst/web/plot.TOXSWA_cwa.html b/inst/web/plot.TOXSWA_cwa.html new file mode 100644 index 0000000..a6118df --- /dev/null +++ b/inst/web/plot.TOXSWA_cwa.html @@ -0,0 +1,119 @@ + + + + +plot.TOXSWA_cwa. pfm 0.3-7 + + + + + + + + + + + + + + + +
          +
          +
          + pfm 0.3-7 +
          + +
          +
          +
          +
          + +
          +
          + +
          + +

          Plot TOXSWA surface water concentrations

          + +
          +
          +

          Usage

          + 
          "plot"(x, time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE, total = FALSE, LC_TIME = "C", ...)
          + +

          Arguments

          +
          +
          x
          +
          The TOXSWA_cwa object to be plotted.
          +
          time_column
          +
          What should be used for the time axis. If "t_firstjan" is chosen, +the time is given in days relative to the first of January in the first year.
          +
          xlab, ylab
          +
          Labels for x and y axis.
          +
          add
          +
          Should we add to an existing plot?
          +
          total
          +
          Should the total concentration in water be plotted, including substance sorbed +to suspended matter?
          +
          LC_TIME
          +
          Specification of the locale used to format dates
          +
          ...
          +
          Further arguments passed to plot if we are not adding to an existing plot
          +
          + +
          +

          Description

          + +

          Plot TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body.

          + +
          + +

          Examples

          + 
          H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                             package = "pfm"))
+plot(H_sw_D4_pond)
+
          
+
          +
          +
          + + + +

          Author

          + +Johannes Ranke + + +
          +
          + + +
          + + \ No newline at end of file diff --git a/inst/web/read.TOXSWA_cwa.html b/inst/web/read.TOXSWA_cwa.html new file mode 100644 index 0000000..3f2d997 --- /dev/null +++ b/inst/web/read.TOXSWA_cwa.html @@ -0,0 +1,138 @@ + + + + +read.TOXSWA_cwa. pfm 0.3-7 + + + + + + + + + + + + + + + +
          +
          +
          + pfm 0.3-7 +
          + +
          +
          +
          +
          + +
          +
          + +
          + +

          Read TOXSWA surface water concentrations

          + +
          +
          +

          Usage

          + 
          read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", substance = "parent", total = FALSE, windows = NULL, thresholds = NULL)
          + +

          Arguments

          +
          +
          filename
          +
          The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).
          +
          basedir
          +
          The path to the directory where the cwa file resides.
          +
          zipfile
          +
          Optional path to a zip file containing the cwa file.
          +
          segment
          +
          The segment for which the data should be read. Either "last", or +the segment number.
          +
          substance
          +
          For TOXSWA 4 .out files, the default value "parent" leads +to reading concentrations of the parent compound. Alternatively, the substance +of interested can be selected by its code name.
          +
          total
          +
          Set this to TRUE in order to read total concentrations as well. This is +only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa +files. For .cwa files, the total concentration is always read as well.
          +
          windows
          +
          Numeric vector of width of moving windows in days, for calculating +maximum time weighted average concentrations and areas under the curve.
          +
          thresholds
          +
          Numeric vector of threshold concentrations in µg/L for +generating event statistics.
          +
          + +
          +

          Value

          + +

          +An instance of an R6 object of class +TOXSWA_cwa. +

          + +
          + +
          +

          Description

          + +

          Read TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body. Per default, the data for the last +segment are imported. As TOXSWA 4 reports the values at the end of the hour +(ConLiqWatLayCur) in its summary file, we use this value as well instead +of the hourly averages (ConLiqWatLay).

          + +
          + +

          Examples

          + 
          H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                 zipfile = system.file("testdata/SwashProjects.zip",
+                                                       package = "pfm"))
+
          +
          +
          + + + +

          Author

          + +Johannes Ranke + + +
          +
          + + +
          + + \ No newline at end of file diff --git a/inst/web/soil_DT50.html b/inst/web/soil_DT50.html new file mode 100644 index 0000000..0e142ae --- /dev/null +++ b/inst/web/soil_DT50.html @@ -0,0 +1,104 @@ + + + + +soil_DT50. pfm 0.2-4 + + + + + + + + + + + + + + + +
          +
          +
          + pfm 0.2-4 +
          + +
          +
          +
          +
          + +
          +
          + +
          + +

          Obtain soil DT50

          + +
          +
          +

          Usage

          + 
          soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)
          + +

          Arguments

          +
          +
          chent
          +
          The chent object to get the information from
          +
          aggregator
          +
          The aggregator function. Can be mean, +geomean, or identity, for example.
          +
          signif
          +
          How many significant digits do we want
          +
          lab_field
          +
          If not NA, do we want laboratory or field endpoints
          +
          value
          +
          The name of the value we want. The list given in the +usage section is not exclusive
          +
          redox
          +
          If not NA, are we looking for aerobic or anaerobic data
          +
          raw
          +
          Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?
          +
          + +
          +

          Description

          + +

          Obtain soil DT50

          + +
          +
          +
          + + + +
          +
          + + +
          + + \ No newline at end of file diff --git a/inst/web/soil_Kfoc.html b/inst/web/soil_Kfoc.html new file mode 100644 index 0000000..ace5f4b --- /dev/null +++ b/inst/web/soil_Kfoc.html @@ -0,0 +1,100 @@ + + + + +soil_Kfoc. pfm 0.2-4 + + + + + + + + + + + + + + + +
          +
          +
          + pfm 0.2-4 +
          + +
          +
          +
          +
          + +
          +
          + +
          + +

          Obtain soil Kfoc

          + +
          +
          +

          Usage

          + 
          soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)
          + +

          Arguments

          +
          +
          chent
          +
          The chent object to get the information from
          +
          aggregator
          +
          The aggregator function. Can be mean, +geomean, or identity, for example.
          +
          signif
          +
          How many significant digits do we want
          +
          value
          +
          The name of the value we want. The list given in the +usage section is not exclusive
          +
          raw
          +
          Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?
          +
          + +
          +

          Description

          + +

          Obtain soil Kfoc

          + +
          +
          +
          + + + +
          +
          + + +
          + + \ No newline at end of file diff --git a/inst/web/soil_N.html b/inst/web/soil_N.html new file mode 100644 index 0000000..886bbc7 --- /dev/null +++ b/inst/web/soil_N.html @@ -0,0 +1,98 @@ + + + + +soil_N. pfm 0.2-4 + + + + + + + + + + + + + + + +
          +
          +
          + pfm 0.2-4 +
          + +
          +
          +
          +
          + +
          +
          + +
          + +

          Obtain soil Freundlich exponent

          + +
          +
          +

          Usage

          + 
          soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
          + +

          Arguments

          +
          +
          chent
          +
          The chent object to get the information from
          +
          aggregator
          +
          The aggregator function. Can be mean, +geomean, or identity, for example.
          +
          signif
          +
          How many significant digits do we want
          +
          raw
          +
          Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?
          +
          + +
          +

          Description

          + +

          In pesticide fate modelling, this exponent is often called 1/n. Here, in +order to facilitate dealing with such data in R, it is called N.

          + +
          +
          +
          + + + +
          +
          + + +
          + + \ No newline at end of file diff --git a/inst/web/soil_scenario_data_EFSA_2015.html b/inst/web/soil_scenario_data_EFSA_2015.html new file mode 100644 index 0000000..0230afb --- /dev/null +++ b/inst/web/soil_scenario_data_EFSA_2015.html @@ -0,0 +1,141 @@ + + + + +soil_scenario_data_EFSA_2015. pfm 0.3-7 + + + + + + + + + + + + + + + +
          +
          +
          + pfm 0.3-7 +
          + +
          +
          +
          +
          + +
          +
          + +
          + +

          Properties of the predefined scenarios from the EFSA guidance from 2015

          + +
          +
          + +
          +

          Format

          + +

          A data frame with one row for each scenario. Row names are the scenario codes, + e.g. CTN for the Northern scenario for the total concentration in soil. Columns are + mostly self-explanatory. rho is the dry bulk density of the top soil.

          + +
          + +
          +

          Source

          + +

          EFSA (European Food Safety Authority) (2015) +EFSA guidance document for predicting environmental concentrations +of active substances of plant protection products and transformation products of these +active substances in soil. EFSA Journal 13(4) 4093 +doi:10.2903/j.efsa.2015.4093

          + +
          + +
          +

          Description

          + +

          Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the +scenario and model adjustment factors from p. 15 and p. 17 are included.

          + +
          + +

          Examples

          + 
          ## Not run: 
+#   # This is the code that was used to define the data
+#   soil_scenario_data_EFSA_2015 <- data.frame(
+#     Zone = rep(c("North", "Central", "South"), 2),
+#     Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),
+#     T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),
+#     T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),
+#     Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),
+#     f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),
+#     theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),
+#     rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),
+#     f_sce = c(3, 2, 2, 2, 1.5, 1.5),
+#     f_mod = c(2, 2, 2, 4, 4, 4),
+#     stringsAsFactors = FALSE,
+#     row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")
+#   )
+#   save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')
+# ## End(Not run)
+
+# And this is the resulting dataframe
+soil_scenario_data_EFSA_2015
+
          
+
                 Zone        Country T_arit T_arr     Texture  f_om theta_fc  rho f_sce
+CTN   North        Estonia    4.7   7.0      Coarse 0.118    0.244 0.95   3.0
+CTC Central        Germany    8.0  10.1      Coarse 0.086    0.244 1.05   2.0
+CTS   South         France   11.0  12.3 Medium fine 0.048    0.385 1.22   2.0
+CLN   North        Denmark    8.2   9.8      Medium 0.023    0.347 1.39   2.0
+CLC Central Czech Republik    9.1  11.2      Medium 0.018    0.347 1.43   1.5
+CLS   South          Spain   12.8  14.7      Medium 0.011    0.347 1.51   1.5
+    f_mod
+CTN     2
+CTC     2
+CTS     2
+CLN     4
+CLC     4
+CLS     4
+
          +
          +
          + + + +
          +
          + + +
          + + \ No newline at end of file diff --git a/inst/web/soil_sorption.html b/inst/web/soil_sorption.html new file mode 100644 index 0000000..152fc5e --- /dev/null +++ b/inst/web/soil_sorption.html @@ -0,0 +1,98 @@ + + + + +soil_sorption. pfm 0.2-4 + + + + + + + + + + + + + + + +
          +
          +
          + pfm 0.2-4 +
          + +
          +
          +
          +
          + +
          +
          + +
          + +

          Obtain soil sorption data

          + +
          +
          +

          Usage

          + 
          soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = rep(3, length(values)), raw = FALSE)
          + +

          Arguments

          +
          +
          chent
          +
          The chent object to get the information from
          +
          values
          +
          The values to be returned
          +
          aggregators
          +
          A named vector of aggregator functions to be used
          +
          signif
          +
          How many significant digits do we want
          +
          raw
          +
          Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?
          +
          + +
          +

          Description

          + +

          Obtain soil sorption data

          + +
          +
          +
          + + + +
          +
          + + +
          + + \ No newline at end of file diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd new file mode 100644 index 0000000..3ae151b --- /dev/null +++ b/man/FOCUS_GW_scenarios_2012.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/FOCUS_GW_scenarios_2012.R +\name{FOCUS_GW_scenarios_2012} +\alias{FOCUS_GW_scenarios_2012} +\title{A very small subset of the FOCUS Groundwater scenario defitions} +\description{ +Currently, only a small subset of the soil definitions are provided. +} +\examples{ +FOCUS_GW_scenarios_2012 +} +\references{ +FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. + FOrum for the Co-ordination of pesticde fate models and their USe. + http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf +} + diff --git a/man/GUS.Rd b/man/GUS.Rd new file mode 100644 index 0000000..f1f5f28 --- /dev/null +++ b/man/GUS.Rd @@ -0,0 +1,81 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/GUS.R +\name{GUS} +\alias{GUS} +\alias{GUS.chent} +\alias{GUS.numeric} +\alias{print.GUS_result} +\title{Groundwater ubiquity score based on Gustafson (1989)} +\usage{ +GUS(...) + +\method{GUS}{numeric}(DT50, Koc, ...) + +\method{GUS}{chent}(chent, degradation_value = "DT50ref", + lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc", + degradation_aggregator = geomean, sorption_aggregator = geomean, ...) + +\method{print}{GUS_result}(x, ..., digits = 1) +} +\arguments{ +\item{...}{Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.} + +\item{DT50}{Half-life of the chemical in soil. Should be a field +half-life according to Gustafson (1989). However, leaching to the sub-soil +can not completely be excluded in field dissipation experiments and Gustafson +did not refer to any normalisation procedure, but says the field study should +be conducted under use conditions.} + +\item{Koc}{The sorption constant normalised to organic carbon. Gustafson +does not mention the nonlinearity of the sorption constant commonly +found and usually described by Freundlich sorption, therefore it is +unclear at which reference concentration the Koc should be observed +(and if the reference concentration would be in soil or in porewater).} + +\item{chent}{If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.} + +\item{degradation_value}{Which of the available degradation values should +be used?} + +\item{lab_field}{Should laboratory or field half-lives be used? This +defaults to lab in this implementation, in order to avoid +double-accounting for mobility. If comparability with the original GUS +values given by Gustafson (1989) is desired, non-normalised first-order +field half-lives obtained under actual use conditions should be used.} + +\item{redox}{Aerobic or anaerobic degradation data} + +\item{sorption_value}{Which of the available sorption values should be used? +Defaults to Kfoc as this is what is generally available from the European +pesticide peer review process. These values generally use a reference +concentration of 1 mg/L in porewater, that means they would be expected to +be Koc values at a concentration of 1 mg/L in the water phase.} + +\item{degradation_aggregator}{Function for aggregating half-lives} + +\item{sorption_aggregator}{Function for aggregation Koc values} + +\item{x}{An object of class GUS_result to be printed} + +\item{digits}{The number of digits used in the print method} +} +\value{ +A list with the DT50 and Koc used as well as the resulting score + of class GUS_result +} +\description{ +The groundwater ubiquity score GUS is calculated according to +the following equation +\deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)} +} +\author{ +Johannes Ranke +} +\references{ +Gustafson, David I. (1989) Groundwater ubiquity score: a simple +method for assessing pesticide leachability. \emph{Environmental +toxicology and chemistry} \bold{8}(4) 339–57. +} + diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd new file mode 100644 index 0000000..c0b5201 --- /dev/null +++ b/man/PEC_soil.Rd @@ -0,0 +1,119 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PEC_soil.R +\name{PEC_soil} +\alias{PEC_soil} +\title{Calculate predicted environmental concentrations in soil} +\usage{ +PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, + PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA, + n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA, + Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default", + "EFSA_2015"), porewater = FALSE) +} +\arguments{ +\item{rate}{Application rate in units specified below} + +\item{rate_units}{Defaults to g/ha} + +\item{interception}{The fraction of the application rate that does not reach the soil} + +\item{mixing_depth}{Mixing depth in cm} + +\item{PEC_units}{Requested units for the calculated PEC. Only mg/kg currently supported} + +\item{PEC_pw_units}{Only mg/L currently supported} + +\item{interval}{Period of the deeper mixing, defaults to 365, which is a year if +rate units are in days} + +\item{n_periods}{Number of periods to be considered for long term PEC calculations} + +\item{tillage_depth}{Periodic (see interval) deeper mixing in cm} + +\item{chent}{An optional chent object holding substance specific information. Can +also be a name for the substance as a character string} + +\item{DT50}{If specified, overrides soil DT50 endpoints from a chent object +If DT50 is not specified here and not available from the chent object, zero +degradation is assumed} + +\item{Koc}{If specified, overrides Koc endpoints from a chent object} + +\item{Kom}{Calculated from Koc by default, but can explicitly be specified +as Kom here} + +\item{t_avg}{Averaging times for time weighted average concentrations} + +\item{scenarios}{If this is 'default', the DT50 will be used without correction +and soil properties as specified in the REACH guidance (R.16, Table +R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", +the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when +'chents' is specified, the DegT50 with destination 'PECgw' will be used), +and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also +model and scenario adjustment factors from the EFSA guidance are used.} + +\item{porewater}{Should equilibrium porewater concentrations be estimated +based on Kom and the organic carbon fraction of the soil instead of total +soil concentrations? Based on equation (7) given in the PPR panel opinion +(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, +p. 13).} +} +\value{ +The predicted concentration in soil +} +\description{ +This is a basic calculation of a contaminant concentration in bulk soil +based on complete, instantaneous mixing. If an interval is given, an +attempt is made at calculating a long term maximum concentration using +the concepts layed out for example in the PPR panel opinion (EFSA 2012). +} +\details{ +This assumes that the complete load to soil during the time specified by +'interval' (typically 365 days) is dosed at once. As in the PPR panel +opinion cited below (PPR panel 2012), only temperature correction using the +Arrhenius equation is performed. + +Total soil and porewater PEC values for the scenarios as defined in the EFSA +guidance (2015, p. 13) can easily be calculated. +} +\note{ +If temperature information is available in the selected scenarios, as + e.g. in the EFSA scenarios, the DT50 for groundwater modelling + (destination 'PECgw') is taken from the chent object, otherwise the DT50 + with destination 'PECsoil'. +} +\examples{ +PEC_soil(100, interception = 0.25) + +# This is example 1 starting at p. 79 of the EFSA guidance (2015) +PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + scenarios = "EFSA_2015") +PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) + +# The following is from example 4 starting at p. 85 of the EFSA guidance (2015) +# Metabolite M2 +# Calculate total and porewater soil concentrations for tier 1 scenarios +# Relative molar mass is 100/300, formation fraction is 0.7 * 1 +results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + scenarios = "EFSA_2015") +results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) +} +\author{ +Johannes Ranke +} +\references{ +EFSA Panel on Plant Protection Products and their Residues (2012) + Scientific Opinion on the science behind the guidance for scenario + selection and scenario parameterisation for predicting environmental + concentrations of plant protection products in soil. \emph{EFSA Journal} + \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562 + + EFSA (European Food Safety Authority) (2015) EFSA guidance document for + predicting environmental concentrations of active substances of plant + protection products and transformation products of these active substances + in soil. \emph{EFSA Journal} \bold{13}(4) 4093 + doi:10.2903/j.efsa.2015.4093 +} + diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd new file mode 100644 index 0000000..cb64bde --- /dev/null +++ b/man/PEC_sw_drainage_UK.Rd @@ -0,0 +1,39 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PEC_sw_drainage_UK.R +\name{PEC_sw_drainage_UK} +\alias{PEC_sw_drainage_UK} +\title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method} +\usage{ +PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL, + soil_DT50 = NULL, model = NULL, model_parms = NULL) +} +\arguments{ +\item{rate}{Application rate in g/ha} + +\item{interception}{The fraction of the application rate that does not reach the soil} + +\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg} + +\item{latest_application}{Latest application date, formatted as e.g. "01 July"} + +\item{soil_DT50}{Soil degradation half-life, if SFO kinetics are to be used} + +\item{model}{The soil degradation model to be used. Either one of "FOMC", +"DFOP", "HS", or "IORE", or an mkinmod object} + +\item{model_parms}{A named numeric vector containing the model parameters} +} +\value{ +The predicted concentration in surface water in µg/L +} +\description{ +This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet +published on the CRC website +} +\examples{ +PEC_sw_drainage_UK(150, Koc = 100) +} +\author{ +Johannes Ranke +} + diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd new file mode 100644 index 0000000..20fa921 --- /dev/null +++ b/man/PEC_sw_drift.Rd @@ -0,0 +1,45 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PEC_sw_drift.R +\name{PEC_sw_drift} +\alias{PEC_sw_drift} +\title{Calculate predicted environmental concentrations in surface water due to drift} +\usage{ +PEC_sw_drift(rate, applications = 1, water_depth = 30, + drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", + distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L") +} +\arguments{ +\item{rate}{Application rate in units specified below} + +\item{applications}{Number of applications for selection of drift percentile} + +\item{water_depth}{Depth of the water body in cm} + +\item{drift_percentages}{Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.} + +\item{drift_data}{Source of drift percentage data} + +\item{crop}{Crop name (use German names for JKI data), defaults to "Ackerbau"} + +\item{distances}{The distances in m for which to get PEC values} + +\item{rate_units}{Defaults to g/ha} + +\item{PEC_units}{Requested units for the calculated PEC. Only µg/L currently supported} +} +\value{ +The predicted concentration in surface water +} +\description{ +This is a basic, vectorised form of a simple calculation of a contaminant +concentration in surface water based on complete, instantaneous mixing +with input via spray drift. +} +\examples{ +PEC_sw_drift(100) +} +\author{ +Johannes Ranke +} + diff --git a/man/PEC_sw_sed.Rd b/man/PEC_sw_sed.Rd new file mode 100644 index 0000000..3140eb0 --- /dev/null +++ b/man/PEC_sw_sed.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PEC_sw_sed.R +\name{PEC_sw_sed} +\alias{PEC_sw_sed} +\title{Calculate predicted environmental concentrations in sediment from surface +water concentrations} +\usage{ +PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage", + sediment_depth = 5, water_depth = 30, sediment_density = 1.3, + PEC_sed_units = c("µg/kg", "mg/kg")) +} +\arguments{ +\item{PEC_sw}{Numeric vector or matrix of surface water concentrations in µg/L for +which the corresponding sediment concentration is to be estimated} + +\item{percentage}{The percentage in sediment, used for the percentage method} + +\item{method}{The method used for the calculation} + +\item{sediment_depth}{Depth of the sediment layer} + +\item{water_depth}{Depth of the water body in cm} + +\item{sediment_density}{The density of the sediment in L/kg (equivalent to +g/cm3)} + +\item{PEC_sed_units}{The units of the estimated sediment PEC value} +} +\value{ +The predicted concentration in sediment +} +\description{ +The method 'percentage' is equivalent to what is used in the CRD spreadsheet +PEC calculator +} +\examples{ +PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) +} +\author{ +Johannes Ranke +} + diff --git a/man/SFO_actual_twa.Rd b/man/SFO_actual_twa.Rd new file mode 100644 index 0000000..573ea03 --- /dev/null +++ b/man/SFO_actual_twa.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/SFO_actual_twa.R +\name{SFO_actual_twa} +\alias{SFO_actual_twa} +\title{Actual and maximum moving window time average concentrations for SFO kinetics} +\source{ +FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, + 18 December 2014, p. 251 +} +\usage{ +SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, + 100)) +} +\arguments{ +\item{DT50}{The half-life.} + +\item{times}{The output times, and window sizes for time weighted average concentrations} +} +\description{ +Actual and maximum moving window time average concentrations for SFO kinetics +} +\examples{ +SFO_actual_twa(10) +} +\author{ +Johannes Ranke +} + diff --git a/man/SSLRC_mobility_classification.Rd b/man/SSLRC_mobility_classification.Rd new file mode 100644 index 0000000..04aa01d --- /dev/null +++ b/man/SSLRC_mobility_classification.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/SSLRC_mobility_classification.R +\name{SSLRC_mobility_classification} +\alias{SSLRC_mobility_classification} +\title{Determine the SSLRC mobility classification for a chemical substance from its Koc} +\usage{ +SSLRC_mobility_classification(Koc) +} +\arguments{ +\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg} +} +\value{ +A list containing the classification and the percentage of the + compound transported per 10 mm drain water +} +\description{ +This implements the method specified in the UK data requirements handbook and was +checked against the spreadsheet published on the CRC website +} +\examples{ +SSLRC_mobility_classification(100) +} +\author{ +Johannes Ranke +} + diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd new file mode 100644 index 0000000..de87510 --- /dev/null +++ b/man/TOXSWA_cwa.Rd @@ -0,0 +1,58 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/TOXSWA_cwa.R +\docType{class} +\name{TOXSWA_cwa} +\alias{TOXSWA_cwa} +\title{R6 class for holding TOXSWA cwa concentration data and associated statistics} +\format{An \code{\link{R6Class}} generator object.} +\usage{ +TOXSWA_cwa +} +\description{ +An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. +} +\section{Fields}{ + +\describe{ +\item{\code{filename}}{Length one character vector.} + +\item{\code{basedir}}{Length one character vector.} + +\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.} + +\item{\code{cwas}}{Dataframe holding the concentrations.} + +\item{\code{events}}{List of dataframes holding the event statistics for each threshold.} + +\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max) +and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) +for the requested moving window sizes in days.} +}} +\section{Methods}{ + +\describe{ + \item{\code{get_events(threshold, total = FALSE)}}{ + Populate a datataframe with event information for the specified threshold value + in µg/L. If \code{total = TRUE}, the total concentration including the amount + adsorbed to suspended matter will be used. The resulting dataframe is stored in the + \code{events} field of the object. + } + \item{\code{moving_windows(windows, total = FALSE)}}{ + Add to the \code{windows} field described above. + Again, if \code{total = TRUE}, the total concentration including the amount + adsorbed to suspended matter will be used. + } +} +} +\examples{ +H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", + basedir = "SwashProjects/project_H_sw/TOXSWA", + zipfile = system.file("testdata/SwashProjects.zip", + package = "pfm")) +H_sw_R1_stream$get_events(c(2, 10)) +H_sw_R1_stream$moving_windows(c(7, 21)) +print(H_sw_R1_stream) +} +\keyword{data} + diff --git a/man/drift_data_JKI.Rd b/man/drift_data_JKI.Rd new file mode 100644 index 0000000..c193c0d --- /dev/null +++ b/man/drift_data_JKI.Rd @@ -0,0 +1,50 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/drift_data_JKI.R +\docType{data} +\name{drift_data_JKI} +\alias{drift_data_JKI} +\title{Deposition from spray drift expressed as percent of the applied dose as +published by the JKI} +\format{A list currently containing matrices with spray drift percentage +data for field crops (Ackerbau), and Pome/stone fruit, early and late +(Obstbau frueh, spaet).} +\source{ +JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved +from +http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html +on 2015-06-11 +} +\description{ +Deposition from spray drift expressed as percent of the applied dose as +published by the German Julius-Kühn Institute (JKI). +} +\details{ +The data were extracted from the spreadsheet cited below using the R code +given in the example section. The spreadsheet is not included in the package +as its licence is not clear. +} +\examples{ + +\dontrun{ + # This is the code that was used to extract the data + library(readxl) + abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" + JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet") + names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late") + drift_data_JKI <- list() + + for (n in 1:8) { + drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) + drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) + dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]), + crop = JKI_crops) + drift_data_JKI[[n]] <- drift_data + } + save(drift_data_JKI, file = "data/drift_data_JKI.RData") +} + +# And this is the resulting data +drift_data_JKI +} +\keyword{datasets} + diff --git a/man/endpoint.Rd b/man/endpoint.Rd new file mode 100644 index 0000000..0350a51 --- /dev/null +++ b/man/endpoint.Rd @@ -0,0 +1,75 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/endpoint.R +\name{endpoint} +\alias{endpoint} +\alias{soil_DT50} +\alias{soil_Kfoc} +\alias{soil_N} +\alias{soil_sorption} +\title{Retrieve endpoint information from the chyaml field of a chent object} +\usage{ +endpoint(chent, medium = "soil", type = c("degradation", "sorption"), + lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", + "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, + raw = FALSE, signif = 3) + +soil_DT50(chent, aggregator = geomean, signif = 3, + lab_field = "laboratory", value = "DT50ref", redox = "aerobic", + raw = FALSE) + +soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", + raw = FALSE) + +soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) + +soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = + geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), + raw = FALSE) +} +\arguments{ +\item{chent}{The chent object to get the information from} + +\item{medium}{The medium for which information is sought} + +\item{type}{The information type} + +\item{lab_field}{If not NA, do we want laboratory or field endpoints} + +\item{redox}{If not NA, are we looking for aerobic or anaerobic data} + +\item{value}{The name of the value we want. The list given in the +usage section is not exclusive} + +\item{aggregator}{The aggregator function. Can be mean, +\code{\link{geomean}}, or identity, for example.} + +\item{raw}{Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?} + +\item{signif}{How many significant digits do we want} + +\item{values}{The values to be returned} + +\item{aggregators}{A named vector of aggregator functions to be used} +} +\value{ +The result from applying the aggregator function to + the values converted to a numeric vector, rounded to the + given number of significant digits, or, if raw = TRUE, + the values as a character value, retaining any implicit + information on precision that may be present. +} +\description{ +R6 class objects of class chent represent chemical entities +and can hold a list of information loaded from a chemical yaml file in their +chyaml field. Such information is extracted and optionally aggregated by +this function. +} +\details{ +The functions \code{soil_*} are functions to extract soil specific endpoints. +For the Freundlich exponent, the capital letter \code{N} is used in order to +facilitate dealing with such data in R. In pesticide fate modelling, this +exponent is often called 1/n. +} + diff --git a/man/geomean.Rd b/man/geomean.Rd new file mode 100644 index 0000000..ed82294 --- /dev/null +++ b/man/geomean.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/geomean.R +\name{geomean} +\alias{geomean} +\title{Calculate the geometric mean} +\usage{ +geomean(x, na.rm = TRUE) +} +\arguments{ +\item{x}{Vector of numbers} + +\item{na.rm}{Should NA values be omitted?} +} +\value{ +The geometric mean +} +\description{ +Based on some posts in a thread on Stackoverflow +\url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in} +This function checks for negative values, removes NA values per default and +returns 0 if at least one element of the vector is 0. +} +\examples{ +geomean(c(1, 3, 9)) +geomean(c(1, 3, NA, 9)) +\dontrun{geomean(c(1, -3, 9)) # returns an error} +} +\author{ +Johannes Ranke +} + diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd new file mode 100644 index 0000000..9ab1d0a --- /dev/null +++ b/man/pfm_degradation.Rd @@ -0,0 +1,35 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pfm_degradation.R +\name{pfm_degradation} +\alias{pfm_degradation} +\title{Calculate a time course of relative concentrations based on an mkinmod model} +\usage{ +pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = + log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = + step_days)) +} +\arguments{ +\item{model}{The degradation model to be used. Either a parent only model like +'SFO' or 'FOMC', or an mkinmod object} + +\item{DT50}{The half-life. This is only used when simple exponential decline +is calculated (SFO model).} + +\item{parms}{The parameters used for the degradation model} + +\item{years}{For how many years should the degradation be predicted?} + +\item{step_days}{What step size in days should the output have?} + +\item{times}{The output times} +} +\description{ +Calculate a time course of relative concentrations based on an mkinmod model +} +\examples{ +head(pfm_degradation("SFO", DT50 = 10)) +} +\author{ +Johannes Ranke +} + diff --git a/man/plot.TOXSWA_cwa.Rd b/man/plot.TOXSWA_cwa.Rd new file mode 100644 index 0000000..b5f0163 --- /dev/null +++ b/man/plot.TOXSWA_cwa.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/TOXSWA_cwa.R +\name{plot.TOXSWA_cwa} +\alias{plot.TOXSWA_cwa} +\title{Plot TOXSWA surface water concentrations} +\usage{ +\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t", "t_firstjan", + "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE, + total = FALSE, LC_TIME = "C", ...) +} +\arguments{ +\item{x}{The TOXSWA_cwa object to be plotted.} + +\item{time_column}{What should be used for the time axis. If "t_firstjan" is chosen, +the time is given in days relative to the first of January in the first year.} + +\item{xlab, ylab}{Labels for x and y axis.} + +\item{add}{Should we add to an existing plot?} + +\item{total}{Should the total concentration in water be plotted, including substance sorbed +to suspended matter?} + +\item{LC_TIME}{Specification of the locale used to format dates} + +\item{...}{Further arguments passed to \code{plot} if we are not adding to an existing plot} +} +\description{ +Plot TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body. +} +\examples{ +H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", + basedir = "SwashProjects/project_H_sw/TOXSWA", + zipfile = system.file("testdata/SwashProjects.zip", + package = "pfm")) +plot(H_sw_D4_pond) +} +\author{ +Johannes Ranke +} + diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd new file mode 100644 index 0000000..84ef3da --- /dev/null +++ b/man/read.TOXSWA_cwa.Rd @@ -0,0 +1,56 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/TOXSWA_cwa.R +\name{read.TOXSWA_cwa} +\alias{read.TOXSWA_cwa} +\title{Read TOXSWA surface water concentrations} +\usage{ +read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", + substance = "parent", total = FALSE, windows = NULL, + thresholds = NULL) +} +\arguments{ +\item{filename}{The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).} + +\item{basedir}{The path to the directory where the cwa file resides.} + +\item{zipfile}{Optional path to a zip file containing the cwa file.} + +\item{segment}{The segment for which the data should be read. Either "last", or +the segment number.} + +\item{substance}{For TOXSWA 4 .out files, the default value "parent" leads +to reading concentrations of the parent compound. Alternatively, the substance +of interested can be selected by its code name.} + +\item{total}{Set this to TRUE in order to read total concentrations as well. This is +only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa +files. For .cwa files, the total concentration is always read as well.} + +\item{windows}{Numeric vector of width of moving windows in days, for calculating +maximum time weighted average concentrations and areas under the curve.} + +\item{thresholds}{Numeric vector of threshold concentrations in µg/L for +generating event statistics.} +} +\value{ +An instance of an R6 object of class +\code{\link{TOXSWA_cwa}}. +} +\description{ +Read TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body. Per default, the data for the last +segment are imported. As TOXSWA 4 reports the values at the end of the hour +(ConLiqWatLayCur) in its summary file, we use this value as well instead +of the hourly averages (ConLiqWatLay). +} +\examples{ +H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", + basedir = "SwashProjects/project_H_sw/TOXSWA", + zipfile = system.file("testdata/SwashProjects.zip", + package = "pfm")) +} +\author{ +Johannes Ranke +} + diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd new file mode 100644 index 0000000..b45af4a --- /dev/null +++ b/man/soil_scenario_data_EFSA_2015.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/soil_scenario_data_EFSA_2015.R +\docType{data} +\name{soil_scenario_data_EFSA_2015} +\alias{soil_scenario_data_EFSA_2015} +\title{Properties of the predefined scenarios from the EFSA guidance from 2015} +\format{A data frame with one row for each scenario. Row names are the scenario codes, + e.g. CTN for the Northern scenario for the total concentration in soil. Columns are + mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.} +\source{ +EFSA (European Food Safety Authority) (2015) +EFSA guidance document for predicting environmental concentrations +of active substances of plant protection products and transformation products of these +active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 +doi:10.2903/j.efsa.2015.4093 +} +\description{ +Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the +scenario and model adjustment factors from p. 15 and p. 17 are included. +} +\examples{ +\dontrun{ + # This is the code that was used to define the data + soil_scenario_data_EFSA_2015 <- data.frame( + Zone = rep(c("North", "Central", "South"), 2), + Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), + T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), + T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), + Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), + f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), + theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), + rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), + f_sce = c(3, 2, 2, 2, 1.5, 1.5), + f_mod = c(2, 2, 2, 4, 4, 4), + stringsAsFactors = FALSE, + row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") + ) + save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') +} + +# And this is the resulting dataframe +soil_scenario_data_EFSA_2015 +} +\keyword{datasets} + diff --git a/pkg/.Rbuildignore b/pkg/.Rbuildignore deleted file mode 100644 index c48d8e3..0000000 --- a/pkg/.Rbuildignore +++ /dev/null @@ -1,3 +0,0 @@ -inst/testdata/SwashProjects/project_H_sw/MACRO/*/*.bin -inst/testdata/Swash/ -inst/extdata/Tabelle\ der\ Abdrifteckwerte.xls diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION deleted file mode 100644 index f9de23c..0000000 --- a/pkg/DESCRIPTION +++ /dev/null @@ -1,25 +0,0 @@ -Package: pfm -Type: Package -Title: Utilities for Pesticide Fate Modelling -Version: 0.3-8 -Date: 2016-09-26 -Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", - role = c("aut", "cre", "cph")) -Description: Utilities for simple calculations of predicted environmental - concentrations (PECs) and for dealing with data from some FOCUS pesticide - fate modelling software packages. -Depends: - R6, - mkin -Imports: - graphics, - readr, - methods -Suggests: - testthat, - chents -License: GPL -LazyLoad: yes -LazyData: yes -Encoding: UTF-8 -RoxygenNote: 5.0.1 diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE deleted file mode 100644 index 572ec80..0000000 --- a/pkg/NAMESPACE +++ /dev/null @@ -1,29 +0,0 @@ -# Generated by roxygen2: do not edit by hand - -S3method(GUS,chent) -S3method(GUS,numeric) -S3method(plot,TOXSWA_cwa) -S3method(print,GUS_result) -export(GUS) -export(PEC_soil) -export(PEC_sw_drainage_UK) -export(PEC_sw_drift) -export(PEC_sw_sed) -export(SFO_actual_twa) -export(SSLRC_mobility_classification) -export(TOXSWA_cwa) -export(endpoint) -export(geomean) -export(pfm_degradation) -export(read.TOXSWA_cwa) -export(soil_DT50) -export(soil_Kfoc) -export(soil_N) -export(soil_sorption) -import(chents) -import(graphics) -import(mkin) -importFrom(R6,R6Class) -importFrom(methods,is) -importFrom(readr,fwf_empty) -importFrom(readr,read_fwf) diff --git a/pkg/R/FOCUS_GW_scenarios_2012.R b/pkg/R/FOCUS_GW_scenarios_2012.R deleted file mode 100644 index 49cf7dd..0000000 --- a/pkg/R/FOCUS_GW_scenarios_2012.R +++ /dev/null @@ -1,11 +0,0 @@ -#' A very small subset of the FOCUS Groundwater scenario defitions -#' -#' Currently, only a small subset of the soil definitions are provided. -#' -#' @name FOCUS_GW_scenarios_2012 -#' @references FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. -#' FOrum for the Co-ordination of pesticde fate models and their USe. -#' http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf -#' @examples -#' FOCUS_GW_scenarios_2012 -NULL diff --git a/pkg/R/GUS.R b/pkg/R/GUS.R deleted file mode 100644 index 4a6532d..0000000 --- a/pkg/R/GUS.R +++ /dev/null @@ -1,98 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Groundwater ubiquity score based on Gustafson (1989) -#' -#' The groundwater ubiquity score GUS is calculated according to -#' the following equation -#' \deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)} -#' -#' @references Gustafson, David I. (1989) Groundwater ubiquity score: a simple -#' method for assessing pesticide leachability. \emph{Environmental -#' toxicology and chemistry} \bold{8}(4) 339–57. -#' @inheritParams endpoint -#' @param DT50 Half-life of the chemical in soil. Should be a field -#' half-life according to Gustafson (1989). However, leaching to the sub-soil -#' can not completely be excluded in field dissipation experiments and Gustafson -#' did not refer to any normalisation procedure, but says the field study should -#' be conducted under use conditions. -#' @param Koc The sorption constant normalised to organic carbon. Gustafson -#' does not mention the nonlinearity of the sorption constant commonly -#' found and usually described by Freundlich sorption, therefore it is -#' unclear at which reference concentration the Koc should be observed -#' (and if the reference concentration would be in soil or in porewater). -#' @param chent If a chent is given with appropriate information present in its -#' chyaml field, this information is used, with defaults specified below. -#' @param degradation_value Which of the available degradation values should -#' be used? -#' @param lab_field Should laboratory or field half-lives be used? This -#' defaults to lab in this implementation, in order to avoid -#' double-accounting for mobility. If comparability with the original GUS -#' values given by Gustafson (1989) is desired, non-normalised first-order -#' field half-lives obtained under actual use conditions should be used. -#' @param redox Aerobic or anaerobic degradation data -#' @param sorption_value Which of the available sorption values should be used? -#' Defaults to Kfoc as this is what is generally available from the European -#' pesticide peer review process. These values generally use a reference -#' concentration of 1 mg/L in porewater, that means they would be expected to -#' be Koc values at a concentration of 1 mg/L in the water phase. -#' @param degradation_aggregator Function for aggregating half-lives -#' @param sorption_aggregator Function for aggregation Koc values -#' @param ... Included in the generic to allow for further arguments later. Therefore -#' this also had to be added to the specific methods. -#' @return A list with the DT50 and Koc used as well as the resulting score -#' of class GUS_result -#' @author Johannes Ranke -#' @export -GUS <- function(...) UseMethod("GUS") - -#' @rdname GUS -#' @export -GUS.numeric <- function(DT50, Koc, ...) { - score <- log10(DT50) * (4 - log10(Koc)) - res <- list(DT50 = DT50, Koc = Koc, score = score) - class(res) <- "GUS_result" - return(res) -} - -#' @rdname GUS -#' @export -GUS.chent <- function(chent, - degradation_value = "DT50ref", - lab_field = "laboratory", - redox = "aerobic", - sorption_value = "Kfoc", - degradation_aggregator = geomean, - sorption_aggregator = geomean, - ...) -{ - DT50 = soil_DT50(chent, lab_field = lab_field, redox = redox, - value = degradation_value, - aggregator = degradation_aggregator, signif = 5) - Koc = soil_Kfoc(chent, value = sorption_value, - aggregator = sorption_aggregator, signif = 5) - GUS.numeric(DT50, Koc) -} - -#' @rdname GUS -#' @export -#' @param x An object of class GUS_result to be printed -#' @param digits The number of digits used in the print method -print.GUS_result = function(x, ..., digits = 1) { - cat("GUS: ", round(x$score, digits = 1), "\n") - cat("calculated from DT50 ", x$DT50, " and Koc ", x$Koc, "\n") -} diff --git a/pkg/R/PEC_soil.R b/pkg/R/PEC_soil.R deleted file mode 100644 index 0263e47..0000000 --- a/pkg/R/PEC_soil.R +++ /dev/null @@ -1,215 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -# Register global variables -if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_type", "TP_identifier", - "soil_scenario_data_EFSA_2015")) - -#' Calculate predicted environmental concentrations in soil -#' -#' This is a basic calculation of a contaminant concentration in bulk soil -#' based on complete, instantaneous mixing. If an interval is given, an -#' attempt is made at calculating a long term maximum concentration using -#' the concepts layed out for example in the PPR panel opinion (EFSA 2012). -#' -#' This assumes that the complete load to soil during the time specified by -#' 'interval' (typically 365 days) is dosed at once. As in the PPR panel -#' opinion cited below (PPR panel 2012), only temperature correction using the -#' Arrhenius equation is performed. -#' -#' Total soil and porewater PEC values for the scenarios as defined in the EFSA -#' guidance (2015, p. 13) can easily be calculated. -#' -#' @note If temperature information is available in the selected scenarios, as -#' e.g. in the EFSA scenarios, the DT50 for groundwater modelling -#' (destination 'PECgw') is taken from the chent object, otherwise the DT50 -#' with destination 'PECsoil'. -#' @importFrom methods is -#' @param rate Application rate in units specified below -#' @param rate_units Defaults to g/ha -#' @param interception The fraction of the application rate that does not reach the soil -#' @param mixing_depth Mixing depth in cm -#' @param interval Period of the deeper mixing, defaults to 365, which is a year if -#' rate units are in days -#' @param n_periods Number of periods to be considered for long term PEC calculations -#' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported -#' @param PEC_pw_units Only mg/L currently supported -#' @param tillage_depth Periodic (see interval) deeper mixing in cm -#' @param chent An optional chent object holding substance specific information. Can -#' also be a name for the substance as a character string -#' @param DT50 If specified, overrides soil DT50 endpoints from a chent object -#' If DT50 is not specified here and not available from the chent object, zero -#' degradation is assumed -#' @param Koc If specified, overrides Koc endpoints from a chent object -#' @param Kom Calculated from Koc by default, but can explicitly be specified -#' as Kom here -#' @param t_avg Averaging times for time weighted average concentrations -#' @param scenarios If this is 'default', the DT50 will be used without correction -#' and soil properties as specified in the REACH guidance (R.16, Table -#' R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", -#' the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -#' 'chents' is specified, the DegT50 with destination 'PECgw' will be used), -#' and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -#' model and scenario adjustment factors from the EFSA guidance are used. -#' @param porewater Should equilibrium porewater concentrations be estimated -#' based on Kom and the organic carbon fraction of the soil instead of total -#' soil concentrations? Based on equation (7) given in the PPR panel opinion -#' (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -#' p. 13). -#' @return The predicted concentration in soil -#' @references EFSA Panel on Plant Protection Products and their Residues (2012) -#' Scientific Opinion on the science behind the guidance for scenario -#' selection and scenario parameterisation for predicting environmental -#' concentrations of plant protection products in soil. \emph{EFSA Journal} -#' \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562 -#' -#' EFSA (European Food Safety Authority) (2015) EFSA guidance document for -#' predicting environmental concentrations of active substances of plant -#' protection products and transformation products of these active substances -#' in soil. \emph{EFSA Journal} \bold{13}(4) 4093 -#' doi:10.2903/j.efsa.2015.4093 -#' @author Johannes Ranke -#' @export -#' @examples -#' PEC_soil(100, interception = 0.25) -#' -#' # This is example 1 starting at p. 79 of the EFSA guidance (2015) -#' PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), -#' scenarios = "EFSA_2015") -#' PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), -#' Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) -#' -#' # The following is from example 4 starting at p. 85 of the EFSA guidance (2015) -#' # Metabolite M2 -#' # Calculate total and porewater soil concentrations for tier 1 scenarios -#' # Relative molar mass is 100/300, formation fraction is 0.7 * 1 -#' results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), -#' scenarios = "EFSA_2015") -#' results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), -#' Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) - -PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, - mixing_depth = 5, - PEC_units = "mg/kg", PEC_pw_units = "mg/L", - interval = NA, n_periods = Inf, - tillage_depth = 20, - chent = NA, - DT50 = NA, - Koc = NA, Kom = Koc / 1.724, - t_avg = 0, - scenarios = c("default", "EFSA_2015"), - porewater = FALSE) -{ - rate_to_soil = (1 - interception) * rate - rate_units = match.arg(rate_units) - PEC_units = match.arg(PEC_units) - scenarios = match.arg(scenarios) - sce <- switch(scenarios, - default = data.frame(rho = 1.5, T_arr = NA, theta_fc = 0.2, f_oc = 0.02, - f_sce = 1, f_mod = 1, row.names = "default"), - EFSA_2015 = if (porewater) soil_scenario_data_EFSA_2015[4:6, ] - else soil_scenario_data_EFSA_2015[1:3, ] - ) - n_sce = nrow(sce) - - soil_volume = 100 * 100 * (mixing_depth/100) # in m3 - soil_mass = soil_volume * sce$rho * 1000 # in kg - - # The following is C_T,ini from EFSA 2012, p. 22, but potentially with interception > 0 - PEC_soil_ini = rate_to_soil * 1000 / soil_mass # in mg/kg - - # Decide which DT50 to take, or set degradation to zero if no DT50 available - if (is.na(DT50) & is(chent, "chent")) { - if (all(is.na(sce$T_arr))) { # No temperature correction - DT50 <- subset(chent$soil_degradation_endpoints, destination == "PECsoil")$DT50 - } else { - DT50 <- subset(chent$soil_degradation_endpoints, destination == "PECgw")$DT50 - } - if (length(DT50) > 1) stop("More than one PECsoil DT50 in chent object") - if (length(DT50) == 0) DT50 <- Inf - } - k = log(2)/DT50 - - # Temperature correction of degradation (accumulation) - if (all(is.na(sce$T_arr))) { # No temperature correction - f_T = 1 - } else { - # Temperature correction as in EFSA 2012 p. 23 - f_T = ifelse(sce$T_arr == 0, - 0, - exp(- (65.4 / 0.008314) * (1/(sce$T_arr + 273.15) - 1/293.15))) - } - - # X is the fraction left after one period (EFSA guidance p. 23) - X = exp(- k * f_T * interval) - - # f_accu is the fraction left after n periods (X + X^2 + ...) - f_accu = 0 - if (!is.na(interval)) { - if (n_periods == Inf) { - f_accu = X/(1 - X) - } else { - for (i in 1:n_periods) { - f_accu = f_accu + X^i - } - } - } - - f_tillage = mixing_depth / tillage_depth - - PEC_background = f_accu * f_tillage * PEC_soil_ini - - PEC_soil = (1 + f_accu * f_tillage) * PEC_soil_ini - - # Get porewater PEC if requested - if (porewater) { - - # If Kom is not specified, try to get K(f)oc - if (is.na(Kom)) { - # If Koc not specified, try to get K(f)oc from chent - if (is.na(Koc) & is(chent, "chent")) { - Koc <- soil_Kfoc(chent) - } - Kom <- Koc / 1.724 - } - - if (is.na(Kom)) stop("No Kom information specified") - - PEC_soil = PEC_soil/((sce$theta_fc/sce$rho) + sce$f_om * Kom) - } - - # Scenario adjustment factors - PEC_soil_sce = PEC_soil * sce$f_sce - - # Model adjustment factors - PEC_soil_sce_mod = PEC_soil_sce * sce$f_mod - - result <- matrix(NA, ncol = n_sce, nrow = length(t_avg), - dimnames = list(t_avg = t_avg, scenario = rownames(sce))) - - result[1, ] <- PEC_soil_sce_mod - - for (i in seq_along(t_avg)) { - t_av_i <- t_avg[i] - if (t_av_i > 0) { - # Equation 10 from p. 24 (EFSA 2015) - result[i, ] <- PEC_soil_sce_mod/(t_av_i * f_T * k) * (1 - exp(- f_T * k * t_av_i)) - } - } - - return(result) -} diff --git a/pkg/R/PEC_sw_drainage_UK.R b/pkg/R/PEC_sw_drainage_UK.R deleted file mode 100644 index e53f179..0000000 --- a/pkg/R/PEC_sw_drainage_UK.R +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method -#' -#' This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -#' published on the CRC website -#' -#' @param rate Application rate in g/ha -#' @param interception The fraction of the application rate that does not reach the soil -#' @param Koc The sorption coefficient normalised to organic carbon in L/kg -#' @param latest_application Latest application date, formatted as e.g. "01 July" -#' @param soil_DT50 Soil degradation half-life, if SFO kinetics are to be used -#' @param model The soil degradation model to be used. Either one of "FOMC", -#' "DFOP", "HS", or "IORE", or an mkinmod object -#' @param model_parms A named numeric vector containing the model parameters -#' @return The predicted concentration in surface water in µg/L -#' @export -#' @author Johannes Ranke -#' @examples -#' PEC_sw_drainage_UK(150, Koc = 100) -PEC_sw_drainage_UK <- function(rate, interception = 0, Koc, - latest_application = NULL, soil_DT50 = NULL, - model = NULL, model_parms = NULL) -{ - percentage_lost <- SSLRC_mobility_classification(Koc)[[2]] - amount_available <- rate * (1 - interception) # g/ha - - if (!missing(latest_application)) { - lct <- Sys.getlocale("LC_TIME") - tmp <- Sys.setlocale("LC_TIME", "C") - latest <- as.Date(paste(latest_application, "1999"), "%d %b %Y") - tmp <- Sys.setlocale("LC_TIME", lct) - degradation_time <- as.numeric(difftime(as.Date("1999-10-01"), units = "days", latest)) - if (!missing(soil_DT50)) { - k = log(2)/soil_DT50 - as.Date(paste(latest_application, "1999"), "%d %B %Y") - - amount_available <- amount_available * exp(-k * degradation_time) - if (!missing(model)) stop("You already supplied a soil_DT50 value, implying SFO kinetics") - } - if (!missing(model)) { - fraction_left <- pfm_degradation(model, parms = model_parms, - times = degradation_time)[1, "parent"] - amount_available <- fraction_left * amount_available - } - } - - volume = 130000 # L/ha - PEC = 1e6 * (percentage_lost/100) * amount_available / volume - return(PEC) -} diff --git a/pkg/R/PEC_sw_drift.R b/pkg/R/PEC_sw_drift.R deleted file mode 100644 index 261706c..0000000 --- a/pkg/R/PEC_sw_drift.R +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate predicted environmental concentrations in surface water due to drift -#' -#' This is a basic, vectorised form of a simple calculation of a contaminant -#' concentration in surface water based on complete, instantaneous mixing -#' with input via spray drift. -#' -#' @param rate Application rate in units specified below -#' @param applications Number of applications for selection of drift percentile -#' @param drift_percentages Percentage drift values for which to calculate PECsw. -#' 'drift_data' and 'distances' if not NULL. -#' @param drift_data Source of drift percentage data -#' @param crop Crop name (use German names for JKI data), defaults to "Ackerbau" -#' @param distances The distances in m for which to get PEC values -#' @param water_depth Depth of the water body in cm -#' @param rate_units Defaults to g/ha -#' @param PEC_units Requested units for the calculated PEC. Only µg/L currently supported -#' @return The predicted concentration in surface water -#' @export -#' @author Johannes Ranke -#' @examples -#' PEC_sw_drift(100) -PEC_sw_drift <- function(rate, - applications = 1, - water_depth = 30, - drift_percentages = NULL, - drift_data = "JKI", - crop = "Ackerbau", - distances = c(1, 5, 10, 20), - rate_units = "g/ha", - PEC_units = "\u00B5g/L") -{ - rate_units <- match.arg(rate_units) - PEC_units <- match.arg(PEC_units) - drift_data <- match.arg(drift_data) - water_volume <- 100 * 100 * (water_depth/100) * 1000 # in L (for 1 ha) - PEC_sw_overspray <- rate * 1e6 / water_volume # in µg/L - dist_index <- as.character(distances) - - if (is.null(drift_percentages)) { - drift_percentages <- pfm::drift_data_JKI[[applications]][dist_index, crop] - names(drift_percentages) <- paste(dist_index, "m") - } else { - names(drift_percentages) <- paste(drift_percentages, "%") - } - - PEC_sw_drift <- PEC_sw_overspray * drift_percentages / 100 - return(PEC_sw_drift) -} diff --git a/pkg/R/PEC_sw_sed.R b/pkg/R/PEC_sw_sed.R deleted file mode 100644 index a4a3d6a..0000000 --- a/pkg/R/PEC_sw_sed.R +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate predicted environmental concentrations in sediment from surface -#' water concentrations -#' -#' The method 'percentage' is equivalent to what is used in the CRD spreadsheet -#' PEC calculator -#' -#' @param PEC_sw Numeric vector or matrix of surface water concentrations in µg/L for -#' which the corresponding sediment concentration is to be estimated -#' @param percentage The percentage in sediment, used for the percentage method -#' @param method The method used for the calculation -#' @param sediment_depth Depth of the sediment layer -#' @param water_depth Depth of the water body in cm -#' @param sediment_density The density of the sediment in L/kg (equivalent to -#' g/cm3) -#' @param PEC_sed_units The units of the estimated sediment PEC value -#' @return The predicted concentration in sediment -#' @export -#' @author Johannes Ranke -#' @examples -#' PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) -PEC_sw_sed <- function(PEC_sw, percentage = 100, method = "percentage", - sediment_depth = 5, water_depth = 30, - sediment_density = 1.3, - PEC_sed_units = c("\u00B5g/kg", "mg/kg")) -{ - method = match.arg(method) - PEC_sed_units = match.arg(PEC_sed_units) - if (method == "percentage") { - PEC_sed = PEC_sw * (percentage/100) * (water_depth / sediment_depth) * (1 / sediment_density) - if (PEC_sed_units == "mg/kg") PEC_sed <- PEC_sed / 1000 - } - return(PEC_sed) -} diff --git a/pkg/R/SFO_actual_twa.R b/pkg/R/SFO_actual_twa.R deleted file mode 100644 index 7facb6a..0000000 --- a/pkg/R/SFO_actual_twa.R +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Actual and maximum moving window time average concentrations for SFO kinetics -#' -#' @param DT50 The half-life. -#' @param times The output times, and window sizes for time weighted average concentrations -#' @export -#' @author Johannes Ranke -#' @source FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation -#' Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, -#' 18 December 2014, p. 251 -#' @examples -#' SFO_actual_twa(10) -SFO_actual_twa <- function(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100)) -{ - k = log(2)/DT50 - result <- data.frame(actual = 1 * exp(-k * times), - twa = (1 - exp(-k * times))/(k * times), - row.names = times) - return(result) -} diff --git a/pkg/R/SSLRC_mobility_classification.R b/pkg/R/SSLRC_mobility_classification.R deleted file mode 100644 index deda5cf..0000000 --- a/pkg/R/SSLRC_mobility_classification.R +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Determine the SSLRC mobility classification for a chemical substance from its Koc -#' -#' This implements the method specified in the UK data requirements handbook and was -#' checked against the spreadsheet published on the CRC website -#' -#' @param Koc The sorption coefficient normalised to organic carbon in L/kg -#' @return A list containing the classification and the percentage of the -#' compound transported per 10 mm drain water -#' @export -#' @author Johannes Ranke -#' @examples -#' SSLRC_mobility_classification(100) -SSLRC_mobility_classification <- function(Koc) -{ - if (!is.numeric(Koc) | length(Koc) != 1) stop("Please give a single number") - result <- list("Non mobile", 0.01) - if (Koc < 4000) result <- list("Slightly mobile", 0.02) - if (Koc < 1000) result <- list("Slightly mobile", 0.5) - if (Koc < 500) result <- list("Moderately mobile", 0.7) - if (Koc < 75) result <- list("Mobile", 1.9) - if (Koc < 15) result <- list("Very mobile", 1.9) - names(result) <- c("Mobility classification", - "Percentage drained per mm of drain water") - return(result) -} diff --git a/pkg/R/TOXSWA_cwa.R b/pkg/R/TOXSWA_cwa.R deleted file mode 100644 index c5ddce9..0000000 --- a/pkg/R/TOXSWA_cwa.R +++ /dev/null @@ -1,380 +0,0 @@ -# Copyright (C) 2014,2015,2016 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Read TOXSWA surface water concentrations -#' -#' Read TOXSWA hourly concentrations of a chemical substance in a specific -#' segment of a TOXSWA surface water body. Per default, the data for the last -#' segment are imported. As TOXSWA 4 reports the values at the end of the hour -#' (ConLiqWatLayCur) in its summary file, we use this value as well instead -#' of the hourly averages (ConLiqWatLay). -#' -#' @param filename The filename of the cwa file (TOXSWA 2.x.y or similar) or the -#' out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar). -#' @param basedir The path to the directory where the cwa file resides. -#' @param zipfile Optional path to a zip file containing the cwa file. -#' @param segment The segment for which the data should be read. Either "last", or -#' the segment number. -#' @param total Set this to TRUE in order to read total concentrations as well. This is -#' only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -#' files. For .cwa files, the total concentration is always read as well. -#' @param substance For TOXSWA 4 .out files, the default value "parent" leads -#' to reading concentrations of the parent compound. Alternatively, the substance -#' of interested can be selected by its code name. -#' @param windows Numeric vector of width of moving windows in days, for calculating -#' maximum time weighted average concentrations and areas under the curve. -#' @param thresholds Numeric vector of threshold concentrations in µg/L for -#' generating event statistics. -#' @importFrom readr read_fwf fwf_empty -#' @return An instance of an R6 object of class -#' \code{\link{TOXSWA_cwa}}. -#' @export -#' @author Johannes Ranke -#' @examples -#' H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", -#' basedir = "SwashProjects/project_H_sw/TOXSWA", -#' zipfile = system.file("testdata/SwashProjects.zip", -#' package = "pfm")) -read.TOXSWA_cwa <- function(filename, basedir = ".", zipfile = NULL, - segment = "last", substance = "parent", - total = FALSE, - windows = NULL, thresholds = NULL) -{ - if (!missing(filename)) { - cwa <- TOXSWA_cwa$new(filename, basedir, zipfile, - substance = substance, total = total) - if (!is.null(windows[1])) cwa$moving_windows(windows) - if (!is.null(thresholds[1])) cwa$get_events(thresholds) - invisible(cwa) - } else { - message("You need to specify a filename for the cwa file to be read") - } -} - -#' Plot TOXSWA surface water concentrations -#' -#' Plot TOXSWA hourly concentrations of a chemical substance in a specific -#' segment of a TOXSWA surface water body. -#' -#' @import graphics -#' @param x The TOXSWA_cwa object to be plotted. -#' @param xlab,ylab Labels for x and y axis. -#' @param time_column What should be used for the time axis. If "t_firstjan" is chosen, -#' the time is given in days relative to the first of January in the first year. -#' @param add Should we add to an existing plot? -#' @param total Should the total concentration in water be plotted, including substance sorbed -#' to suspended matter? -#' @param LC_TIME Specification of the locale used to format dates -#' @param ... Further arguments passed to \code{plot} if we are not adding to an existing plot -#' @export -#' @author Johannes Ranke -#' @examples -#' H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", -#' basedir = "SwashProjects/project_H_sw/TOXSWA", -#' zipfile = system.file("testdata/SwashProjects.zip", -#' package = "pfm")) -#' plot(H_sw_D4_pond) -plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"), - xlab = "default", ylab = "default", - add = FALSE, - total = FALSE, LC_TIME = "C", ...) -{ - time_column = match.arg(time_column) - cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L") - lct <- Sys.getlocale("LC_TIME") - tmp <- Sys.setlocale("LC_TIME", LC_TIME) - if (xlab == "default") { - xlab = switch(time_column, - datetime = "Time", - t = "Time [days]", - t_firstjan = "Time since first of January [days]", - t_rel_to_max = "Time relative to maximum concentration [days]") - } - if (ylab == "default") { - ylab = paste( ifelse(total, "Total concentration", "Concentration"), "[\u03bcg/L]") - } - if (add) { - lines(x$cwas[c(time_column, cwa_column)], xlab = xlab, ylab = ylab, ...) - } else{ - if (time_column == "datetime") { - plot(x$cwas$datetime, x$cwas[[cwa_column]], type = "l", - xlab = xlab, ylab = ylab, xaxt = "n", ...) - seq_x <- seq(min(x$cwas$datetime), max(x$cwas$datetime), by = "quarter") - axis(1, at = seq_x, labels = format(seq_x, "%b %Y")) - } else { - plot(x$cwas[c(time_column, cwa_column)], type = "l", - xlab = xlab, ylab = ylab, ...) - } - } - tmp <- Sys.setlocale("LC_TIME", lct) -} - -#' R6 class for holding TOXSWA cwa concentration data and associated statistics -#' -#' An R6 class for holding TOXSWA cwa concentration data and some associated statistics. -#' Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. -#' -#' @docType class -#' @importFrom R6 R6Class -#' @export -#' @format An \code{\link{R6Class}} generator object. -#' @field filename Length one character vector. -#' @field basedir Length one character vector. -#' @field segment Length one integer, specifying for which segment the cwa data were read. -#' @field cwas Dataframe holding the concentrations. -#' @field events List of dataframes holding the event statistics for each threshold. -#' @field windows Matrix of maximum time weighted average concentrations (TWAC_max) -#' and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) -#' for the requested moving window sizes in days. -#' @section Methods: -#' \describe{ -#' \item{\code{get_events(threshold, total = FALSE)}}{ -#' Populate a datataframe with event information for the specified threshold value -#' in µg/L. If \code{total = TRUE}, the total concentration including the amount -#' adsorbed to suspended matter will be used. The resulting dataframe is stored in the -#' \code{events} field of the object. -#' } -#' \item{\code{moving_windows(windows, total = FALSE)}}{ -#' Add to the \code{windows} field described above. -#' Again, if \code{total = TRUE}, the total concentration including the amount -#' adsorbed to suspended matter will be used. -#' } -#' } -#' @examples -#' H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", -#' basedir = "SwashProjects/project_H_sw/TOXSWA", -#' zipfile = system.file("testdata/SwashProjects.zip", -#' package = "pfm")) -#' H_sw_R1_stream$get_events(c(2, 10)) -#' H_sw_R1_stream$moving_windows(c(7, 21)) -#' print(H_sw_R1_stream) -#' @keywords data - -TOXSWA_cwa <- R6Class("TOXSWA_cwa", - public = list( - filename = NULL, - basedir = NULL, - zipfile = NULL, - segment = NULL, - substance = NULL, - cwas = NULL, - windows = NULL, - events = list(), - initialize = function(filename, basedir, zipfile = NULL, - segment = "last", substance = "parent", total = FALSE) { - self$filename <- filename - self$basedir <- basedir - self$zipfile <- zipfile - if (!is.null(zipfile)) { - try(file_connection <- unz(zipfile, paste0(basedir, "/", filename))) - } else { - try(file_connection <- file(file.path(basedir, filename), "rt")) - } - - - if (grepl(".cwa$", filename)) { - # cwa file from FOCUS TOXSWA 3 (TOXSWA 2.x.y) - cwa_all_segments <- try( - read.table(file_connection, - sep = "", skip = 40, - encoding = "UTF-8", - colClasses = c("character", "numeric", - "integer", rep("numeric", 5)), - col.names = c("datetime", "t", "segment", - "xcd", "cwa_tot", "cwa", "Xss", "Xmp"))) - - if (is.null(zipfile)) close(file_connection) # only needed for files - - if (!inherits(cwa_all_segments, "try-error")) { - available_segments = 1:max(cwa_all_segments$segment) - if (segment == "last") segment = max(available_segments) - if (!segment %in% available_segments) stop("Invalid segment specified") - self$segment <- segment - cwa <- subset(cwa_all_segments, segment == self$segment, - c("datetime", "t", "segment", "cwa", "cwa_tot")) - lct <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C") - cwa$datetime <- strptime(cwa$datetime, "%d-%b-%Y-%H:%M") - Sys.setlocale("LC_TIME", lct) - startyear = format(cwa$datetime[1], "%Y") - firstjan <- strptime(paste0(startyear, "-01-01"), "%Y-%m-%d") - cwa$t_firstjan <- as.numeric(difftime(cwa$datetime, - firstjan, units = "days")) - - t_max = cwa[which.max(cwa$cwa), "t"] - cwa$t_rel_to_max = cwa$t - t_max - cwa$cwa_mug_per_L <- cwa$cwa * 1000 - cwa$cwa_tot_mug_per_L <- cwa$cwa_tot * 1000 - self$cwas <- cwa[c("datetime", "t", "t_firstjan", - "t_rel_to_max", - "cwa_mug_per_L", - "cwa_tot_mug_per_L")] - } else { - stop("Could not read ", filename) - } - } else { - # out file from FOCUS TOXSWA 4 (TOXSWA 4.4.2 or similar) - outfile <- try(readLines(file_connection)) - - close(file_connection) # only needed for files - - if (inherits(outfile, "try-error")) { - stop("Could not read ", filename) - } else { - # Get the substance name(s) - sub_lines <- grep(".*0.000.*ConLiqWatLayCur_", outfile[1:50], value = TRUE) - substances <- gsub(".*ConLiqWatLayCur_(.*?) *[0-9].*", "\\1", sub_lines) - if (!substance %in% c("parent", substances)) { - stop("No data for substance ", substance, " present in the .out file.") - } - - # Generate field name for the concentrations at end of hour for the - # substance of interest - if (substance == "parent") { - cwa_string = paste0("ConLiqWatLayCur_", substances[1]) - } else { - cwa_string = paste0("ConLiqWatLayCur_", substance) - } - - cwa_lines <- grep(cwa_string, outfile, value = TRUE) - - cwa_all_segments <- read_fwf(paste(cwa_lines, collapse = "\n"), - fwf_empty(paste(tail(cwa_lines), collapse = "\n"))) - - # Append time "-00h00" to datetime in first row, as this is not (always?) present - # in the line ConLiqWatLayCur - if (nchar(cwa_all_segments[1, "X2"]) == 11) { - cwa_all_segments[1, "X2"] = paste0(cwa_all_segments[1, "X2"], "-00h00") - } - - available_segments = 1:(ncol(cwa_all_segments) - 3) - if (segment == "last") segment = max(available_segments) - if (!segment %in% available_segments) stop("Invalid segment specified") - self$segment <- segment - cwa <- data.frame( - datetime = as.character(cwa_all_segments$X2), - t = cwa_all_segments$X1, - cwa = cwa_all_segments[[3 + segment]] - ) - if (total) { - cwa_tot_lines <- outfile[grep("ConSysWatLay_", outfile)] # hourly total conc. - cwa_tot_all_segments <- read.table(text = cwa_lines) - cwa$cwa_tot = cwa_tot_all_segments[[3 + segment]] - } - lct <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C") - cwa$datetime <- strptime(cwa$datetime, "%d-%b-%Y-%Hh%M") - Sys.setlocale("LC_TIME", lct) - - startyear = format(cwa$datetime[1], "%Y") - firstjan <- strptime(paste0(startyear, "-01-01"), "%Y-%m-%d") - cwa$t_firstjan <- as.numeric(difftime(cwa$datetime, - firstjan, units = "days")) - t_max = cwa[which.max(cwa$cwa), "t"] - cwa$t_rel_to_max = cwa$t - t_max - cwa$cwa_mug_per_L <- cwa$cwa * 1000 - self$cwas <- cwa[c("datetime", "t", "t_firstjan", - "t_rel_to_max", - "cwa_mug_per_L")] - if (total) { - self$cwas$cwa_tot_mug_per_L <- cwa$cwa_tot * 1000 - } - } - } - }, - moving_windows = function(windows, total = FALSE) { - window_names = paste(windows, "days") - n = length(window_names) - self$windows <- data.frame(window = window_names, - max_TWAC = numeric(n), - max_AUC_h = numeric(n), - max_AUC_d = numeric(n)) - if (missing(windows)) { - stop("You need to specify at least one moving window size in days") - } - cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L") - for (i in seq_along(windows)) { - window_size = windows[i] - filter_size = window_size * 24 - max_TWAC = max(filter(self$cwas[cwa_column], rep(1/filter_size, filter_size), - "convolution"), na.rm = TRUE) - max_AUC_h = max_TWAC * filter_size - max_AUC_d = max_TWAC * window_size - - self$windows[i, -1] = c(max_TWAC, max_AUC_h, max_AUC_d) - } - invisible(self) - }, - get_events = function(thresholds, total = FALSE) { - if (missing(thresholds)) { - stop("You need to specify at least one threshold concentration in \u03bcg/L") - } - for (threshold in thresholds) { - events = data.frame(t_start = numeric(), cwa_max = numeric(), - duration = numeric(), pre_interval = numeric(), - AUC_h = numeric(), AUC_d = numeric()) - cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L") - - event_end = 0 - event = FALSE - event_max = 0 - event_nr = 0 - n_rows = nrow(self$cwas) - for (i in 1:n_rows) { - cwa_cur = self$cwas[i, cwa_column] - if (event == FALSE) { - if (cwa_cur > threshold) { - event_start = self$cwas[i, "t"] - pre_interval = event_start - event_end - i_start = i - event = TRUE - event_max = cwa_cur - } - } else { - if (cwa_cur > event_max) event_max = cwa_cur - if (cwa_cur < threshold || i == n_rows) { - event_nr = event_nr + 1 - i_end = i - if (i == n_rows) i_end = i - event_end = self$cwas[i_end, "t"] - event_length = event_end - event_start - event_cwas <- self$cwas[i_start:(i_end - 1), cwa_column] - event_AUC_h = sum(event_cwas) - event_AUC_d = event_AUC_h / 24 - events[event_nr, ] = c(event_start, event_max, event_length, - pre_interval, event_AUC_h, event_AUC_d) - event = FALSE - } - } - } - - self$events[[as.character(threshold)]] <- events - } - invisible(self) - }, - print = function() { - cat(" data from file", self$filename, "segment", self$segment, "\n") - print(head(self$cwas)) - cat("Moving window analysis\n") - print(self$windows) - for (threshold in names(self$events)) { - cat("Event statistics for threshold", threshold, "\n") - if (nrow(self$events[[threshold]]) == 0) cat("No events found\n") - else print(self$events[[threshold]]) - } - } - ) -) -# vim: set ts=2 sw=2 expandtab: diff --git a/pkg/R/drift_data_JKI.R b/pkg/R/drift_data_JKI.R deleted file mode 100644 index 888d3b5..0000000 --- a/pkg/R/drift_data_JKI.R +++ /dev/null @@ -1,44 +0,0 @@ -#' Deposition from spray drift expressed as percent of the applied dose as -#' published by the JKI -#' -#' Deposition from spray drift expressed as percent of the applied dose as -#' published by the German Julius-Kühn Institute (JKI). -#' -#' The data were extracted from the spreadsheet cited below using the R code -#' given in the example section. The spreadsheet is not included in the package -#' as its licence is not clear. -#' -#' -#' @name drift_data_JKI -#' @docType data -#' @format A list currently containing matrices with spray drift percentage -#' data for field crops (Ackerbau), and Pome/stone fruit, early and late -#' (Obstbau frueh, spaet). -#' @source JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved -#' from -#' http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -#' on 2015-06-11 -#' @keywords datasets -#' @examples -#' -#' \dontrun{ -#' # This is the code that was used to extract the data -#' library(readxl) -#' abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" -#' JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet") -#' names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late") -#' drift_data_JKI <- list() -#' -#' for (n in 1:8) { -#' drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) -#' drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) -#' dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]), -#' crop = JKI_crops) -#' drift_data_JKI[[n]] <- drift_data -#' } -#' save(drift_data_JKI, file = "data/drift_data_JKI.RData") -#' } -#' -#' # And this is the resulting data -#' drift_data_JKI -NULL diff --git a/pkg/R/endpoint.R b/pkg/R/endpoint.R deleted file mode 100644 index 314acd2..0000000 --- a/pkg/R/endpoint.R +++ /dev/null @@ -1,110 +0,0 @@ -#' Retrieve endpoint information from the chyaml field of a chent object -#' -#' R6 class objects of class \code{\link{chent}} represent chemical entities -#' and can hold a list of information loaded from a chemical yaml file in their -#' chyaml field. Such information is extracted and optionally aggregated by -#' this function. -#' -#' The functions \code{soil_*} are functions to extract soil specific endpoints. -#' For the Freundlich exponent, the capital letter \code{N} is used in order to -#' facilitate dealing with such data in R. In pesticide fate modelling, this -#' exponent is often called 1/n. -#' -#' @import chents -#' @export -#' @param chent The \code{\link{chent}} object to get the information from -#' @param medium The medium for which information is sought -#' @param type The information type -#' @param lab_field If not NA, do we want laboratory or field endpoints -#' @param redox If not NA, are we looking for aerobic or anaerobic data -#' @param value The name of the value we want. The list given in the -#' usage section is not exclusive -#' @param aggregator The aggregator function. Can be mean, -#' \code{\link{geomean}}, or identity, for example. -#' @param raw Should the number(s) be returned as stored in the chent -#' object (could be a character value) to retain original information -#' about precision? -#' @param signif How many significant digits do we want -#' @return The result from applying the aggregator function to -#' the values converted to a numeric vector, rounded to the -#' given number of significant digits, or, if raw = TRUE, -#' the values as a character value, retaining any implicit -#' information on precision that may be present. -#' -endpoint <- function(chent, - medium = "soil", - type = c("degradation", "sorption"), - lab_field = c(NA, "laboratory", "field"), - redox = c(NA, "aerobic", "anaerobic"), - value = c("DT50ref", "Kfoc", "N"), - aggregator = geomean, - raw = FALSE, - signif = 3) -{ - if (!is(chent, "chent")) { - stop("Please supply a chent object as created using the package 'chents' available from jrwb.de") - } - ep_list <- chent$chyaml[[medium]][[type]] - if (!is.na(lab_field[1])) { - ep_list <- ep_list[[lab_field]] - } - if (!is.na(redox[1])) { - ep_list <- ep_list[[redox]] - } - values <- ep_list$data[[value]] - if (raw) return(values) - else return(signif(aggregator(as.numeric(values)), signif)) -} - -#' @inheritParams endpoint -#' @rdname endpoint -#' @export -soil_DT50 <- function(chent, aggregator = geomean, signif = 3, - lab_field = "laboratory", value = "DT50ref", - redox = "aerobic", raw = FALSE) { - ep <- endpoint(chent, medium = "soil", type = "degradation", - lab_field = "laboratory", redox = redox, - signif = signif, - value = value, aggregator = aggregator, raw = raw) - return(ep) -} - -#' @inheritParams endpoint -#' @rdname endpoint -#' @export -soil_Kfoc <- function(chent, aggregator = geomean, signif = 3, - value = "Kfoc", raw = FALSE) { - ep <- endpoint(chent, medium = "soil", type = "sorption", - signif = signif, - value = value, aggregator = aggregator, raw = raw) - return(ep) -} - -#' @inheritParams endpoint -#' @rdname endpoint -#' @export -soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) { - ep <- endpoint(chent, medium = "soil", type = "sorption", - signif = signif, - value = "N", aggregator = aggregator, raw = raw) - return(ep) -} - -#' @inheritParams endpoint -#' @rdname endpoint -#' @param values The values to be returned -#' @param aggregators A named vector of aggregator functions to be used -#' @export -soil_sorption <- function(chent, values = c("Kfoc", "N"), - aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), - signif = c(Kfoc = 3, N = 3), - raw = FALSE) { - res <- sapply(values, - function(x) { - endpoint(chent, medium = "soil", type = "sorption", - signif = signif[[x]], - value = x, aggregator = aggregators[[x]], raw = raw) - } - ) - return(res) -} diff --git a/pkg/R/geomean.R b/pkg/R/geomean.R deleted file mode 100644 index 626829b..0000000 --- a/pkg/R/geomean.R +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate the geometric mean -#' -#' Based on some posts in a thread on Stackoverflow -#' \url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in} -#' This function checks for negative values, removes NA values per default and -#' returns 0 if at least one element of the vector is 0. -#' -#' @param x Vector of numbers -#' @param na.rm Should NA values be omitted? -#' @return The geometric mean -#' @export -#' @author Johannes Ranke -#' @examples -#' geomean(c(1, 3, 9)) -#' geomean(c(1, 3, NA, 9)) -#' \dontrun{geomean(c(1, -3, 9)) # returns an error} -geomean = function(x, na.rm = TRUE){ - if (any(is.na(x)) & na.rm == FALSE) stop("Removal of NA values was not requested") - if (any(x < 0, na.rm = na.rm)) stop("Only defined for positive numbers") - exp(mean(log(x), na.rm = na.rm)) -} diff --git a/pkg/R/pfm_degradation.R b/pkg/R/pfm_degradation.R deleted file mode 100644 index 6c8610e..0000000 --- a/pkg/R/pfm_degradation.R +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' Calculate a time course of relative concentrations based on an mkinmod model -#' -#' @import mkin -#' @param model The degradation model to be used. Either a parent only model like -#' 'SFO' or 'FOMC', or an mkinmod object -#' @param DT50 The half-life. This is only used when simple exponential decline -#' is calculated (SFO model). -#' @param parms The parameters used for the degradation model -#' @param years For how many years should the degradation be predicted? -#' @param step_days What step size in days should the output have? -#' @param times The output times -#' @export -#' @author Johannes Ranke -#' @examples -#' head(pfm_degradation("SFO", DT50 = 10)) -pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50), - years = 1, step_days = 1, - times = seq(0, years * 365, by = step_days)) -{ - if (model %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) { - model <- mkinmod(parent = list(type = model)) - } - initial_state = c(1, rep(0, length(model$diffs) - 1)) - names(initial_state) <- names(model$diffs) - time_course <- mkinpredict(model, odeparms = parms, - odeini = initial_state, - outtimes = times, - solution_type = ifelse(length(model$spec) == 1, - "analytical", "deSolve")) - invisible(time_course) -} diff --git a/pkg/R/soil_scenario_data_EFSA_2015.R b/pkg/R/soil_scenario_data_EFSA_2015.R deleted file mode 100644 index fb096bc..0000000 --- a/pkg/R/soil_scenario_data_EFSA_2015.R +++ /dev/null @@ -1,40 +0,0 @@ -#' Properties of the predefined scenarios from the EFSA guidance from 2015 -#' -#' Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the -#' concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the -#' scenario and model adjustment factors from p. 15 and p. 17 are included. -#' -#' @name soil_scenario_data_EFSA_2015 -#' @docType data -#' @format A data frame with one row for each scenario. Row names are the scenario codes, -#' e.g. CTN for the Northern scenario for the total concentration in soil. Columns are -#' mostly self-explanatory. \code{rho} is the dry bulk density of the top soil. -#' @source EFSA (European Food Safety Authority) (2015) -#' EFSA guidance document for predicting environmental concentrations -#' of active substances of plant protection products and transformation products of these -#' active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 -#' doi:10.2903/j.efsa.2015.4093 -#' @keywords datasets -#' @examples -#' \dontrun{ -#' # This is the code that was used to define the data -#' soil_scenario_data_EFSA_2015 <- data.frame( -#' Zone = rep(c("North", "Central", "South"), 2), -#' Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), -#' T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), -#' T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), -#' Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), -#' f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), -#' theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), -#' rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), -#' f_sce = c(3, 2, 2, 2, 1.5, 1.5), -#' f_mod = c(2, 2, 2, 4, 4, 4), -#' stringsAsFactors = FALSE, -#' row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") -#' ) -#' save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') -#' } -#' -#' # And this is the resulting dataframe -#' soil_scenario_data_EFSA_2015 -NULL diff --git a/pkg/data/FOCUS_GW_scenarios_2012.RData b/pkg/data/FOCUS_GW_scenarios_2012.RData deleted file mode 100644 index 4b2622e..0000000 Binary files a/pkg/data/FOCUS_GW_scenarios_2012.RData and /dev/null differ diff --git a/pkg/data/drift_data_JKI.RData b/pkg/data/drift_data_JKI.RData deleted file mode 100644 index 0a2f05e..0000000 Binary files a/pkg/data/drift_data_JKI.RData and /dev/null differ diff --git a/pkg/data/soil_scenario_data_EFSA_2015.RData b/pkg/data/soil_scenario_data_EFSA_2015.RData deleted file mode 100644 index b30076f..0000000 Binary files a/pkg/data/soil_scenario_data_EFSA_2015.RData and /dev/null differ diff --git a/pkg/inst/extdata/FOCUS_GW_scenarios_2012.R b/pkg/inst/extdata/FOCUS_GW_scenarios_2012.R deleted file mode 100644 index 3715325..0000000 --- a/pkg/inst/extdata/FOCUS_GW_scenarios_2012.R +++ /dev/null @@ -1,59 +0,0 @@ -# FOCUS 2012 p. 46 ff -FOCUS_GW_scenarios_2012 = list() - -n_layers = c(7, 6, 6, 5, 5, 6, 4, 6, 6) -acronyms = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi") -FOCUS_GW_scenarios_2012$names = c("Ch\u00e2teadun", "Hamburg", "Jokioinen", - "Kremsm\u00fcnster", "Okehampton", - "Piacenza", "Porto", "Sevilla", "Thiva") - -names(FOCUS_GW_scenarios_2012$names) = acronyms -FOCUS_GW_scenarios_2012$soils <- data.frame( - location= rep(acronyms, times = n_layers), - horizon = c("Ap", "B1", "B2", "II C1", "II C1", "II C2", "M", - "Ap", "BvI", "BvII", "Bv/Cv", "Cv", "Cv", - "Ap", "Bs", "BC1", "BC2", "BC2", "Cg", - rep(NA, 5), - "A", "Bw1", "BC", "C", "C", - "Ap", "Ap", "Bw", "Bw", "2C", "2C", - rep(NA, 4), - rep(NA, 6), - "Ap1", "Ap2", "Bw", "Bw", "Ck1", "Ck1"), - number = unlist(sapply(n_layers, function(x) 1:x)), - pH_H2O = c(8.0, 8.1, 8.2, 8.5, 8.5, 8.5, 8.3, - 6.4, 5.6, 5.6, 5.7, 5.5, 5.5, - 6.2, 5.6, 5.4, 5.4, 5.4, 5.3, - 7.7, 7.0, 7.1, 7.1, 7.1, - 5.8, 6.3, 6.5, 6.6, 6.6, - 7, 7, 6.3, 6.3, 6.4, 6.4, - 4.9, 4.8, 4.8, 4.8, - 7.3, 7.3, 7.8, 8.1, 8.1, 8.2, - 7.7, 7.7, 7.8, 7.8, 7.8, 7.8), - perc_clay = c(30, 31, 25, 26, 26, 24, 31, - 7.2, 6.7, 0.9, 0, 0, 0, - 3.6, 1.8, 1.2, 1.7, 1.7, 1.9, - 14, 25, 27, 27, 27, - 18, 17, 14, 9, 9, - 15, 15, 7, 7, 0, 0, - 10, 8, 8, 8, - 14, 13, 15, 16, 16, 22, - 25.3, 25.3, 29.6, 31.9, 32.9, 32.9), - perc_oc = c(1.39, 0.93, 0.7, 0.3, 0.3, 0.27, 0.21, - 1.5, 1, 0.2, 0, 0, 0, - 4.06, 0.84, 0.36, 0.29, 0.29, 0.21, - 3.6, 1.0, 0.5, 0.5, 0.5, - 2.2, 0.7, 0.4, 0.1, 0.1, - 1.26, 1.26, 0.47, 0.47, 0, 0, - 1.42, 0.78, 0.78, 0.78, - 0.93, 0.93, 0.70, 0.58, 0.58, 0.49, - 0.74, 0.74, 0.57, 0.31, 0.18, 0.18), - rel_deg = c(1, 0.5, 0.5, 0.3, 0, 0, 0, - 1, 0.5, 0.3, 0.3, 0.3, 0, - 1, 0.5, 0.3, 0.3, 0, 0, - 1, 0.5, 0.5, 0.3, 0, - 1, 0.5, 0.3, 0.3, 0, - 1, 0.5, 0.5, 0.3, 0.3, 0, - 1, 0.5, 0.3, 0, - 1, 1, 0.5, 0.3, 0, 0, - 1, 0.5, 0.5, 0.3, 0.3, 0)) -save(FOCUS_GW_scenarios_2012, file = "../../data/FOCUS_GW_scenarios_2012.RData") diff --git a/pkg/inst/staticdocs/index.r b/pkg/inst/staticdocs/index.r deleted file mode 100644 index 421071c..0000000 --- a/pkg/inst/staticdocs/index.r +++ /dev/null @@ -1,42 +0,0 @@ -sd_section( - "Degradation", - "Functions related to degradation", - c("pfm_degradation", "SFO_actual_twa") -) -sd_section( - "Mobility", - "Indicators related to mobility", - c("GUS", "SSLRC_mobility_classification") -) -sd_section( - "Soil", - "Predicted environmental concentrations in soil", - c("PEC_soil", "soil_scenario_data_EFSA_2015") -) -sd_section( - "Surface water", - "Predicted environmental concentrations in surface water", - c( - "PEC_sw_drift", "PEC_sw_sed", - "drift_data_JKI", - "PEC_sw_drainage_UK", - "TOXSWA_cwa", - "read.TOXSWA_cwa", - "plot.TOXSWA_cwa" - ) -) -sd_section( - "Groundwater", - "Predicted environmental concentrations in groundwater", - c("FOCUS_GW_scenarios_2012") -) -sd_section( - "Chemical entities", - "Work with input stored in chemical entites as R objects using the chent package", - c("endpoint") -) -sd_section( - "General", - "Utilities that are generally useful", - c("geomean") -) diff --git a/pkg/inst/testdata/SwashProjects.zip b/pkg/inst/testdata/SwashProjects.zip deleted file mode 100644 index 5b9ff49..0000000 Binary files a/pkg/inst/testdata/SwashProjects.zip and /dev/null differ diff --git a/pkg/inst/web/FOCUS_GW_scenarios_2012.html b/pkg/inst/web/FOCUS_GW_scenarios_2012.html deleted file mode 100644 index 43ac090..0000000 --- a/pkg/inst/web/FOCUS_GW_scenarios_2012.html +++ /dev/null @@ -1,154 +0,0 @@ - - - - -FOCUS_GW_scenarios_2012. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          A very small subset of the FOCUS Groundwater scenario defitions

          - -
          -
          - -
          -

          Description

          - -

          Currently, only a small subset of the soil definitions are provided.

          - -
          - -
          -

          References

          - -

          FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. - FOrum for the Co-ordination of pesticde fate models and their USe. - http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf

          - -
          - -

          Examples

          - 
          FOCUS_GW_scenarios_2012
-
          
-
          $names
-           Cha            Ham            Jok            Kre            Oke 
-  "Châteaudun"      "Hamburg"    "Jokioinen" "Kremsmünster"   "Okehampton" 
-           Pia            Por            Sev            Thi 
-    "Piacenza"        "Porto"      "Sevilla"        "Thiva" 
-
-$soils
-   location horizon number pH_H2O perc_clay perc_oc rel_deg
-1       Cha      Ap      1    8.0      30.0    1.39     1.0
-2       Cha      B1      2    8.1      31.0    0.93     0.5
-3       Cha      B2      3    8.2      25.0    0.70     0.5
-4       Cha   II C1      4    8.5      26.0    0.30     0.3
-5       Cha   II C1      5    8.5      26.0    0.30     0.0
-6       Cha   II C2      6    8.5      24.0    0.27     0.0
-7       Cha       M      7    8.3      31.0    0.21     0.0
-8       Ham      Ap      1    6.4       7.2    1.50     1.0
-9       Ham     BvI      2    5.6       6.7    1.00     0.5
-10      Ham    BvII      3    5.6       0.9    0.20     0.3
-11      Ham   Bv/Cv      4    5.7       0.0    0.00     0.3
-12      Ham      Cv      5    5.5       0.0    0.00     0.3
-13      Ham      Cv      6    5.5       0.0    0.00     0.0
-14      Jok      Ap      1    6.2       3.6    4.06     1.0
-15      Jok      Bs      2    5.6       1.8    0.84     0.5
-16      Jok     BC1      3    5.4       1.2    0.36     0.3
-17      Jok     BC2      4    5.4       1.7    0.29     0.3
-18      Jok     BC2      5    5.4       1.7    0.29     0.0
-19      Jok      Cg      6    5.3       1.9    0.21     0.0
-20      Kre    <NA>      1    7.7      14.0    3.60     1.0
-21      Kre    <NA>      2    7.0      25.0    1.00     0.5
-22      Kre    <NA>      3    7.1      27.0    0.50     0.5
-23      Kre    <NA>      4    7.1      27.0    0.50     0.3
-24      Kre    <NA>      5    7.1      27.0    0.50     0.0
-25      Oke       A      1    5.8      18.0    2.20     1.0
-26      Oke     Bw1      2    6.3      17.0    0.70     0.5
-27      Oke      BC      3    6.5      14.0    0.40     0.3
-28      Oke       C      4    6.6       9.0    0.10     0.3
-29      Oke       C      5    6.6       9.0    0.10     0.0
-30      Pia      Ap      1    7.0      15.0    1.26     1.0
-31      Pia      Ap      2    7.0      15.0    1.26     0.5
-32      Pia      Bw      3    6.3       7.0    0.47     0.5
-33      Pia      Bw      4    6.3       7.0    0.47     0.3
-34      Pia      2C      5    6.4       0.0    0.00     0.3
-35      Pia      2C      6    6.4       0.0    0.00     0.0
-36      Por    <NA>      1    4.9      10.0    1.42     1.0
-37      Por    <NA>      2    4.8       8.0    0.78     0.5
-38      Por    <NA>      3    4.8       8.0    0.78     0.3
-39      Por    <NA>      4    4.8       8.0    0.78     0.0
-40      Sev    <NA>      1    7.3      14.0    0.93     1.0
-41      Sev    <NA>      2    7.3      13.0    0.93     1.0
-42      Sev    <NA>      3    7.8      15.0    0.70     0.5
-43      Sev    <NA>      4    8.1      16.0    0.58     0.3
-44      Sev    <NA>      5    8.1      16.0    0.58     0.0
-45      Sev    <NA>      6    8.2      22.0    0.49     0.0
-46      Thi     Ap1      1    7.7      25.3    0.74     1.0
-47      Thi     Ap2      2    7.7      25.3    0.74     0.5
-48      Thi      Bw      3    7.8      29.6    0.57     0.5
-49      Thi      Bw      4    7.8      31.9    0.31     0.3
-50      Thi     Ck1      5    7.8      32.9    0.18     0.3
-51      Thi     Ck1      6    7.8      32.9    0.18     0.0
-
-
          -
          -
          - - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/GUS.html b/pkg/inst/web/GUS.html deleted file mode 100644 index a330be2..0000000 --- a/pkg/inst/web/GUS.html +++ /dev/null @@ -1,160 +0,0 @@ - - - - -GUS. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Groundwater ubiquity score based on Gustafson (1989)

          - -
          -
          -

          Usage

          - 
          GUS(...)
          
-
          "GUS"(DT50, Koc, ...)
          
-
          "GUS"(chent, degradation_value = "DT50ref", lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc", degradation_aggregator = geomean, sorption_aggregator = geomean, ...)
          
-
          "print"(x, ..., digits = 1)
          - -

          Arguments

          -
          -
          ...
          -
          Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.
          -
          DT50
          -
          Half-life of the chemical in soil. Should be a field -half-life according to Gustafson (1989). However, leaching to the sub-soil -can not completely be excluded in field dissipation experiments and Gustafson -did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions.
          -
          Koc
          -
          The sorption constant normalised to organic carbon. Gustafson -does not mention the nonlinearity of the sorption constant commonly -found and usually described by Freundlich sorption, therefore it is -unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater).
          -
          chent
          -
          If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.
          -
          degradation_value
          -
          Which of the available degradation values should -be used?
          -
          lab_field
          -
          Should laboratory or field half-lives be used? This -defaults to lab in this implementation, in order to avoid -double-accounting for mobility. If comparability with the original GUS -values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used.
          -
          redox
          -
          Aerobic or anaerobic degradation data
          -
          sorption_value
          -
          Which of the available sorption values should be used? -Defaults to Kfoc as this is what is generally available from the European -pesticide peer review process. These values generally use a reference -concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase.
          -
          degradation_aggregator
          -
          Function for aggregating half-lives
          -
          sorption_aggregator
          -
          Function for aggregation Koc values
          -
          x
          -
          An object of class GUS_result to be printed
          -
          digits
          -
          The number of digits used in the print method
          -
          - -
          -

          Value

          - -

          -A list with the DT50 and Koc used as well as the resulting score - of class GUS_result -

          - -
          - -
          -

          Description

          - -

          The groundwater ubiquity score GUS is calculated according to -the following equation -$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$

          - -
          - -
          -

          References

          - -

          Gustafson, David I. (1989) Groundwater ubiquity score: a simple -method for assessing pesticide leachability. Environmental -toxicology and chemistry 8(4) 339–57.

          - -
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/PEC_soil.html b/pkg/inst/web/PEC_soil.html deleted file mode 100644 index 1304d19..0000000 --- a/pkg/inst/web/PEC_soil.html +++ /dev/null @@ -1,228 +0,0 @@ - - - - -PEC_soil. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Calculate predicted environmental concentrations in soil

          - -
          -
          -

          Usage

          - 
          PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA, n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default", "EFSA_2015"), porewater = FALSE)
          - -

          Arguments

          -
          -
          rate
          -
          Application rate in units specified below
          -
          rate_units
          -
          Defaults to g/ha
          -
          interception
          -
          The fraction of the application rate that does not reach the soil
          -
          mixing_depth
          -
          Mixing depth in cm
          -
          PEC_units
          -
          Requested units for the calculated PEC. Only mg/kg currently supported
          -
          PEC_pw_units
          -
          Only mg/L currently supported
          -
          interval
          -
          Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days
          -
          n_periods
          -
          Number of periods to be considered for long term PEC calculations
          -
          tillage_depth
          -
          Periodic (see interval) deeper mixing in cm
          -
          chent
          -
          An optional chent object holding substance specific information. Can -also be a name for the substance as a character string
          -
          DT50
          -
          If specified, overrides soil DT50 endpoints from a chent object -If DT50 is not specified here and not available from the chent object, zero -degradation is assumed
          -
          Koc
          -
          If specified, overrides Koc endpoints from a chent object
          -
          Kom
          -
          Calculated from Koc by default, but can explicitly be specified -as Kom here
          -
          t_avg
          -
          Averaging times for time weighted average concentrations
          -
          scenarios
          -
          If this is 'default', the DT50 will be used without correction -and soil properties as specified in the REACH guidance (R.16, Table -R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", -the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -'chents' is specified, the DegT50 with destination 'PECgw' will be used), -and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used.
          -
          porewater
          -
          Should equilibrium porewater concentrations be estimated -based on Kom and the organic carbon fraction of the soil instead of total -soil concentrations? Based on equation (7) given in the PPR panel opinion -(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -p. 13).
          -
          - -
          -

          Value

          - -

          -The predicted concentration in soil -

          - -
          - -
          -

          Description

          - -

          This is a basic calculation of a contaminant concentration in bulk soil -based on complete, instantaneous mixing. If an interval is given, an -attempt is made at calculating a long term maximum concentration using -the concepts layed out for example in the PPR panel opinion (EFSA 2012).

          - -
          - -
          -

          Details

          - -

          This assumes that the complete load to soil during the time specified by -'interval' (typically 365 days) is dosed at once. As in the PPR panel -opinion cited below (PPR panel 2012), only temperature correction using the -Arrhenius equation is performed.

          - -

          Total soil and porewater PEC values for the scenarios as defined in the EFSA -guidance (2015, p. 13) can easily be calculated.

          - -
          - -
          -

          Note

          - -

          If temperature information is available in the selected scenarios, as - e.g. in the EFSA scenarios, the DT50 for groundwater modelling - (destination 'PECgw') is taken from the chent object, otherwise the DT50 - with destination 'PECsoil'.

          - -
          - -
          -

          References

          - -

          EFSA Panel on Plant Protection Products and their Residues (2012) - Scientific Opinion on the science behind the guidance for scenario - selection and scenario parameterisation for predicting environmental - concentrations of plant protection products in soil. EFSA Journal - 10(2) 2562, doi:10.2903/j.efsa.2012.2562

          - -

          EFSA (European Food Safety Authority) (2015) EFSA guidance document for - predicting environmental concentrations of active substances of plant - protection products and transformation products of these active substances - in soil. EFSA Journal 13(4) 4093 - doi:10.2903/j.efsa.2015.4093

          - -
          - -

          Examples

          - 
          PEC_soil(100, interception = 0.25)
-
          
-
               scenario
-t_avg default
-    0     0.1
-
          
-
          
-# This is example 1 starting at p. 79 of the EFSA guidance (2015)
-PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
-               scenarios = "EFSA_2015")
-
          
-
               scenario
-t_avg      CTN      CTC      CTS
-   0  21.96827 11.53750 9.145259
-   21 21.78517 11.40701 9.017370
-
          
-
          PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21),
-               Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE)
-
          
-
               scenario
-t_avg       CLN       CLC       CLS
-   0  0.7589401 0.6674322 0.9147861
-   21 0.7506036 0.6590345 0.8987279
-
          
-
          
-# The following is from example 4 starting at p. 85 of the EFSA guidance (2015)
-# Metabolite M2
-# Calculate total and porewater soil concentrations for tier 1 scenarios
-# Relative molar mass is 100/300, formation fraction is 0.7 * 1
-results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
-                        scenarios = "EFSA_2015")
-results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21),
-                           Kom = 100, scenarios = "EFSA_2015", porewater = TRUE)
-
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/PEC_soil_product.html b/pkg/inst/web/PEC_soil_product.html deleted file mode 100644 index 9704de2..0000000 --- a/pkg/inst/web/PEC_soil_product.html +++ /dev/null @@ -1,141 +0,0 @@ - - - - -PEC_soil_product. pfm 0.2-4 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.2-4 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Calculate predicted environmental concentrations in soil for a product

          - -
          -
          -

          Usage

          - 
          PEC_soil_product(product, rate, rate_units = "L/ha", interception = 0, mixing_depth = 5, tillage_depth = 20, interval = 365, PEC_units = "mg/kg", scenarios = "EFSA_2015")
          - -

          Arguments

          -
          -
          product
          -
          An object of class pp
          -
          rate
          -
          Application rate in units specified below
          -
          rate_units
          -
          Defaults to g/ha
          -
          interception
          -
          The fraction of the application rate that does not reach the soil
          -
          mixing_depth
          -
          Mixing depth in cm
          -
          tillage_depth
          -
          Periodic (see interval) deeper mixing in cm
          -
          interval
          -
          Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days
          -
          PEC_units
          -
          Requested units for the calculated PEC. Only mg/kg currently supported
          -
          - -
          -

          Source

          - -

          EFSA Panel on Plant Protection Products and their Residues (2012) -Scientific Opinion on the science behind the guidance for scenario selection -and scenario parameterisation for predicting environmental concentrations -of plant protection products in soil. EFSA Journal 10(2) 2562, -doi:10.2903/j.efsa.2012.2562

          - -

          EFSA (European Food Safety Authority) (2015) -EFSA guidance document for predicting environmental concentrations -of active substances of plant protection products and transformation products of these -active substances in soil. EFSA Journal 13(4) 4093 -doi:10.2903/j.efsa.2015.4093

          - -
          - -
          -

          Value

          - -

          -A data frame with compound names, and initial, background (plateau minimum) - and long term maximum predicted concentrations in soil -

          - -
          - -
          -

          Description

          - -

          Calculates long term accumulation PEC values. Assumes that the complete load to soil during the -time specified by 'interval' (typically 365 days) is dosed at once. As in the PPR panel opinion -cited below (PPR panel 2012), only temperature correction using the Arrhenius equation is performed. -By default, PEC values for the scenarios as defined in the EFSA guidance -(2015, p. 13) are calculated.

          - -
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drainage_UK.html b/pkg/inst/web/PEC_sw_drainage_UK.html deleted file mode 100644 index bf97fea..0000000 --- a/pkg/inst/web/PEC_sw_drainage_UK.html +++ /dev/null @@ -1,124 +0,0 @@ - - - - -PEC_sw_drainage_UK. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

          - -
          -
          -

          Usage

          - 
          PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL)
          - -

          Arguments

          -
          -
          rate
          -
          Application rate in g/ha
          -
          interception
          -
          The fraction of the application rate that does not reach the soil
          -
          Koc
          -
          The sorption coefficient normalised to organic carbon in L/kg
          -
          latest_application
          -
          Latest application date, formatted as e.g. "01 July"
          -
          soil_DT50
          -
          Soil degradation half-life, if SFO kinetics are to be used
          -
          model
          -
          The soil degradation model to be used. Either one of "FOMC", -"DFOP", "HS", or "IORE", or an mkinmod object
          -
          model_parms
          -
          A named numeric vector containing the model parameters
          -
          - -
          -

          Value

          - -

          -The predicted concentration in surface water in µg/L -

          - -
          - -
          -

          Description

          - -

          This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -published on the CRC website

          - -
          - -

          Examples

          - 
          PEC_sw_drainage_UK(150, Koc = 100)
-
          
-
          [1] 8.076923
-
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drainage_UK_ini.html b/pkg/inst/web/PEC_sw_drainage_UK_ini.html deleted file mode 100644 index 0d55bd9..0000000 --- a/pkg/inst/web/PEC_sw_drainage_UK_ini.html +++ /dev/null @@ -1,124 +0,0 @@ - - - - -PEC_sw_drainage_UK_ini. pfm 0.2-4 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.2-4 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

          - -
          -
          -

          Usage

          - 
          PEC_sw_drainage_UK_ini(rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL)
          - -

          Arguments

          -
          -
          rate
          -
          Application rate in g/ha
          -
          interception
          -
          The fraction of the application rate that does not reach the soil
          -
          Koc
          -
          The sorption coefficient normalised to organic carbon in L/kg
          -
          latest_application
          -
          Latest application date, formatted as e.g. "01 July"
          -
          soil_DT50
          -
          Soil degradation half-life, if SFO kinetics are to be used
          -
          model
          -
          The degradation model to be used. Either one of "FOMC", "DFOP", -"HS", or "IORE", or an mkinmod object
          -
          model_parms
          -
          A named numeric vector containing the model parameters
          -
          - -
          -

          Value

          - -

          -The predicted concentration in surface water in µg/L -

          - -
          - -
          -

          Description

          - -

          This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -published on the CRC website

          - -
          - -

          Examples

          - 
          PEC_sw_drainage_UK_ini(150, Koc = 100)
-
          
-
          [1] 8.076923
-
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drift.html b/pkg/inst/web/PEC_sw_drift.html deleted file mode 100644 index 5d4bb47..0000000 --- a/pkg/inst/web/PEC_sw_drift.html +++ /dev/null @@ -1,130 +0,0 @@ - - - - -PEC_sw_drift. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Calculate predicted environmental concentrations in surface water due to drift

          - -
          -
          -

          Usage

          - 
          PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
          - -

          Arguments

          -
          -
          rate
          -
          Application rate in units specified below
          -
          applications
          -
          Number of applications for selection of drift percentile
          -
          water_depth
          -
          Depth of the water body in cm
          -
          drift_percentages
          -
          Percentage drift values for which to calculate PECsw. -'drift_data' and 'distances' if not NULL.
          -
          drift_data
          -
          Source of drift percentage data
          -
          crop
          -
          Crop name (use German names for JKI data), defaults to "Ackerbau"
          -
          distances
          -
          The distances in m for which to get PEC values
          -
          rate_units
          -
          Defaults to g/ha
          -
          PEC_units
          -
          Requested units for the calculated PEC. Only µg/L currently supported
          -
          - -
          -

          Value

          - -

          -The predicted concentration in surface water -

          - -
          - -
          -

          Description

          - -

          This is a basic, vectorised form of a simple calculation of a contaminant -concentration in surface water based on complete, instantaneous mixing -with input via spray drift.

          - -
          - -

          Examples

          - 
          PEC_sw_drift(100)
-
          
-
                 1 m        5 m       10 m       20 m 
-0.92333333 0.19000000 0.09666667 0.05000000 
-
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drift_ini.html b/pkg/inst/web/PEC_sw_drift_ini.html deleted file mode 100644 index bc7eed5..0000000 --- a/pkg/inst/web/PEC_sw_drift_ini.html +++ /dev/null @@ -1,127 +0,0 @@ - - - - -PEC_sw_drift_ini. pfm 0.2-4 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.2-4 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Calculate initial predicted environmental concentrations in surface water due to drift

          - -
          -
          -

          Usage

          - 
          PEC_sw_drift_ini(rate, applications = 1, water_depth = 30, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
          - -

          Arguments

          -
          -
          rate
          -
          Application rate in units specified below
          -
          applications
          -
          Number of applications for selection of drift percentile
          -
          water_depth
          -
          Depth of the water body in cm
          -
          drift_data
          -
          Source of drift percentage data
          -
          crop
          -
          Crop name (use German names for JKI data), defaults to "Ackerbau"
          -
          distances
          -
          The distances in m for which to get PEC values
          -
          rate_units
          -
          Defaults to g/ha
          -
          PEC_units
          -
          Requested units for the calculated PEC. Only µg/L currently supported
          -
          - -
          -

          Value

          - -

          -The predicted concentration in surface water -

          - -
          - -
          -

          Description

          - -

          This is a basic, vectorised form of a simple calculation of a contaminant -concentration in surface water based on complete, instantaneous mixing -with input via spray drift.

          - -
          - -

          Examples

          - 
          PEC_sw_drift_ini(100)
-
          
-
                 1 m        5 m       10 m       20 m 
-0.92333333 0.19000000 0.09666667 0.05000000 
-
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_sed.html b/pkg/inst/web/PEC_sw_sed.html deleted file mode 100644 index 4eda1d7..0000000 --- a/pkg/inst/web/PEC_sw_sed.html +++ /dev/null @@ -1,127 +0,0 @@ - - - - -PEC_sw_sed. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Calculate predicted environmental concentrations in sediment from surface -water concentrations

          - -
          -
          -

          Usage

          - 
          PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage", sediment_depth = 5, water_depth = 30, sediment_density = 1.3, PEC_sed_units = c("µg/kg", "mg/kg"))
          - -

          Arguments

          -
          -
          PEC_sw
          -
          Numeric vector or matrix of surface water concentrations in µg/L for -which the corresponding sediment concentration is to be estimated
          -
          percentage
          -
          The percentage in sediment, used for the percentage method
          -
          method
          -
          The method used for the calculation
          -
          sediment_depth
          -
          Depth of the sediment layer
          -
          water_depth
          -
          Depth of the water body in cm
          -
          sediment_density
          -
          The density of the sediment in L/kg (equivalent to -g/cm3)
          -
          PEC_sed_units
          -
          The units of the estimated sediment PEC value
          -
          - -
          -

          Value

          - -

          -The predicted concentration in sediment -

          - -
          - -
          -

          Description

          - -

          The method 'percentage' is equivalent to what is used in the CRD spreadsheet -PEC calculator

          - -
          - -

          Examples

          - 
          PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50)
-
          
-
               1 m 
-2.130769 
-
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/SFO_actual_twa.html b/pkg/inst/web/SFO_actual_twa.html deleted file mode 100644 index 3ce9220..0000000 --- a/pkg/inst/web/SFO_actual_twa.html +++ /dev/null @@ -1,123 +0,0 @@ - - - - -SFO_actual_twa. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Actual and maximum moving window time average concentrations for SFO kinetics

          - -
          -
          -

          Usage

          - 
          SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))
          - -

          Arguments

          -
          -
          DT50
          -
          The half-life.
          -
          times
          -
          The output times, and window sizes for time weighted average concentrations
          -
          - -
          -

          Source

          - -

          FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, - 18 December 2014, p. 251

          - -
          - -
          -

          Description

          - -

          Actual and maximum moving window time average concentrations for SFO kinetics

          - -
          - -

          Examples

          - 
          SFO_actual_twa(10)
-
          
-
                    actual       twa
-0   1.0000000000       NaN
-1   0.9330329915 0.9661297
-2   0.8705505633 0.9337803
-4   0.7578582833 0.8733416
-7   0.6155722067 0.7923030
-14  0.3789291416 0.6400113
-21  0.2332582479 0.5267498
-28  0.1435872944 0.4412651
-42  0.0544094102 0.3248093
-50  0.0312500000 0.2795222
-100 0.0009765625 0.1441286
-
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/SSLRC_mobility_classification.html b/pkg/inst/web/SSLRC_mobility_classification.html deleted file mode 100644 index 43d701e..0000000 --- a/pkg/inst/web/SSLRC_mobility_classification.html +++ /dev/null @@ -1,117 +0,0 @@ - - - - -SSLRC_mobility_classification. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Determine the SSLRC mobility classification for a chemical substance from its Koc

          - -
          -
          -

          Usage

          - 
          SSLRC_mobility_classification(Koc)
          - -

          Arguments

          -
          -
          Koc
          -
          The sorption coefficient normalised to organic carbon in L/kg
          -
          - -
          -

          Value

          - -

          -A list containing the classification and the percentage of the - compound transported per 10 mm drain water -

          - -
          - -
          -

          Description

          - -

          This implements the method specified in the UK data requirements handbook and was -checked against the spreadsheet published on the CRC website

          - -
          - -

          Examples

          - 
          SSLRC_mobility_classification(100)
-
          
-
          $`Mobility classification`
-[1] "Moderately mobile"
-
-$`Percentage drained per mm of drain water`
-[1] 0.7
-
-
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/TOXSWA_cwa.html b/pkg/inst/web/TOXSWA_cwa.html deleted file mode 100644 index 0d8ae17..0000000 --- a/pkg/inst/web/TOXSWA_cwa.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - -TOXSWA_cwa. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          R6 class for holding TOXSWA cwa concentration data and associated statistics

          - -
          -
          -

          Usage

          - 
          TOXSWA_cwa
          - -
          -

          Format

          - -

          An R6Class generator object.

          - -
          - -
          -

          Description

          - -

          An R6 class for holding TOXSWA cwa concentration data and some associated statistics. -Usually, an instance of this class will be generated by read.TOXSWA_cwa.

          - -
          - -
          -

          Fields

          - -

          - -

          -
          filename
          Length one character vector.

          - -

          basedir
          Length one character vector.

          - -

          segment
          Length one integer, specifying for which segment the cwa data were read.

          - -

          cwas
          Dataframe holding the concentrations.

          - -

          events
          List of dataframes holding the event statistics for each threshold.

          - -

          windows
          Matrix of maximum time weighted average concentrations (TWAC_max) -and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) -for the requested moving window sizes in days.

          - -

          - -
          - -
          -

          Methods

          - -

          - -

          -
          get_events(threshold, total = FALSE)
          - Populate a datataframe with event information for the specified threshold value - in µg/L. If total = TRUE, the total concentration including the amount - adsorbed to suspended matter will be used. The resulting dataframe is stored in the - events field of the object. -

          - -

          moving_windows(windows, total = FALSE)
          - Add to the windows field described above. - Again, if total = TRUE, the total concentration including the amount - adsorbed to suspended matter will be used. -

          - -

          - -

          - -
          - -

          Examples

          - 
          H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
-                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                 zipfile = system.file("testdata/SwashProjects.zip",
-                                             package = "pfm"))
-H_sw_R1_stream$get_events(c(2, 10))
-H_sw_R1_stream$moving_windows(c(7, 21))
-print(H_sw_R1_stream)
-
          
-
          <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 
-               datetime     t t_firstjan t_rel_to_max cwa_mug_per_L
-20  1978-10-01 00:00:00 0.000   273.0000      -55.333             0
-40  1978-10-01 01:00:00 0.042   273.0417      -55.291             0
-60  1978-10-01 02:00:00 0.083   273.0833      -55.250             0
-80  1978-10-01 03:00:00 0.125   273.1250      -55.208             0
-100 1978-10-01 04:00:00 0.167   273.1667      -55.166             0
-120 1978-10-01 05:00:00 0.208   273.2083      -55.125             0
-    cwa_tot_mug_per_L
-20                  0
-40                  0
-60                  0
-80                  0
-100                 0
-120                 0
-Moving window analysis
-   window  max_TWAC max_AUC_h max_AUC_d
-1  7 days 2.3926551  401.9660  16.74859
-2 21 days 0.8369248  421.8101  17.57542
-Event statistics for threshold 2 
-  t_start   cwa_max duration pre_interval     AUC_h     AUC_d
-1  44.375  4.167238    0.208       44.375  17.77202  0.740501
-2  55.042 40.584010    0.583       10.459 398.21189 16.592162
-Event statistics for threshold 10 
-  t_start  cwa_max duration pre_interval   AUC_h    AUC_d
-1  55.083 40.58401    0.459       55.083 379.433 15.80971
-
          -
          -
          - - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/css/bootstrap-responsive.css b/pkg/inst/web/css/bootstrap-responsive.css deleted file mode 100644 index 06e55c0..0000000 --- a/pkg/inst/web/css/bootstrap-responsive.css +++ /dev/null @@ -1,815 +0,0 @@ -/*! - * Bootstrap Responsive v2.0.4 - * - * Copyright 2012 Twitter, Inc - * Licensed under the Apache License v2.0 - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Designed and built with all the love in the world @twitter by @mdo and @fat. - */ - -.clearfix { - *zoom: 1; -} - -.clearfix:before, -.clearfix:after { - display: table; - content: ""; -} - -.clearfix:after { - clear: both; -} - -.hide-text { - font: 0/0 a; - color: transparent; - text-shadow: none; - background-color: transparent; - border: 0; -} - -.input-block-level { - display: block; - width: 100%; - min-height: 28px; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - -ms-box-sizing: border-box; - box-sizing: border-box; -} - -.hidden { - display: none; - visibility: hidden; -} - -.visible-phone { - display: none !important; -} - -.visible-tablet { - display: none !important; -} - -.hidden-desktop { - display: none !important; -} - -@media (max-width: 767px) { - .visible-phone { - display: inherit !important; - } - .hidden-phone { - display: none !important; - } - .hidden-desktop { - display: inherit !important; - } - .visible-desktop { - display: none !important; - } -} - -@media (min-width: 768px) and (max-width: 979px) { - .visible-tablet { - display: inherit !important; - } - .hidden-tablet { - display: none !important; - } - .hidden-desktop { - display: inherit !important; - } - .visible-desktop { - display: none !important ; - } -} - -@media (max-width: 480px) { - .nav-collapse { - -webkit-transform: translate3d(0, 0, 0); - } - .page-header h1 small { - display: block; - line-height: 18px; - } - input[type="checkbox"], - input[type="radio"] { - border: 1px solid #ccc; - } - .form-horizontal .control-group > label { - float: none; - width: auto; - padding-top: 0; - text-align: left; - } - .form-horizontal .controls { - margin-left: 0; - } - .form-horizontal .control-list { - padding-top: 0; - } - .form-horizontal .form-actions { - padding-right: 10px; - padding-left: 10px; - } - .modal { - position: absolute; - top: 10px; - right: 10px; - left: 10px; - width: auto; - margin: 0; - } - .modal.fade.in { - top: auto; - } - .modal-header .close { - padding: 10px; - margin: -10px; - } - .carousel-caption { - position: static; - } -} - -@media (max-width: 767px) { - body { - padding-right: 20px; - padding-left: 20px; - } - .navbar-fixed-top, - .navbar-fixed-bottom { - margin-right: -20px; - margin-left: -20px; - } - .container-fluid { - padding: 0; - } - .dl-horizontal dt { - float: none; - width: auto; - clear: none; - text-align: left; - } - .dl-horizontal dd { - margin-left: 0; - } - .container { - width: auto; - } - .row-fluid { - width: 100%; - } - .row, - .thumbnails { - margin-left: 0; - } - [class*="span"], - .row-fluid [class*="span"] { - display: block; - float: none; - width: auto; - margin-left: 0; - } - .input-large, - .input-xlarge, - .input-xxlarge, - input[class*="span"], - select[class*="span"], - textarea[class*="span"], - .uneditable-input { - display: block; - width: 100%; - min-height: 28px; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - -ms-box-sizing: border-box; - box-sizing: border-box; - } - .input-prepend input, - .input-append input, - .input-prepend input[class*="span"], - .input-append input[class*="span"] { - display: inline-block; - width: auto; - } -} - -@media (min-width: 768px) and (max-width: 979px) { - .row { - margin-left: -20px; - *zoom: 1; - } - .row:before, - .row:after { - display: table; - content: ""; - } - .row:after { - clear: both; - } - [class*="span"] { - float: left; - margin-left: 20px; - } - .container, - .navbar-fixed-top .container, - .navbar-fixed-bottom .container { - width: 724px; - } - .span12 { - width: 724px; - } - .span11 { - width: 662px; - } - .span10 { - width: 600px; - } - .span9 { - width: 538px; - } - .span8 { - width: 476px; - } - .span7 { - width: 414px; - } - .span6 { - width: 352px; - } - .span5 { - width: 290px; - } - .span4 { - width: 228px; - } - .span3 { - width: 166px; - } - .span2 { - width: 104px; - } - .span1 { - width: 42px; - } - .offset12 { - margin-left: 764px; - } - .offset11 { - margin-left: 702px; - } - .offset10 { - margin-left: 640px; - } - .offset9 { - margin-left: 578px; - } - .offset8 { - margin-left: 516px; - } - .offset7 { - margin-left: 454px; - } - .offset6 { - margin-left: 392px; - } - .offset5 { - margin-left: 330px; - } - .offset4 { - margin-left: 268px; - } - .offset3 { - margin-left: 206px; - } - .offset2 { - margin-left: 144px; - } - .offset1 { - margin-left: 82px; - } - .row-fluid { - width: 100%; - *zoom: 1; - } - .row-fluid:before, - .row-fluid:after { - display: table; - content: ""; - } - .row-fluid:after { - clear: both; - } - .row-fluid [class*="span"] { - display: block; - float: left; - width: 100%; - min-height: 28px; - margin-left: 2.762430939%; - *margin-left: 2.709239449638298%; - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - -ms-box-sizing: border-box; - box-sizing: border-box; - } - .row-fluid [class*="span"]:first-child { - margin-left: 0; - } - .row-fluid .span12 { - width: 99.999999993%; - *width: 99.9468085036383%; - } - .row-fluid .span11 { - width: 91.436464082%; - *width: 91.38327259263829%; - } - .row-fluid .span10 { - width: 82.87292817100001%; - *width: 82.8197366816383%; - } - .row-fluid .span9 { - width: 74.30939226%; - *width: 74.25620077063829%; - } - .row-fluid .span8 { - width: 65.74585634900001%; - *width: 65.6926648596383%; - } - .row-fluid .span7 { - width: 57.182320438000005%; - *width: 57.129128948638304%; - } - .row-fluid .span6 { - width: 48.618784527%; - *width: 48.5655930376383%; - } - .row-fluid .span5 { - width: 40.055248616%; - *width: 40.0020571266383%; - } - .row-fluid .span4 { - width: 31.491712705%; - *width: 31.4385212156383%; - } - .row-fluid .span3 { - width: 22.928176794%; - *width: 22.874985304638297%; - } - .row-fluid .span2 { - width: 14.364640883%; - *width: 14.311449393638298%; - } - .row-fluid .span1 { - width: 5.801104972%; - *width: 5.747913482638298%; - } - input, - textarea, - .uneditable-input { - margin-left: 0; - } - input.span12, - textarea.span12, - .uneditable-input.span12 { - width: 714px; - } - input.span11, - textarea.span11, - .uneditable-input.span11 { - width: 652px; - } - input.span10, - textarea.span10, - .uneditable-input.span10 { - width: 590px; - } - input.span9, - textarea.span9, - .uneditable-input.span9 { - width: 528px; - } - input.span8, - textarea.span8, - .uneditable-input.span8 { - width: 466px; - } - input.span7, - textarea.span7, - .uneditable-input.span7 { - width: 404px; - } - input.span6, - textarea.span6, - .uneditable-input.span6 { - width: 342px; - } - input.span5, - textarea.span5, - .uneditable-input.span5 { - width: 280px; - } - input.span4, - textarea.span4, - .uneditable-input.span4 { - width: 218px; - } - input.span3, - textarea.span3, - .uneditable-input.span3 { - width: 156px; - } - input.span2, - textarea.span2, - .uneditable-input.span2 { - width: 94px; - } - input.span1, - textarea.span1, - .uneditable-input.span1 { - width: 32px; - } -} - -@media (min-width: 1200px) { - .row { - margin-left: -30px; - *zoom: 1; - } - .row:before, - .row:after { - display: table; - content: ""; - } - .row:after { - clear: both; - } - [class*="span"] { - float: left; - margin-left: 30px; - } - .container, - .navbar-fixed-top .container, - .navbar-fixed-bottom .container { - width: 1170px; - } - .span12 { - width: 1170px; - } - .span11 { - width: 1070px; - } - .span10 { - width: 970px; - } - .span9 { - width: 870px; - } - .span8 { - width: 770px; - } - .span7 { - width: 670px; - } - .span6 { - width: 570px; - } - .span5 { - width: 470px; - } - .span4 { - 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#fff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:.5;filter:alpha(opacity=50)}.carousel-control.right{right:15px;left:auto}.carousel-control:hover{color:#fff;text-decoration:none;opacity:.9;filter:alpha(opacity=90)}.carousel-caption{position:absolute;right:0;bottom:0;left:0;padding:10px 15px 5px;background:#333;background:rgba(0,0,0,0.75)}.carousel-caption h4,.carousel-caption p{color:#fff}.hero-unit{padding:60px;margin-bottom:30px;background-color:#eee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;letter-spacing:-1px;color:inherit}.hero-unit p{font-size:18px;font-weight:200;line-height:27px;color:inherit}.pull-right{float:right}.pull-left{float:left}.hide{display:none}.show{display:block}.invisible{visibility:hidden} diff --git a/pkg/inst/web/css/highlight.css b/pkg/inst/web/css/highlight.css deleted file mode 100644 index 4b85237..0000000 --- a/pkg/inst/web/css/highlight.css +++ /dev/null @@ -1,28 +0,0 @@ -/* Syntax highlighting ---------------------------------------------------- */ - -pre .input { - border-left: 3px solid #ccc; - padding-left: 0.5em; -} -pre .output { - background-color: #eee; -} - -.number {color:rgb(21,20,181);} -.functioncall {color:#264D66 ;} -.string {color:#375D81 ;} -.keyword {font-weight:bolder ;color:black;} -.argument {color:#264D66 ;} -.comment {color: #333;} -.formalargs {color: #264D66;} -.eqformalargs {color:#264D66;} -.slot {font-style:italic;} -.symbol {color:black ;} -.prompt {color:black ;} - -pre img { - background-color: #fff; - border: 1px solid #ccc; - display: block; - margin: 0.5em auto 0.5em auto; -} diff --git a/pkg/inst/web/css/staticdocs.css b/pkg/inst/web/css/staticdocs.css deleted file mode 100644 index 9fee28b..0000000 --- a/pkg/inst/web/css/staticdocs.css +++ /dev/null @@ -1,18 +0,0 @@ -h2 {padding-top: 20px} - -.icon img { - float: right; - border: 1px solid #ccc; -} -.index .internal {display: none;} -ul.index li {margin-bottom: 0.5em; clear: both;} - -footer { - margin-top: 45px; - padding: 35px 0 36px; - border-top: 1px solid #e5e5e5; -} -footer p { - margin-bottom: 0; - color: #555; -} diff --git a/pkg/inst/web/drift_data_JKI.html b/pkg/inst/web/drift_data_JKI.html deleted file mode 100644 index c3471c9..0000000 --- a/pkg/inst/web/drift_data_JKI.html +++ /dev/null @@ -1,239 +0,0 @@ - - - - -drift_data_JKI. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Deposition from spray drift expressed as percent of the applied dose as -published by the JKI

          - -
          -
          - -
          -

          Format

          - -

          A list currently containing matrices with spray drift percentage -data for field crops (Ackerbau), and Pome/stone fruit, early and late -(Obstbau frueh, spaet).

          - -
          - -
          -

          Source

          - -

          JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved -from -http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11

          - -
          - -
          -

          Description

          - -

          Deposition from spray drift expressed as percent of the applied dose as -published by the German Julius-Kühn Institute (JKI).

          - -
          - -
          -

          Details

          - -

          The data were extracted from the spreadsheet cited below using the R code -given in the example section. The spreadsheet is not included in the package -as its licence is not clear.

          - -
          - -

          Examples

          - 
          
-## Not run: 
-#   # This is the code that was used to extract the data
-#   library(readxl)
-#   abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"
-#   JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")
-#   names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")
-#   drift_data_JKI <- list()
-# 
-#   for (n in 1:8) {
-#     drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2)
-#     drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) 
-#     dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]),
-#                                             crop = JKI_crops)
-#     drift_data_JKI[[n]] <- drift_data
-#   }
-#   save(drift_data_JKI, file = "data/drift_data_JKI.RData")
-# ## End(Not run)
-
-# And this is the resulting data
-drift_data_JKI
-
          
-
          [[1]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      2.77            NA            NA
-      3        NA         29.20         15.73
-      5      0.57         19.89          8.41
-      10     0.29         11.81          3.60
-      15     0.20          5.55          1.81
-      20     0.15          2.77          1.09
-      30     0.10          1.04          0.54
-      40     0.07          0.52          0.32
-      50     0.06          0.30          0.22
-
-[[2]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      2.38            NA            NA
-      3        NA         25.53         12.13
-      5      0.47         16.87          6.81
-      10     0.24          9.61          3.11
-      15     0.16          5.61          1.58
-      20     0.12          2.59          0.90
-      30     0.08          0.87          0.40
-      40     0.06          0.40          0.23
-      50     0.05          0.22          0.15
-
-[[3]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      2.01            NA            NA
-      3        NA         23.96         11.01
-      5      0.41         15.79          6.04
-      10     0.20          8.96          2.67
-      15     0.14          4.24          1.39
-      20     0.10          2.01          0.80
-      30     0.07          0.70          0.36
-      40     0.05          0.33          0.21
-      50     0.04          0.19          0.13
-
-[[4]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.85            NA            NA
-      3        NA         23.61         10.12
-      5      0.38         15.42          5.60
-      10     0.19          8.66          2.50
-      15     0.13          4.01          1.28
-      20     0.10          1.89          0.75
-      30     0.06          0.66          0.35
-      40     0.05          0.31          0.20
-      50     0.04          0.17          0.13
-
-[[5]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.75            NA            NA
-      3        NA         23.12          9.74
-      5      0.36         15.06          5.41
-      10     0.18          8.42          2.43
-      15     0.12          3.83          1.24
-      20     0.09          1.81          0.72
-      30     0.06          0.63          0.34
-      40     0.05          0.30          0.20
-      50     0.04          0.17          0.13
-
-[[6]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.64            NA            NA
-      3        NA         22.76          9.21
-      5      0.34         14.64          5.18
-      10     0.17          8.04          2.38
-      15     0.11          3.71          1.20
-      20     0.09          1.75          0.68
-      30     0.06          0.61          0.31
-      40     0.04          0.29          0.17
-      50     0.03          0.16          0.11
-
-[[7]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.61            NA            NA
-      3        NA         22.69          9.10
-      5      0.33         14.45          5.11
-      10     0.17          7.83          2.33
-      15     0.11          3.62          1.20
-      20     0.08          1.71          0.67
-      30     0.06          0.60          0.30
-      40     0.04          0.28          0.17
-      50     0.03          0.16          0.11
-
-[[8]]
-        crop
-distance Ackerbau Obstbau frueh Obstbau spaet
-      1      1.52            NA            NA
-      3        NA         22.24          8.66
-      5      0.31         14.09          4.92
-      10     0.16          7.58          2.29
-      15     0.11          3.48          1.14
-      20     0.08          1.65          0.65
-      30     0.05          0.57          0.29
-      40     0.04          0.27          0.16
-      50     0.03          0.15          0.11
-
-
          -
          -
          - - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/endpoint.html b/pkg/inst/web/endpoint.html deleted file mode 100644 index 521f7f4..0000000 --- a/pkg/inst/web/endpoint.html +++ /dev/null @@ -1,142 +0,0 @@ - - - - -endpoint. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Retrieve endpoint information from the chyaml field of a chent object

          - -
          -
          -

          Usage

          - 
          endpoint(chent, medium = "soil", type = c("degradation", "sorption"), lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, raw = FALSE, signif = 3)
          
-
          soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)
          
-
          soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)
          
-
          soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
          
-
          soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE)
          - -

          Arguments

          -
          -
          chent
          -
          The chent object to get the information from
          -
          medium
          -
          The medium for which information is sought
          -
          type
          -
          The information type
          -
          lab_field
          -
          If not NA, do we want laboratory or field endpoints
          -
          redox
          -
          If not NA, are we looking for aerobic or anaerobic data
          -
          value
          -
          The name of the value we want. The list given in the -usage section is not exclusive
          -
          aggregator
          -
          The aggregator function. Can be mean, -geomean, or identity, for example.
          -
          raw
          -
          Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
          -
          signif
          -
          How many significant digits do we want
          -
          values
          -
          The values to be returned
          -
          aggregators
          -
          A named vector of aggregator functions to be used
          -
          - -
          -

          Value

          - -

          -The result from applying the aggregator function to - the values converted to a numeric vector, rounded to the - given number of significant digits, or, if raw = TRUE, - the values as a character value, retaining any implicit - information on precision that may be present. -

          - -
          - -
          -

          Description

          - -

          R6 class objects of class chent represent chemical entities -and can hold a list of information loaded from a chemical yaml file in their -chyaml field. Such information is extracted and optionally aggregated by -this function.

          - -
          - -
          -

          Details

          - -

          The functions soil_* are functions to extract soil specific endpoints. -For the Freundlich exponent, the capital letter N is used in order to -facilitate dealing with such data in R. In pesticide fate modelling, this -exponent is often called 1/n.

          - -
          -
          -
          - - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/geomean.html b/pkg/inst/web/geomean.html deleted file mode 100644 index 672e9b5..0000000 --- a/pkg/inst/web/geomean.html +++ /dev/null @@ -1,121 +0,0 @@ - - - - -geomean. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -

          Calculate the geometric mean

          - -
          -
          -

          Usage

          - 
          geomean(x, na.rm = TRUE)
          - -

          Arguments

          -
          -
          x
          -
          Vector of numbers
          -
          na.rm
          -
          Should NA values be omitted?
          -
          - -
          -

          Value

          - -

          -The geometric mean -

          - -
          - -
          -

          Description

          - -

          Based on some posts in a thread on Stackoverflow -http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in -This function checks for negative values, removes NA values per default and -returns 0 if at least one element of the vector is 0.

          - -
          - -

          Examples

          - 
          geomean(c(1, 3, 9))
-
          
-
          [1] 3
-
          
-
          geomean(c(1, 3, NA, 9))
-
          
-
          [1] 3
-
          
-
          ## Not run: geomean(c(1, -3, 9)) # returns an error
-
          -
          -
          - - - -

          Author

          - -Johannes Ranke - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/img/glyphicons-halflings-white.png b/pkg/inst/web/img/glyphicons-halflings-white.png deleted file mode 100644 index 3bf6484..0000000 Binary files a/pkg/inst/web/img/glyphicons-halflings-white.png and /dev/null differ diff --git a/pkg/inst/web/img/glyphicons-halflings.png b/pkg/inst/web/img/glyphicons-halflings.png deleted file mode 100644 index 79bc568..0000000 Binary files a/pkg/inst/web/img/glyphicons-halflings.png and /dev/null differ diff --git a/pkg/inst/web/index.html b/pkg/inst/web/index.html deleted file mode 100644 index 54f0f35..0000000 --- a/pkg/inst/web/index.html +++ /dev/null @@ -1,182 +0,0 @@ - - - - -Index. pfm 0.3-7 - - - - - - - - - - - - - - - -
          -
          -
          - pfm 0.3-7 -
          - -
          -
          -
          -
          - -
          -
          - -
          - -
          -
          - Utilities for simple calculations of predicted environmental -concentrations (PECs) and for dealing with data from some FOCUS pesticide -fate modelling software packages. - -

          Help topics

          - -

          Degradation

          -

          Functions related to degradation

          - - -
            - -
          • - pfm_degradation
            Calculate a time course of relative concentrations based on an mkinmod model
            • - -
          • - SFO_actual_twa
            Actual and maximum moving window time average concentrations for SFO kinetics
            • - -
          -

          Mobility

          -

          Indicators related to mobility

          - - -
            - -
          • - GUS(GUS.chent, GUS.numeric, print.GUS_result)
            Groundwater ubiquity score based on Gustafson (1989)
            • - -
          • - SSLRC_mobility_classification
            Determine the SSLRC mobility classification for a chemical substance from its Koc
            • - -
          -

          Soil

          -

          Predicted environmental concentrations in soil

          - - -
            - -
          • - PEC_soil
            Calculate predicted environmental concentrations in soil
            • - -
          • - soil_scenario_data_EFSA_2015
            Properties of the predefined scenarios from the EFSA guidance from 2015
            • - -
          -

          Surface water

          -

          Predicted environmental concentrations in surface water

          - - -
            - -
          • - PEC_sw_drift
            Calculate predicted environmental concentrations in surface water due to drift
            • - -
          • - PEC_sw_sed
            Calculate predicted environmental concentrations in sediment from surface -
            • - -
          • - drift_data_JKI
            Deposition from spray drift expressed as percent of the applied dose as -
            • - -
          • - PEC_sw_drainage_UK
            Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method
            • - -
          • - TOXSWA_cwa
            R6 class for holding TOXSWA cwa concentration data and associated statistics
            • - -
          • - read.TOXSWA_cwa
            Read TOXSWA surface water concentrations
            • - -
          • - plot.TOXSWA_cwa
            Plot TOXSWA surface water concentrations
            • - -
          -

          Groundwater

          -

          Predicted environmental concentrations in groundwater

          - - - -

          Chemical entities

          -

          Work with input stored in chemical entites as R objects using the chent package

          - - -
            - -
          • - endpoint(soil_DT50, soil_Kfoc, soil_N, soil_sorption)
            Retrieve endpoint information from the chyaml field of a chent object
            • - -
          -

          General

          -

          Utilities that are generally useful

          - - -
            - -
          • - geomean
            Calculate the geometric mean
            • - -
          -
          - -
          - -

          Dependencies

          -
            -
          • Depends: R6, mkin
            • -
          • Imports: graphics, chents, readr, methods
            • -
          • Suggests: testthat
            • - -
          -

          Authors

          - - -
          -
          - - -
          - - \ No newline at end of file diff --git a/pkg/inst/web/js/bootstrap.js b/pkg/inst/web/js/bootstrap.js deleted file mode 100644 index 5d6e65b..0000000 --- a/pkg/inst/web/js/bootstrap.js +++ /dev/null @@ -1,1825 +0,0 @@ -/* =================================================== - * bootstrap-transition.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#transitions - * =================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - $(function () { - - "use strict"; // jshint ;_; - - - /* CSS TRANSITION SUPPORT (http://www.modernizr.com/) - * ======================================================= */ - - $.support.transition = (function () { - - var transitionEnd = (function () { - - var el = document.createElement('bootstrap') - , transEndEventNames = { - 'WebkitTransition' : 'webkitTransitionEnd' - , 'MozTransition' : 'transitionend' - , 'OTransition' : 'oTransitionEnd' - , 'msTransition' : 'MSTransitionEnd' - , 'transition' : 'transitionend' - } - , name - - for (name in transEndEventNames){ - if (el.style[name] !== undefined) { - return transEndEventNames[name] - } - } - - }()) - - return transitionEnd && { - end: transitionEnd - } - - })() - - }) - -}(window.jQuery);/* ========================================================== - * bootstrap-alert.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#alerts - * ========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* ALERT CLASS DEFINITION - * ====================== */ - - var dismiss = '[data-dismiss="alert"]' - , Alert = function (el) { - $(el).on('click', dismiss, this.close) - } - - Alert.prototype.close = function (e) { - var $this = $(this) - , selector = $this.attr('data-target') - , $parent - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - $parent = $(selector) - - e && e.preventDefault() - - $parent.length || ($parent = $this.hasClass('alert') ? $this : $this.parent()) - - $parent.trigger(e = $.Event('close')) - - if (e.isDefaultPrevented()) return - - $parent.removeClass('in') - - function removeElement() { - $parent - .trigger('closed') - .remove() - } - - $.support.transition && $parent.hasClass('fade') ? - $parent.on($.support.transition.end, removeElement) : - removeElement() - } - - - /* ALERT PLUGIN DEFINITION - * ======================= */ - - $.fn.alert = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('alert') - if (!data) $this.data('alert', (data = new Alert(this))) - if (typeof option == 'string') data[option].call($this) - }) - } - - $.fn.alert.Constructor = Alert - - - /* ALERT DATA-API - * ============== */ - - $(function () { - $('body').on('click.alert.data-api', dismiss, Alert.prototype.close) - }) - -}(window.jQuery);/* ============================================================ - * bootstrap-button.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#buttons - * ============================================================ - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* BUTTON PUBLIC CLASS DEFINITION - * ============================== */ - - var Button = function (element, options) { - this.$element = $(element) - this.options = $.extend({}, $.fn.button.defaults, options) - } - - Button.prototype.setState = function (state) { - var d = 'disabled' - , $el = this.$element - , data = $el.data() - , val = $el.is('input') ? 'val' : 'html' - - state = state + 'Text' - data.resetText || $el.data('resetText', $el[val]()) - - $el[val](data[state] || this.options[state]) - - // push to event loop to allow forms to submit - setTimeout(function () { - state == 'loadingText' ? - $el.addClass(d).attr(d, d) : - $el.removeClass(d).removeAttr(d) - }, 0) - } - - Button.prototype.toggle = function () { - var $parent = this.$element.parent('[data-toggle="buttons-radio"]') - - $parent && $parent - .find('.active') - .removeClass('active') - - this.$element.toggleClass('active') - } - - - /* BUTTON PLUGIN DEFINITION - * ======================== */ - - $.fn.button = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('button') - , options = typeof option == 'object' && option - if (!data) $this.data('button', (data = new Button(this, options))) - if (option == 'toggle') data.toggle() - else if (option) data.setState(option) - }) - } - - $.fn.button.defaults = { - loadingText: 'loading...' - } - - $.fn.button.Constructor = Button - - - /* BUTTON DATA-API - * =============== */ - - $(function () { - $('body').on('click.button.data-api', '[data-toggle^=button]', function ( e ) { - var $btn = $(e.target) - if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn') - $btn.button('toggle') - }) - }) - -}(window.jQuery);/* ========================================================== - * bootstrap-carousel.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#carousel - * ========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* CAROUSEL CLASS DEFINITION - * ========================= */ - - var Carousel = function (element, options) { - this.$element = $(element) - this.options = options - this.options.slide && this.slide(this.options.slide) - this.options.pause == 'hover' && this.$element - .on('mouseenter', $.proxy(this.pause, this)) - .on('mouseleave', $.proxy(this.cycle, this)) - } - - Carousel.prototype = { - - cycle: function (e) { - if (!e) this.paused = false - this.options.interval - && !this.paused - && (this.interval = setInterval($.proxy(this.next, this), this.options.interval)) - return this - } - - , to: function (pos) { - var $active = this.$element.find('.active') - , children = $active.parent().children() - , activePos = children.index($active) - , that = this - - if (pos > (children.length - 1) || pos < 0) return - - if (this.sliding) { - return this.$element.one('slid', function () { - that.to(pos) - }) - } - - if (activePos == pos) { - return this.pause().cycle() - } - - return this.slide(pos > activePos ? 'next' : 'prev', $(children[pos])) - } - - , pause: function (e) { - if (!e) this.paused = true - clearInterval(this.interval) - this.interval = null - return this - } - - , next: function () { - if (this.sliding) return - return this.slide('next') - } - - , prev: function () { - if (this.sliding) return - return this.slide('prev') - } - - , slide: function (type, next) { - var $active = this.$element.find('.active') - , $next = next || $active[type]() - , isCycling = this.interval - , direction = type == 'next' ? 'left' : 'right' - , fallback = type == 'next' ? 'first' : 'last' - , that = this - , e = $.Event('slide') - - this.sliding = true - - isCycling && this.pause() - - $next = $next.length ? $next : this.$element.find('.item')[fallback]() - - if ($next.hasClass('active')) return - - if ($.support.transition && this.$element.hasClass('slide')) { - this.$element.trigger(e) - if (e.isDefaultPrevented()) return - $next.addClass(type) - $next[0].offsetWidth // force reflow - $active.addClass(direction) - $next.addClass(direction) - this.$element.one($.support.transition.end, function () { - $next.removeClass([type, direction].join(' ')).addClass('active') - $active.removeClass(['active', direction].join(' ')) - that.sliding = false - setTimeout(function () { that.$element.trigger('slid') }, 0) - }) - } else { - this.$element.trigger(e) - if (e.isDefaultPrevented()) return - $active.removeClass('active') - $next.addClass('active') - this.sliding = false - this.$element.trigger('slid') - } - - isCycling && this.cycle() - - return this - } - - } - - - /* CAROUSEL PLUGIN DEFINITION - * ========================== */ - - $.fn.carousel = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('carousel') - , options = $.extend({}, $.fn.carousel.defaults, typeof option == 'object' && option) - if (!data) $this.data('carousel', (data = new Carousel(this, options))) - if (typeof option == 'number') data.to(option) - else if (typeof option == 'string' || (option = options.slide)) data[option]() - else if (options.interval) data.cycle() - }) - } - - $.fn.carousel.defaults = { - interval: 5000 - , pause: 'hover' - } - - $.fn.carousel.Constructor = Carousel - - - /* CAROUSEL DATA-API - * ================= */ - - $(function () { - $('body').on('click.carousel.data-api', '[data-slide]', function ( e ) { - var $this = $(this), href - , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - , options = !$target.data('modal') && $.extend({}, $target.data(), $this.data()) - $target.carousel(options) - e.preventDefault() - }) - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-collapse.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#collapse - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* COLLAPSE PUBLIC CLASS DEFINITION - * ================================ */ - - var Collapse = function (element, options) { - this.$element = $(element) - this.options = $.extend({}, $.fn.collapse.defaults, options) - - if (this.options.parent) { - this.$parent = $(this.options.parent) - } - - this.options.toggle && this.toggle() - } - - Collapse.prototype = { - - constructor: Collapse - - , dimension: function () { - var hasWidth = this.$element.hasClass('width') - return hasWidth ? 'width' : 'height' - } - - , show: function () { - var dimension - , scroll - , actives - , hasData - - if (this.transitioning) return - - dimension = this.dimension() - scroll = $.camelCase(['scroll', dimension].join('-')) - actives = this.$parent && this.$parent.find('> .accordion-group > .in') - - if (actives && actives.length) { - hasData = actives.data('collapse') - if (hasData && hasData.transitioning) return - actives.collapse('hide') - hasData || actives.data('collapse', null) - } - - this.$element[dimension](0) - this.transition('addClass', $.Event('show'), 'shown') - this.$element[dimension](this.$element[0][scroll]) - } - - , hide: function () { - var dimension - if (this.transitioning) return - dimension = this.dimension() - this.reset(this.$element[dimension]()) - this.transition('removeClass', $.Event('hide'), 'hidden') - this.$element[dimension](0) - } - - , reset: function (size) { - var dimension = this.dimension() - - this.$element - .removeClass('collapse') - [dimension](size || 'auto') - [0].offsetWidth - - this.$element[size !== null ? 'addClass' : 'removeClass']('collapse') - - return this - } - - , transition: function (method, startEvent, completeEvent) { - var that = this - , complete = function () { - if (startEvent.type == 'show') that.reset() - that.transitioning = 0 - that.$element.trigger(completeEvent) - } - - this.$element.trigger(startEvent) - - if (startEvent.isDefaultPrevented()) return - - this.transitioning = 1 - - this.$element[method]('in') - - $.support.transition && this.$element.hasClass('collapse') ? - this.$element.one($.support.transition.end, complete) : - complete() - } - - , toggle: function () { - this[this.$element.hasClass('in') ? 'hide' : 'show']() - } - - } - - - /* COLLAPSIBLE PLUGIN DEFINITION - * ============================== */ - - $.fn.collapse = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('collapse') - , options = typeof option == 'object' && option - if (!data) $this.data('collapse', (data = new Collapse(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.collapse.defaults = { - toggle: true - } - - $.fn.collapse.Constructor = Collapse - - - /* COLLAPSIBLE DATA-API - * ==================== */ - - $(function () { - $('body').on('click.collapse.data-api', '[data-toggle=collapse]', function ( e ) { - var $this = $(this), href - , target = $this.attr('data-target') - || e.preventDefault() - || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7 - , option = $(target).data('collapse') ? 'toggle' : $this.data() - $(target).collapse(option) - }) - }) - -}(window.jQuery);/* ============================================================ - * bootstrap-dropdown.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#dropdowns - * ============================================================ - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* DROPDOWN CLASS DEFINITION - * ========================= */ - - var toggle = '[data-toggle="dropdown"]' - , Dropdown = function (element) { - var $el = $(element).on('click.dropdown.data-api', this.toggle) - $('html').on('click.dropdown.data-api', function () { - $el.parent().removeClass('open') - }) - } - - Dropdown.prototype = { - - constructor: Dropdown - - , toggle: function (e) { - var $this = $(this) - , $parent - , selector - , isActive - - if ($this.is('.disabled, :disabled')) return - - selector = $this.attr('data-target') - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - $parent = $(selector) - $parent.length || ($parent = $this.parent()) - - isActive = $parent.hasClass('open') - - clearMenus() - - if (!isActive) $parent.toggleClass('open') - - return false - } - - } - - function clearMenus() { - $(toggle).parent().removeClass('open') - } - - - /* DROPDOWN PLUGIN DEFINITION - * ========================== */ - - $.fn.dropdown = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('dropdown') - if (!data) $this.data('dropdown', (data = new Dropdown(this))) - if (typeof option == 'string') data[option].call($this) - }) - } - - $.fn.dropdown.Constructor = Dropdown - - - /* APPLY TO STANDARD DROPDOWN ELEMENTS - * =================================== */ - - $(function () { - $('html').on('click.dropdown.data-api', clearMenus) - $('body') - .on('click.dropdown', '.dropdown form', function (e) { e.stopPropagation() }) - .on('click.dropdown.data-api', toggle, Dropdown.prototype.toggle) - }) - -}(window.jQuery);/* ========================================================= - * bootstrap-modal.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#modals - * ========================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================= */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* MODAL CLASS DEFINITION - * ====================== */ - - var Modal = function (content, options) { - this.options = options - this.$element = $(content) - .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this)) - } - - Modal.prototype = { - - constructor: Modal - - , toggle: function () { - return this[!this.isShown ? 'show' : 'hide']() - } - - , show: function () { - var that = this - , e = $.Event('show') - - this.$element.trigger(e) - - if (this.isShown || e.isDefaultPrevented()) return - - $('body').addClass('modal-open') - - this.isShown = true - - escape.call(this) - backdrop.call(this, function () { - var transition = $.support.transition && that.$element.hasClass('fade') - - if (!that.$element.parent().length) { - that.$element.appendTo(document.body) //don't move modals dom position - } - - that.$element - .show() - - if (transition) { - that.$element[0].offsetWidth // force reflow - } - - that.$element.addClass('in') - - transition ? - that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) : - that.$element.trigger('shown') - - }) - } - - , hide: function (e) { - e && e.preventDefault() - - var that = this - - e = $.Event('hide') - - this.$element.trigger(e) - - if (!this.isShown || e.isDefaultPrevented()) return - - this.isShown = false - - $('body').removeClass('modal-open') - - escape.call(this) - - this.$element.removeClass('in') - - $.support.transition && this.$element.hasClass('fade') ? - hideWithTransition.call(this) : - hideModal.call(this) - } - - } - - - /* MODAL PRIVATE METHODS - * ===================== */ - - function hideWithTransition() { - var that = this - , timeout = setTimeout(function () { - that.$element.off($.support.transition.end) - hideModal.call(that) - }, 500) - - this.$element.one($.support.transition.end, function () { - clearTimeout(timeout) - hideModal.call(that) - }) - } - - function hideModal(that) { - this.$element - .hide() - .trigger('hidden') - - backdrop.call(this) - } - - function backdrop(callback) { - var that = this - , animate = this.$element.hasClass('fade') ? 'fade' : '' - - if (this.isShown && this.options.backdrop) { - var doAnimate = $.support.transition && animate - - this.$backdrop = $('
          ') - .appendTo(document.body) - - if (this.options.backdrop != 'static') { - this.$backdrop.click($.proxy(this.hide, this)) - } - - if (doAnimate) this.$backdrop[0].offsetWidth // force reflow - - this.$backdrop.addClass('in') - - doAnimate ? - this.$backdrop.one($.support.transition.end, callback) : - callback() - - } else if (!this.isShown && this.$backdrop) { - this.$backdrop.removeClass('in') - - $.support.transition && this.$element.hasClass('fade')? - this.$backdrop.one($.support.transition.end, $.proxy(removeBackdrop, this)) : - removeBackdrop.call(this) - - } else if (callback) { - callback() - } - } - - function removeBackdrop() { - this.$backdrop.remove() - this.$backdrop = null - } - - function escape() { - var that = this - if (this.isShown && this.options.keyboard) { - $(document).on('keyup.dismiss.modal', function ( e ) { - e.which == 27 && that.hide() - }) - } else if (!this.isShown) { - $(document).off('keyup.dismiss.modal') - } - } - - - /* MODAL PLUGIN DEFINITION - * ======================= */ - - $.fn.modal = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('modal') - , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option) - if (!data) $this.data('modal', (data = new Modal(this, options))) - if (typeof option == 'string') data[option]() - else if (options.show) data.show() - }) - } - - $.fn.modal.defaults = { - backdrop: true - , keyboard: true - , show: true - } - - $.fn.modal.Constructor = Modal - - - /* MODAL DATA-API - * ============== */ - - $(function () { - $('body').on('click.modal.data-api', '[data-toggle="modal"]', function ( e ) { - var $this = $(this), href - , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - , option = $target.data('modal') ? 'toggle' : $.extend({}, $target.data(), $this.data()) - - e.preventDefault() - $target.modal(option) - }) - }) - -}(window.jQuery);/* =========================================================== - * bootstrap-tooltip.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tooltips - * Inspired by the original jQuery.tipsy by Jason Frame - * =========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* TOOLTIP PUBLIC CLASS DEFINITION - * =============================== */ - - var Tooltip = function (element, options) { - this.init('tooltip', element, options) - } - - Tooltip.prototype = { - - constructor: Tooltip - - , init: function (type, element, options) { - var eventIn - , eventOut - - this.type = type - this.$element = $(element) - this.options = this.getOptions(options) - this.enabled = true - - if (this.options.trigger != 'manual') { - eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus' - eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur' - this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this)) - this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this)) - } - - this.options.selector ? - (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : - this.fixTitle() - } - - , getOptions: function (options) { - options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data()) - - if (options.delay && typeof options.delay == 'number') { - options.delay = { - show: options.delay - , hide: options.delay - } - } - - return options - } - - , enter: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) - - if (!self.options.delay || !self.options.delay.show) return self.show() - - clearTimeout(this.timeout) - self.hoverState = 'in' - this.timeout = setTimeout(function() { - if (self.hoverState == 'in') self.show() - }, self.options.delay.show) - } - - , leave: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) - - if (this.timeout) clearTimeout(this.timeout) - if (!self.options.delay || !self.options.delay.hide) return self.hide() - - self.hoverState = 'out' - this.timeout = setTimeout(function() { - if (self.hoverState == 'out') self.hide() - }, self.options.delay.hide) - } - - , show: function () { - var $tip - , inside - , pos - , actualWidth - , actualHeight - , placement - , tp - - if (this.hasContent() && this.enabled) { - $tip = this.tip() - this.setContent() - - if (this.options.animation) { - $tip.addClass('fade') - } - - placement = typeof this.options.placement == 'function' ? - this.options.placement.call(this, $tip[0], this.$element[0]) : - this.options.placement - - inside = /in/.test(placement) - - $tip - .remove() - .css({ top: 0, left: 0, display: 'block' }) - .appendTo(inside ? this.$element : document.body) - - pos = this.getPosition(inside) - - actualWidth = $tip[0].offsetWidth - actualHeight = $tip[0].offsetHeight - - switch (inside ? placement.split(' ')[1] : placement) { - case 'bottom': - tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'top': - tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'left': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth} - break - case 'right': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width} - break - } - - $tip - .css(tp) - .addClass(placement) - .addClass('in') - } - } - - , isHTML: function(text) { - // html string detection logic adapted from jQuery - return typeof text != 'string' - || ( text.charAt(0) === "<" - && text.charAt( text.length - 1 ) === ">" - && text.length >= 3 - ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text) - } - - , setContent: function () { - var $tip = this.tip() - , title = this.getTitle() - - $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title) - $tip.removeClass('fade in top bottom left right') - } - - , hide: function () { - var that = this - , $tip = this.tip() - - $tip.removeClass('in') - - function removeWithAnimation() { - var timeout = setTimeout(function () { - $tip.off($.support.transition.end).remove() - }, 500) - - $tip.one($.support.transition.end, function () { - clearTimeout(timeout) - $tip.remove() - }) - } - - $.support.transition && this.$tip.hasClass('fade') ? - removeWithAnimation() : - $tip.remove() - } - - , fixTitle: function () { - var $e = this.$element - if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { - $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title') - } - } - - , hasContent: function () { - return this.getTitle() - } - - , getPosition: function (inside) { - return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), { - width: this.$element[0].offsetWidth - , height: this.$element[0].offsetHeight - }) - } - - , getTitle: function () { - var title - , $e = this.$element - , o = this.options - - title = $e.attr('data-original-title') - || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) - - return title - } - - , tip: function () { - return this.$tip = this.$tip || $(this.options.template) - } - - , validate: function () { - if (!this.$element[0].parentNode) { - this.hide() - this.$element = null - this.options = null - } - } - - , enable: function () { - this.enabled = true - } - - , disable: function () { - this.enabled = false - } - - , toggleEnabled: function () { - this.enabled = !this.enabled - } - - , toggle: function () { - this[this.tip().hasClass('in') ? 'hide' : 'show']() - } - - } - - - /* TOOLTIP PLUGIN DEFINITION - * ========================= */ - - $.fn.tooltip = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('tooltip') - , options = typeof option == 'object' && option - if (!data) $this.data('tooltip', (data = new Tooltip(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.tooltip.Constructor = Tooltip - - $.fn.tooltip.defaults = { - animation: true - , placement: 'top' - , selector: false - , template: '
          ' - , trigger: 'hover' - , title: '' - , delay: 0 - } - -}(window.jQuery); -/* =========================================================== - * bootstrap-popover.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#popovers - * =========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * =========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* POPOVER PUBLIC CLASS DEFINITION - * =============================== */ - - var Popover = function ( element, options ) { - this.init('popover', element, options) - } - - - /* NOTE: POPOVER EXTENDS BOOTSTRAP-TOOLTIP.js - ========================================== */ - - Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype, { - - constructor: Popover - - , setContent: function () { - var $tip = this.tip() - , title = this.getTitle() - , content = this.getContent() - - $tip.find('.popover-title')[this.isHTML(title) ? 'html' : 'text'](title) - $tip.find('.popover-content > *')[this.isHTML(content) ? 'html' : 'text'](content) - - $tip.removeClass('fade top bottom left right in') - } - - , hasContent: function () { - return this.getTitle() || this.getContent() - } - - , getContent: function () { - var content - , $e = this.$element - , o = this.options - - content = $e.attr('data-content') - || (typeof o.content == 'function' ? o.content.call($e[0]) : o.content) - - return content - } - - , tip: function () { - if (!this.$tip) { - this.$tip = $(this.options.template) - } - return this.$tip - } - - }) - - - /* POPOVER PLUGIN DEFINITION - * ======================= */ - - $.fn.popover = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('popover') - , options = typeof option == 'object' && option - if (!data) $this.data('popover', (data = new Popover(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.popover.Constructor = Popover - - $.fn.popover.defaults = $.extend({} , $.fn.tooltip.defaults, { - placement: 'right' - , content: '' - , template: '

          ' - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-scrollspy.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#scrollspy - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* SCROLLSPY CLASS DEFINITION - * ========================== */ - - function ScrollSpy( element, options) { - var process = $.proxy(this.process, this) - , $element = $(element).is('body') ? $(window) : $(element) - , href - this.options = $.extend({}, $.fn.scrollspy.defaults, options) - this.$scrollElement = $element.on('scroll.scroll.data-api', process) - this.selector = (this.options.target - || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - || '') + ' .nav li > a' - this.$body = $('body') - this.refresh() - this.process() - } - - ScrollSpy.prototype = { - - constructor: ScrollSpy - - , refresh: function () { - var self = this - , $targets - - this.offsets = $([]) - this.targets = $([]) - - $targets = this.$body - .find(this.selector) - .map(function () { - var $el = $(this) - , href = $el.data('target') || $el.attr('href') - , $href = /^#\w/.test(href) && $(href) - return ( $href - && href.length - && [[ $href.position().top, href ]] ) || null - }) - .sort(function (a, b) { return a[0] - b[0] }) - .each(function () { - self.offsets.push(this[0]) - self.targets.push(this[1]) - }) - } - - , process: function () { - var scrollTop = this.$scrollElement.scrollTop() + this.options.offset - , scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight - , maxScroll = scrollHeight - this.$scrollElement.height() - , offsets = this.offsets - , targets = this.targets - , activeTarget = this.activeTarget - , i - - if (scrollTop >= maxScroll) { - return activeTarget != (i = targets.last()[0]) - && this.activate ( i ) - } - - for (i = offsets.length; i--;) { - activeTarget != targets[i] - && scrollTop >= offsets[i] - && (!offsets[i + 1] || scrollTop <= offsets[i + 1]) - && this.activate( targets[i] ) - } - } - - , activate: function (target) { - var active - , selector - - this.activeTarget = target - - $(this.selector) - .parent('.active') - .removeClass('active') - - selector = this.selector - + '[data-target="' + target + '"],' - + this.selector + '[href="' + target + '"]' - - active = $(selector) - .parent('li') - .addClass('active') - - if (active.parent('.dropdown-menu')) { - active = active.closest('li.dropdown').addClass('active') - } - - active.trigger('activate') - } - - } - - - /* SCROLLSPY PLUGIN DEFINITION - * =========================== */ - - $.fn.scrollspy = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('scrollspy') - , options = typeof option == 'object' && option - if (!data) $this.data('scrollspy', (data = new ScrollSpy(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.scrollspy.Constructor = ScrollSpy - - $.fn.scrollspy.defaults = { - offset: 10 - } - - - /* SCROLLSPY DATA-API - * ================== */ - - $(function () { - $('[data-spy="scroll"]').each(function () { - var $spy = $(this) - $spy.scrollspy($spy.data()) - }) - }) - -}(window.jQuery);/* ======================================================== - * bootstrap-tab.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tabs - * ======================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ======================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* TAB CLASS DEFINITION - * ==================== */ - - var Tab = function ( element ) { - this.element = $(element) - } - - Tab.prototype = { - - constructor: Tab - - , show: function () { - var $this = this.element - , $ul = $this.closest('ul:not(.dropdown-menu)') - , selector = $this.attr('data-target') - , previous - , $target - , e - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - if ( $this.parent('li').hasClass('active') ) return - - previous = $ul.find('.active a').last()[0] - - e = $.Event('show', { - relatedTarget: previous - }) - - $this.trigger(e) - - if (e.isDefaultPrevented()) return - - $target = $(selector) - - this.activate($this.parent('li'), $ul) - this.activate($target, $target.parent(), function () { - $this.trigger({ - type: 'shown' - , relatedTarget: previous - }) - }) - } - - , activate: function ( element, container, callback) { - var $active = container.find('> .active') - , transition = callback - && $.support.transition - && $active.hasClass('fade') - - function next() { - $active - .removeClass('active') - .find('> .dropdown-menu > .active') - .removeClass('active') - - element.addClass('active') - - if (transition) { - element[0].offsetWidth // reflow for transition - element.addClass('in') - } else { - element.removeClass('fade') - } - - if ( element.parent('.dropdown-menu') ) { - element.closest('li.dropdown').addClass('active') - } - - callback && callback() - } - - transition ? - $active.one($.support.transition.end, next) : - next() - - $active.removeClass('in') - } - } - - - /* TAB PLUGIN DEFINITION - * ===================== */ - - $.fn.tab = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('tab') - if (!data) $this.data('tab', (data = new Tab(this))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.tab.Constructor = Tab - - - /* TAB DATA-API - * ============ */ - - $(function () { - $('body').on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) { - e.preventDefault() - $(this).tab('show') - }) - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-typeahead.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#typeahead - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function($){ - - "use strict"; // jshint ;_; - - - /* TYPEAHEAD PUBLIC CLASS DEFINITION - * ================================= */ - - var Typeahead = function (element, options) { - this.$element = $(element) - this.options = $.extend({}, $.fn.typeahead.defaults, options) - this.matcher = this.options.matcher || this.matcher - this.sorter = this.options.sorter || this.sorter - this.highlighter = this.options.highlighter || this.highlighter - this.updater = this.options.updater || this.updater - this.$menu = $(this.options.menu).appendTo('body') - this.source = this.options.source - this.shown = false - this.listen() - } - - Typeahead.prototype = { - - constructor: Typeahead - - , select: function () { - var val = this.$menu.find('.active').attr('data-value') - this.$element - .val(this.updater(val)) - .change() - return this.hide() - } - - , updater: function (item) { - return item - } - - , show: function () { - var pos = $.extend({}, this.$element.offset(), { - height: this.$element[0].offsetHeight - }) - - this.$menu.css({ - top: pos.top + pos.height - , left: pos.left - }) - - this.$menu.show() - this.shown = true - return this - } - - , hide: function () { - this.$menu.hide() - this.shown = false - return this - } - - , lookup: function (event) { - var that = this - , items - , q - - this.query = this.$element.val() - - if (!this.query) { - return this.shown ? this.hide() : this - } - - items = $.grep(this.source, function (item) { - return that.matcher(item) - }) - - items = this.sorter(items) - - if (!items.length) { - return this.shown ? this.hide() : this - } - - return this.render(items.slice(0, this.options.items)).show() - } - - , matcher: function (item) { - return ~item.toLowerCase().indexOf(this.query.toLowerCase()) - } - - , sorter: function (items) { - var beginswith = [] - , caseSensitive = [] - , caseInsensitive = [] - , item - - while (item = items.shift()) { - if (!item.toLowerCase().indexOf(this.query.toLowerCase())) beginswith.push(item) - else if (~item.indexOf(this.query)) caseSensitive.push(item) - else caseInsensitive.push(item) - } - - return beginswith.concat(caseSensitive, caseInsensitive) - } - - , highlighter: function (item) { - var query = this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, '\\$&') - return item.replace(new RegExp('(' + query + ')', 'ig'), function ($1, match) { - return '' + match + '' - }) - } - - , render: function (items) { - var that = this - - items = $(items).map(function (i, item) { - i = $(that.options.item).attr('data-value', item) - i.find('a').html(that.highlighter(item)) - return i[0] - }) - - items.first().addClass('active') - this.$menu.html(items) - return this - } - - , next: function (event) { - var active = this.$menu.find('.active').removeClass('active') - , next = active.next() - - if (!next.length) { - next = $(this.$menu.find('li')[0]) - } - - next.addClass('active') - } - - , prev: function (event) { - var active = this.$menu.find('.active').removeClass('active') - , prev = active.prev() - - if (!prev.length) { - prev = this.$menu.find('li').last() - } - - prev.addClass('active') - } - - , listen: function () { - this.$element - .on('blur', $.proxy(this.blur, this)) - .on('keypress', $.proxy(this.keypress, this)) - .on('keyup', $.proxy(this.keyup, this)) - - if ($.browser.webkit || $.browser.msie) { - this.$element.on('keydown', $.proxy(this.keypress, this)) - } - - this.$menu - .on('click', $.proxy(this.click, this)) - .on('mouseenter', 'li', $.proxy(this.mouseenter, this)) - } - - , keyup: function (e) { - switch(e.keyCode) { - case 40: // down arrow - case 38: // up arrow - break - - case 9: // tab - case 13: // enter - if (!this.shown) return - this.select() - break - - case 27: // escape - if (!this.shown) return - this.hide() - break - - default: - this.lookup() - } - - e.stopPropagation() - e.preventDefault() - } - - , keypress: function (e) { - if (!this.shown) return - - switch(e.keyCode) { - case 9: // tab - case 13: // enter - case 27: // escape - e.preventDefault() - break - - case 38: // up arrow - if (e.type != 'keydown') break - e.preventDefault() - this.prev() - break - - case 40: // down arrow - if (e.type != 'keydown') break - e.preventDefault() - this.next() - break - } - - e.stopPropagation() - } - - , blur: function (e) { - var that = this - setTimeout(function () { that.hide() }, 150) - } - - , click: function (e) { - e.stopPropagation() - e.preventDefault() - this.select() - } - - , mouseenter: function (e) { - this.$menu.find('.active').removeClass('active') - $(e.currentTarget).addClass('active') - } - - } - - - /* TYPEAHEAD PLUGIN DEFINITION - * =========================== */ - - $.fn.typeahead = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('typeahead') - , options = typeof option == 'object' && option - if (!data) $this.data('typeahead', (data = new Typeahead(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.typeahead.defaults = { - source: [] - , items: 8 - , menu: '
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              ',item:'
              • '},a.fn.typeahead.Constructor=b,a(function(){a("body").on("focus.typeahead.data-api",'[data-provide="typeahead"]',function(b){var c=a(this);if(c.data("typeahead"))return;b.preventDefault(),c.typeahead(c.data())})})}(window.jQuery); \ No newline at end of file diff --git a/pkg/inst/web/pfm_degradation.html b/pkg/inst/web/pfm_degradation.html deleted file mode 100644 index fad64be..0000000 --- a/pkg/inst/web/pfm_degradation.html +++ /dev/null @@ -1,119 +0,0 @@ - - - - -pfm_degradation. pfm 0.3-7 - - - - - - - - - - - - - - - -
              -
              -
              - pfm 0.3-7 -
              - -
              -
              -
              -
              - -
              -
              - -
              - -

              Calculate a time course of relative concentrations based on an mkinmod model

              - -
              -
              -

              Usage

              - 
              pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = step_days))
              - -

              Arguments

              -
              -
              model
              -
              The degradation model to be used. Either a parent only model like -'SFO' or 'FOMC', or an mkinmod object
              -
              DT50
              -
              The half-life. This is only used when simple exponential decline -is calculated (SFO model).
              -
              parms
              -
              The parameters used for the degradation model
              -
              years
              -
              For how many years should the degradation be predicted?
              -
              step_days
              -
              What step size in days should the output have?
              -
              times
              -
              The output times
              -
              - -
              -

              Description

              - -

              Calculate a time course of relative concentrations based on an mkinmod model

              - -
              - -

              Examples

              - 
              head(pfm_degradation("SFO", DT50 = 10))
-
              
-
                time    parent
-1    0 1.0000000
-2    1 0.9330330
-3    2 0.8705506
-4    3 0.8122524
-5    4 0.7578583
-6    5 0.7071068
-
              -
              -
              - - - -

              Author

              - -Johannes Ranke - - -
              -
              - - -
              - - \ No newline at end of file diff --git a/pkg/inst/web/plot.TOXSWA_cwa-2.png b/pkg/inst/web/plot.TOXSWA_cwa-2.png deleted file mode 100644 index 764c7f4..0000000 Binary files a/pkg/inst/web/plot.TOXSWA_cwa-2.png and /dev/null differ diff --git a/pkg/inst/web/plot.TOXSWA_cwa-4.png b/pkg/inst/web/plot.TOXSWA_cwa-4.png deleted file mode 100644 index 764c7f4..0000000 Binary files a/pkg/inst/web/plot.TOXSWA_cwa-4.png and /dev/null differ diff --git a/pkg/inst/web/plot.TOXSWA_cwa.html b/pkg/inst/web/plot.TOXSWA_cwa.html deleted file mode 100644 index a6118df..0000000 --- a/pkg/inst/web/plot.TOXSWA_cwa.html +++ /dev/null @@ -1,119 +0,0 @@ - - - - -plot.TOXSWA_cwa. pfm 0.3-7 - - - - - - - - - - - - - - - -
              -
              -
              - pfm 0.3-7 -
              - -
              -
              -
              -
              - -
              -
              - -
              - -

              Plot TOXSWA surface water concentrations

              - -
              -
              -

              Usage

              - 
              "plot"(x, time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE, total = FALSE, LC_TIME = "C", ...)
              - -

              Arguments

              -
              -
              x
              -
              The TOXSWA_cwa object to be plotted.
              -
              time_column
              -
              What should be used for the time axis. If "t_firstjan" is chosen, -the time is given in days relative to the first of January in the first year.
              -
              xlab, ylab
              -
              Labels for x and y axis.
              -
              add
              -
              Should we add to an existing plot?
              -
              total
              -
              Should the total concentration in water be plotted, including substance sorbed -to suspended matter?
              -
              LC_TIME
              -
              Specification of the locale used to format dates
              -
              ...
              -
              Further arguments passed to plot if we are not adding to an existing plot
              -
              - -
              -

              Description

              - -

              Plot TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body.

              - -
              - -

              Examples

              - 
              H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
-                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                 zipfile = system.file("testdata/SwashProjects.zip",
-                                             package = "pfm"))
-plot(H_sw_D4_pond)
-
              
-
              -
              -
              - - - -

              Author

              - -Johannes Ranke - - -
              -
              - - -
              - - \ No newline at end of file diff --git a/pkg/inst/web/read.TOXSWA_cwa.html b/pkg/inst/web/read.TOXSWA_cwa.html deleted file mode 100644 index 3f2d997..0000000 --- a/pkg/inst/web/read.TOXSWA_cwa.html +++ /dev/null @@ -1,138 +0,0 @@ - - - - -read.TOXSWA_cwa. pfm 0.3-7 - - - - - - - - - - - - - - - -
              -
              -
              - pfm 0.3-7 -
              - -
              -
              -
              -
              - -
              -
              - -
              - -

              Read TOXSWA surface water concentrations

              - -
              -
              -

              Usage

              - 
              read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", substance = "parent", total = FALSE, windows = NULL, thresholds = NULL)
              - -

              Arguments

              -
              -
              filename
              -
              The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).
              -
              basedir
              -
              The path to the directory where the cwa file resides.
              -
              zipfile
              -
              Optional path to a zip file containing the cwa file.
              -
              segment
              -
              The segment for which the data should be read. Either "last", or -the segment number.
              -
              substance
              -
              For TOXSWA 4 .out files, the default value "parent" leads -to reading concentrations of the parent compound. Alternatively, the substance -of interested can be selected by its code name.
              -
              total
              -
              Set this to TRUE in order to read total concentrations as well. This is -only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -files. For .cwa files, the total concentration is always read as well.
              -
              windows
              -
              Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve.
              -
              thresholds
              -
              Numeric vector of threshold concentrations in µg/L for -generating event statistics.
              -
              - -
              -

              Value

              - -

              -An instance of an R6 object of class -TOXSWA_cwa. -

              - -
              - -
              -

              Description

              - -

              Read TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body. Per default, the data for the last -segment are imported. As TOXSWA 4 reports the values at the end of the hour -(ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay).

              - -
              - -

              Examples

              - 
              H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
-                                 basedir = "SwashProjects/project_H_sw/TOXSWA",
-                                 zipfile = system.file("testdata/SwashProjects.zip",
-                                                       package = "pfm"))
-
              -
              -
              - - - -

              Author

              - -Johannes Ranke - - -
              -
              - - -
              - - \ No newline at end of file diff --git a/pkg/inst/web/soil_DT50.html b/pkg/inst/web/soil_DT50.html deleted file mode 100644 index 0e142ae..0000000 --- a/pkg/inst/web/soil_DT50.html +++ /dev/null @@ -1,104 +0,0 @@ - - - - -soil_DT50. pfm 0.2-4 - - - - - - - - - - - - - - - -
              -
              -
              - pfm 0.2-4 -
              - -
              -
              -
              -
              - -
              -
              - -
              - -

              Obtain soil DT50

              - -
              -
              -

              Usage

              - 
              soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)
              - -

              Arguments

              -
              -
              chent
              -
              The chent object to get the information from
              -
              aggregator
              -
              The aggregator function. Can be mean, -geomean, or identity, for example.
              -
              signif
              -
              How many significant digits do we want
              -
              lab_field
              -
              If not NA, do we want laboratory or field endpoints
              -
              value
              -
              The name of the value we want. The list given in the -usage section is not exclusive
              -
              redox
              -
              If not NA, are we looking for aerobic or anaerobic data
              -
              raw
              -
              Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
              -
              - -
              -

              Description

              - -

              Obtain soil DT50

              - -
              -
              -
              - - - -
              -
              - - -
              - - \ No newline at end of file diff --git a/pkg/inst/web/soil_Kfoc.html b/pkg/inst/web/soil_Kfoc.html deleted file mode 100644 index ace5f4b..0000000 --- a/pkg/inst/web/soil_Kfoc.html +++ /dev/null @@ -1,100 +0,0 @@ - - - - -soil_Kfoc. pfm 0.2-4 - - - - - - - - - - - - - - - -
              -
              -
              - pfm 0.2-4 -
              - -
              -
              -
              -
              - -
              -
              - -
              - -

              Obtain soil Kfoc

              - -
              -
              -

              Usage

              - 
              soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)
              - -

              Arguments

              -
              -
              chent
              -
              The chent object to get the information from
              -
              aggregator
              -
              The aggregator function. Can be mean, -geomean, or identity, for example.
              -
              signif
              -
              How many significant digits do we want
              -
              value
              -
              The name of the value we want. The list given in the -usage section is not exclusive
              -
              raw
              -
              Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
              -
              - -
              -

              Description

              - -

              Obtain soil Kfoc

              - -
              -
              -
              - - - -
              -
              - - -
              - - \ No newline at end of file diff --git a/pkg/inst/web/soil_N.html b/pkg/inst/web/soil_N.html deleted file mode 100644 index 886bbc7..0000000 --- a/pkg/inst/web/soil_N.html +++ /dev/null @@ -1,98 +0,0 @@ - - - - -soil_N. pfm 0.2-4 - - - - - - - - - - - - - - - -
              -
              -
              - pfm 0.2-4 -
              - -
              -
              -
              -
              - -
              -
              - -
              - -

              Obtain soil Freundlich exponent

              - -
              -
              -

              Usage

              - 
              soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
              - -

              Arguments

              -
              -
              chent
              -
              The chent object to get the information from
              -
              aggregator
              -
              The aggregator function. Can be mean, -geomean, or identity, for example.
              -
              signif
              -
              How many significant digits do we want
              -
              raw
              -
              Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
              -
              - -
              -

              Description

              - -

              In pesticide fate modelling, this exponent is often called 1/n. Here, in -order to facilitate dealing with such data in R, it is called N.

              - -
              -
              -
              - - - -
              -
              - - -
              - - \ No newline at end of file diff --git a/pkg/inst/web/soil_scenario_data_EFSA_2015.html b/pkg/inst/web/soil_scenario_data_EFSA_2015.html deleted file mode 100644 index 0230afb..0000000 --- a/pkg/inst/web/soil_scenario_data_EFSA_2015.html +++ /dev/null @@ -1,141 +0,0 @@ - - - - -soil_scenario_data_EFSA_2015. pfm 0.3-7 - - - - - - - - - - - - - - - -
              -
              -
              - pfm 0.3-7 -
              - -
              -
              -
              -
              - -
              -
              - -
              - -

              Properties of the predefined scenarios from the EFSA guidance from 2015

              - -
              -
              - -
              -

              Format

              - -

              A data frame with one row for each scenario. Row names are the scenario codes, - e.g. CTN for the Northern scenario for the total concentration in soil. Columns are - mostly self-explanatory. rho is the dry bulk density of the top soil.

              - -
              - -
              -

              Source

              - -

              EFSA (European Food Safety Authority) (2015) -EFSA guidance document for predicting environmental concentrations -of active substances of plant protection products and transformation products of these -active substances in soil. EFSA Journal 13(4) 4093 -doi:10.2903/j.efsa.2015.4093

              - -
              - -
              -

              Description

              - -

              Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the -concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the -scenario and model adjustment factors from p. 15 and p. 17 are included.

              - -
              - -

              Examples

              - 
              ## Not run: 
-#   # This is the code that was used to define the data
-#   soil_scenario_data_EFSA_2015 <- data.frame(
-#     Zone = rep(c("North", "Central", "South"), 2),
-#     Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),
-#     T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),
-#     T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),
-#     Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),
-#     f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),
-#     theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),
-#     rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),
-#     f_sce = c(3, 2, 2, 2, 1.5, 1.5),
-#     f_mod = c(2, 2, 2, 4, 4, 4),
-#     stringsAsFactors = FALSE,
-#     row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")
-#   )
-#   save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')
-# ## End(Not run)
-
-# And this is the resulting dataframe
-soil_scenario_data_EFSA_2015
-
              
-
                     Zone        Country T_arit T_arr     Texture  f_om theta_fc  rho f_sce
-CTN   North        Estonia    4.7   7.0      Coarse 0.118    0.244 0.95   3.0
-CTC Central        Germany    8.0  10.1      Coarse 0.086    0.244 1.05   2.0
-CTS   South         France   11.0  12.3 Medium fine 0.048    0.385 1.22   2.0
-CLN   North        Denmark    8.2   9.8      Medium 0.023    0.347 1.39   2.0
-CLC Central Czech Republik    9.1  11.2      Medium 0.018    0.347 1.43   1.5
-CLS   South          Spain   12.8  14.7      Medium 0.011    0.347 1.51   1.5
-    f_mod
-CTN     2
-CTC     2
-CTS     2
-CLN     4
-CLC     4
-CLS     4
-
              -
              -
              - - - -
              -
              - - -
              - - \ No newline at end of file diff --git a/pkg/inst/web/soil_sorption.html b/pkg/inst/web/soil_sorption.html deleted file mode 100644 index 152fc5e..0000000 --- a/pkg/inst/web/soil_sorption.html +++ /dev/null @@ -1,98 +0,0 @@ - - - - -soil_sorption. pfm 0.2-4 - - - - - - - - - - - - - - - -
              -
              -
              - pfm 0.2-4 -
              - -
              -
              -
              -
              - -
              -
              - -
              - -

              Obtain soil sorption data

              - -
              -
              -

              Usage

              - 
              soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = rep(3, length(values)), raw = FALSE)
              - -

              Arguments

              -
              -
              chent
              -
              The chent object to get the information from
              -
              values
              -
              The values to be returned
              -
              aggregators
              -
              A named vector of aggregator functions to be used
              -
              signif
              -
              How many significant digits do we want
              -
              raw
              -
              Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?
              -
              - -
              -

              Description

              - -

              Obtain soil sorption data

              - -
              -
              -
              - - - -
              -
              - - -
              - - \ No newline at end of file diff --git a/pkg/man/FOCUS_GW_scenarios_2012.Rd b/pkg/man/FOCUS_GW_scenarios_2012.Rd deleted file mode 100644 index 3ae151b..0000000 --- a/pkg/man/FOCUS_GW_scenarios_2012.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/FOCUS_GW_scenarios_2012.R -\name{FOCUS_GW_scenarios_2012} -\alias{FOCUS_GW_scenarios_2012} -\title{A very small subset of the FOCUS Groundwater scenario defitions} -\description{ -Currently, only a small subset of the soil definitions are provided. -} -\examples{ -FOCUS_GW_scenarios_2012 -} -\references{ -FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. - FOrum for the Co-ordination of pesticde fate models and their USe. - http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf -} - diff --git a/pkg/man/GUS.Rd b/pkg/man/GUS.Rd deleted file mode 100644 index f1f5f28..0000000 --- a/pkg/man/GUS.Rd +++ /dev/null @@ -1,81 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/GUS.R -\name{GUS} -\alias{GUS} -\alias{GUS.chent} -\alias{GUS.numeric} -\alias{print.GUS_result} -\title{Groundwater ubiquity score based on Gustafson (1989)} -\usage{ -GUS(...) - -\method{GUS}{numeric}(DT50, Koc, ...) - -\method{GUS}{chent}(chent, degradation_value = "DT50ref", - lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc", - degradation_aggregator = geomean, sorption_aggregator = geomean, ...) - -\method{print}{GUS_result}(x, ..., digits = 1) -} -\arguments{ -\item{...}{Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.} - -\item{DT50}{Half-life of the chemical in soil. Should be a field -half-life according to Gustafson (1989). However, leaching to the sub-soil -can not completely be excluded in field dissipation experiments and Gustafson -did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions.} - -\item{Koc}{The sorption constant normalised to organic carbon. Gustafson -does not mention the nonlinearity of the sorption constant commonly -found and usually described by Freundlich sorption, therefore it is -unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater).} - -\item{chent}{If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.} - -\item{degradation_value}{Which of the available degradation values should -be used?} - -\item{lab_field}{Should laboratory or field half-lives be used? This -defaults to lab in this implementation, in order to avoid -double-accounting for mobility. If comparability with the original GUS -values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used.} - -\item{redox}{Aerobic or anaerobic degradation data} - -\item{sorption_value}{Which of the available sorption values should be used? -Defaults to Kfoc as this is what is generally available from the European -pesticide peer review process. These values generally use a reference -concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase.} - -\item{degradation_aggregator}{Function for aggregating half-lives} - -\item{sorption_aggregator}{Function for aggregation Koc values} - -\item{x}{An object of class GUS_result to be printed} - -\item{digits}{The number of digits used in the print method} -} -\value{ -A list with the DT50 and Koc used as well as the resulting score - of class GUS_result -} -\description{ -The groundwater ubiquity score GUS is calculated according to -the following equation -\deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)} -} -\author{ -Johannes Ranke -} -\references{ -Gustafson, David I. (1989) Groundwater ubiquity score: a simple -method for assessing pesticide leachability. \emph{Environmental -toxicology and chemistry} \bold{8}(4) 339–57. -} - diff --git a/pkg/man/PEC_soil.Rd b/pkg/man/PEC_soil.Rd deleted file mode 100644 index c0b5201..0000000 --- a/pkg/man/PEC_soil.Rd +++ /dev/null @@ -1,119 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/PEC_soil.R -\name{PEC_soil} -\alias{PEC_soil} -\title{Calculate predicted environmental concentrations in soil} -\usage{ -PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, - PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA, - n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA, - Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default", - "EFSA_2015"), porewater = FALSE) -} -\arguments{ -\item{rate}{Application rate in units specified below} - -\item{rate_units}{Defaults to g/ha} - -\item{interception}{The fraction of the application rate that does not reach the soil} - -\item{mixing_depth}{Mixing depth in cm} - -\item{PEC_units}{Requested units for the calculated PEC. Only mg/kg currently supported} - -\item{PEC_pw_units}{Only mg/L currently supported} - -\item{interval}{Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days} - -\item{n_periods}{Number of periods to be considered for long term PEC calculations} - -\item{tillage_depth}{Periodic (see interval) deeper mixing in cm} - -\item{chent}{An optional chent object holding substance specific information. Can -also be a name for the substance as a character string} - -\item{DT50}{If specified, overrides soil DT50 endpoints from a chent object -If DT50 is not specified here and not available from the chent object, zero -degradation is assumed} - -\item{Koc}{If specified, overrides Koc endpoints from a chent object} - -\item{Kom}{Calculated from Koc by default, but can explicitly be specified -as Kom here} - -\item{t_avg}{Averaging times for time weighted average concentrations} - -\item{scenarios}{If this is 'default', the DT50 will be used without correction -and soil properties as specified in the REACH guidance (R.16, Table -R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", -the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -'chents' is specified, the DegT50 with destination 'PECgw' will be used), -and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used.} - -\item{porewater}{Should equilibrium porewater concentrations be estimated -based on Kom and the organic carbon fraction of the soil instead of total -soil concentrations? Based on equation (7) given in the PPR panel opinion -(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -p. 13).} -} -\value{ -The predicted concentration in soil -} -\description{ -This is a basic calculation of a contaminant concentration in bulk soil -based on complete, instantaneous mixing. If an interval is given, an -attempt is made at calculating a long term maximum concentration using -the concepts layed out for example in the PPR panel opinion (EFSA 2012). -} -\details{ -This assumes that the complete load to soil during the time specified by -'interval' (typically 365 days) is dosed at once. As in the PPR panel -opinion cited below (PPR panel 2012), only temperature correction using the -Arrhenius equation is performed. - -Total soil and porewater PEC values for the scenarios as defined in the EFSA -guidance (2015, p. 13) can easily be calculated. -} -\note{ -If temperature information is available in the selected scenarios, as - e.g. in the EFSA scenarios, the DT50 for groundwater modelling - (destination 'PECgw') is taken from the chent object, otherwise the DT50 - with destination 'PECsoil'. -} -\examples{ -PEC_soil(100, interception = 0.25) - -# This is example 1 starting at p. 79 of the EFSA guidance (2015) -PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") -PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) - -# The following is from example 4 starting at p. 85 of the EFSA guidance (2015) -# Metabolite M2 -# Calculate total and porewater soil concentrations for tier 1 scenarios -# Relative molar mass is 100/300, formation fraction is 0.7 * 1 -results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") -results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) -} -\author{ -Johannes Ranke -} -\references{ -EFSA Panel on Plant Protection Products and their Residues (2012) - Scientific Opinion on the science behind the guidance for scenario - selection and scenario parameterisation for predicting environmental - concentrations of plant protection products in soil. \emph{EFSA Journal} - \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562 - - EFSA (European Food Safety Authority) (2015) EFSA guidance document for - predicting environmental concentrations of active substances of plant - protection products and transformation products of these active substances - in soil. \emph{EFSA Journal} \bold{13}(4) 4093 - doi:10.2903/j.efsa.2015.4093 -} - diff --git a/pkg/man/PEC_sw_drainage_UK.Rd b/pkg/man/PEC_sw_drainage_UK.Rd deleted file mode 100644 index cb64bde..0000000 --- a/pkg/man/PEC_sw_drainage_UK.Rd +++ /dev/null @@ -1,39 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/PEC_sw_drainage_UK.R -\name{PEC_sw_drainage_UK} -\alias{PEC_sw_drainage_UK} -\title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method} -\usage{ -PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL, - soil_DT50 = NULL, model = NULL, model_parms = NULL) -} -\arguments{ -\item{rate}{Application rate in g/ha} - -\item{interception}{The fraction of the application rate that does not reach the soil} - -\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg} - -\item{latest_application}{Latest application date, formatted as e.g. "01 July"} - -\item{soil_DT50}{Soil degradation half-life, if SFO kinetics are to be used} - -\item{model}{The soil degradation model to be used. Either one of "FOMC", -"DFOP", "HS", or "IORE", or an mkinmod object} - -\item{model_parms}{A named numeric vector containing the model parameters} -} -\value{ -The predicted concentration in surface water in µg/L -} -\description{ -This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -published on the CRC website -} -\examples{ -PEC_sw_drainage_UK(150, Koc = 100) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/PEC_sw_drift.Rd b/pkg/man/PEC_sw_drift.Rd deleted file mode 100644 index 20fa921..0000000 --- a/pkg/man/PEC_sw_drift.Rd +++ /dev/null @@ -1,45 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/PEC_sw_drift.R -\name{PEC_sw_drift} -\alias{PEC_sw_drift} -\title{Calculate predicted environmental concentrations in surface water due to drift} -\usage{ -PEC_sw_drift(rate, applications = 1, water_depth = 30, - drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", - distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L") -} -\arguments{ -\item{rate}{Application rate in units specified below} - -\item{applications}{Number of applications for selection of drift percentile} - -\item{water_depth}{Depth of the water body in cm} - -\item{drift_percentages}{Percentage drift values for which to calculate PECsw. -'drift_data' and 'distances' if not NULL.} - -\item{drift_data}{Source of drift percentage data} - -\item{crop}{Crop name (use German names for JKI data), defaults to "Ackerbau"} - -\item{distances}{The distances in m for which to get PEC values} - -\item{rate_units}{Defaults to g/ha} - -\item{PEC_units}{Requested units for the calculated PEC. Only µg/L currently supported} -} -\value{ -The predicted concentration in surface water -} -\description{ -This is a basic, vectorised form of a simple calculation of a contaminant -concentration in surface water based on complete, instantaneous mixing -with input via spray drift. -} -\examples{ -PEC_sw_drift(100) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/PEC_sw_sed.Rd b/pkg/man/PEC_sw_sed.Rd deleted file mode 100644 index 3140eb0..0000000 --- a/pkg/man/PEC_sw_sed.Rd +++ /dev/null @@ -1,42 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/PEC_sw_sed.R -\name{PEC_sw_sed} -\alias{PEC_sw_sed} -\title{Calculate predicted environmental concentrations in sediment from surface -water concentrations} -\usage{ -PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage", - sediment_depth = 5, water_depth = 30, sediment_density = 1.3, - PEC_sed_units = c("µg/kg", "mg/kg")) -} -\arguments{ -\item{PEC_sw}{Numeric vector or matrix of surface water concentrations in µg/L for -which the corresponding sediment concentration is to be estimated} - -\item{percentage}{The percentage in sediment, used for the percentage method} - -\item{method}{The method used for the calculation} - -\item{sediment_depth}{Depth of the sediment layer} - -\item{water_depth}{Depth of the water body in cm} - -\item{sediment_density}{The density of the sediment in L/kg (equivalent to -g/cm3)} - -\item{PEC_sed_units}{The units of the estimated sediment PEC value} -} -\value{ -The predicted concentration in sediment -} -\description{ -The method 'percentage' is equivalent to what is used in the CRD spreadsheet -PEC calculator -} -\examples{ -PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/SFO_actual_twa.Rd b/pkg/man/SFO_actual_twa.Rd deleted file mode 100644 index 573ea03..0000000 --- a/pkg/man/SFO_actual_twa.Rd +++ /dev/null @@ -1,29 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/SFO_actual_twa.R -\name{SFO_actual_twa} -\alias{SFO_actual_twa} -\title{Actual and maximum moving window time average concentrations for SFO kinetics} -\source{ -FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, - 18 December 2014, p. 251 -} -\usage{ -SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, - 100)) -} -\arguments{ -\item{DT50}{The half-life.} - -\item{times}{The output times, and window sizes for time weighted average concentrations} -} -\description{ -Actual and maximum moving window time average concentrations for SFO kinetics -} -\examples{ -SFO_actual_twa(10) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/SSLRC_mobility_classification.Rd b/pkg/man/SSLRC_mobility_classification.Rd deleted file mode 100644 index 04aa01d..0000000 --- a/pkg/man/SSLRC_mobility_classification.Rd +++ /dev/null @@ -1,26 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/SSLRC_mobility_classification.R -\name{SSLRC_mobility_classification} -\alias{SSLRC_mobility_classification} -\title{Determine the SSLRC mobility classification for a chemical substance from its Koc} -\usage{ -SSLRC_mobility_classification(Koc) -} -\arguments{ -\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg} -} -\value{ -A list containing the classification and the percentage of the - compound transported per 10 mm drain water -} -\description{ -This implements the method specified in the UK data requirements handbook and was -checked against the spreadsheet published on the CRC website -} -\examples{ -SSLRC_mobility_classification(100) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/TOXSWA_cwa.Rd b/pkg/man/TOXSWA_cwa.Rd deleted file mode 100644 index de87510..0000000 --- a/pkg/man/TOXSWA_cwa.Rd +++ /dev/null @@ -1,58 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/TOXSWA_cwa.R -\docType{class} -\name{TOXSWA_cwa} -\alias{TOXSWA_cwa} -\title{R6 class for holding TOXSWA cwa concentration data and associated statistics} -\format{An \code{\link{R6Class}} generator object.} -\usage{ -TOXSWA_cwa -} -\description{ -An R6 class for holding TOXSWA cwa concentration data and some associated statistics. -Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. -} -\section{Fields}{ - -\describe{ -\item{\code{filename}}{Length one character vector.} - -\item{\code{basedir}}{Length one character vector.} - -\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.} - -\item{\code{cwas}}{Dataframe holding the concentrations.} - -\item{\code{events}}{List of dataframes holding the event statistics for each threshold.} - -\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max) -and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) -for the requested moving window sizes in days.} -}} -\section{Methods}{ - -\describe{ - \item{\code{get_events(threshold, total = FALSE)}}{ - Populate a datataframe with event information for the specified threshold value - in µg/L. If \code{total = TRUE}, the total concentration including the amount - adsorbed to suspended matter will be used. The resulting dataframe is stored in the - \code{events} field of the object. - } - \item{\code{moving_windows(windows, total = FALSE)}}{ - Add to the \code{windows} field described above. - Again, if \code{total = TRUE}, the total concentration including the amount - adsorbed to suspended matter will be used. - } -} -} -\examples{ -H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", - basedir = "SwashProjects/project_H_sw/TOXSWA", - zipfile = system.file("testdata/SwashProjects.zip", - package = "pfm")) -H_sw_R1_stream$get_events(c(2, 10)) -H_sw_R1_stream$moving_windows(c(7, 21)) -print(H_sw_R1_stream) -} -\keyword{data} - diff --git a/pkg/man/drift_data_JKI.Rd b/pkg/man/drift_data_JKI.Rd deleted file mode 100644 index c193c0d..0000000 --- a/pkg/man/drift_data_JKI.Rd +++ /dev/null @@ -1,50 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/drift_data_JKI.R -\docType{data} -\name{drift_data_JKI} -\alias{drift_data_JKI} -\title{Deposition from spray drift expressed as percent of the applied dose as -published by the JKI} -\format{A list currently containing matrices with spray drift percentage -data for field crops (Ackerbau), and Pome/stone fruit, early and late -(Obstbau frueh, spaet).} -\source{ -JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved -from -http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11 -} -\description{ -Deposition from spray drift expressed as percent of the applied dose as -published by the German Julius-Kühn Institute (JKI). -} -\details{ -The data were extracted from the spreadsheet cited below using the R code -given in the example section. The spreadsheet is not included in the package -as its licence is not clear. -} -\examples{ - -\dontrun{ - # This is the code that was used to extract the data - library(readxl) - abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" - JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet") - names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late") - drift_data_JKI <- list() - - for (n in 1:8) { - drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) - drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) - dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]), - crop = JKI_crops) - drift_data_JKI[[n]] <- drift_data - } - save(drift_data_JKI, file = "data/drift_data_JKI.RData") -} - -# And this is the resulting data -drift_data_JKI -} -\keyword{datasets} - diff --git a/pkg/man/endpoint.Rd b/pkg/man/endpoint.Rd deleted file mode 100644 index fd16650..0000000 --- a/pkg/man/endpoint.Rd +++ /dev/null @@ -1,75 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/endpoint.R -\name{endpoint} -\alias{endpoint} -\alias{soil_DT50} -\alias{soil_Kfoc} -\alias{soil_N} -\alias{soil_sorption} -\title{Retrieve endpoint information from the chyaml field of a chent object} -\usage{ -endpoint(chent, medium = "soil", type = c("degradation", "sorption"), - lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", - "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, - raw = FALSE, signif = 3) - -soil_DT50(chent, aggregator = geomean, signif = 3, - lab_field = "laboratory", value = "DT50ref", redox = "aerobic", - raw = FALSE) - -soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", - raw = FALSE) - -soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) - -soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = - geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), - raw = FALSE) -} -\arguments{ -\item{chent}{The \code{\link{chent}} object to get the information from} - -\item{medium}{The medium for which information is sought} - -\item{type}{The information type} - -\item{lab_field}{If not NA, do we want laboratory or field endpoints} - -\item{redox}{If not NA, are we looking for aerobic or anaerobic data} - -\item{value}{The name of the value we want. The list given in the -usage section is not exclusive} - -\item{aggregator}{The aggregator function. Can be mean, -\code{\link{geomean}}, or identity, for example.} - -\item{raw}{Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?} - -\item{signif}{How many significant digits do we want} - -\item{values}{The values to be returned} - -\item{aggregators}{A named vector of aggregator functions to be used} -} -\value{ -The result from applying the aggregator function to - the values converted to a numeric vector, rounded to the - given number of significant digits, or, if raw = TRUE, - the values as a character value, retaining any implicit - information on precision that may be present. -} -\description{ -R6 class objects of class \code{\link{chent}} represent chemical entities -and can hold a list of information loaded from a chemical yaml file in their -chyaml field. Such information is extracted and optionally aggregated by -this function. -} -\details{ -The functions \code{soil_*} are functions to extract soil specific endpoints. -For the Freundlich exponent, the capital letter \code{N} is used in order to -facilitate dealing with such data in R. In pesticide fate modelling, this -exponent is often called 1/n. -} - diff --git a/pkg/man/geomean.Rd b/pkg/man/geomean.Rd deleted file mode 100644 index ed82294..0000000 --- a/pkg/man/geomean.Rd +++ /dev/null @@ -1,31 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/geomean.R -\name{geomean} -\alias{geomean} -\title{Calculate the geometric mean} -\usage{ -geomean(x, na.rm = TRUE) -} -\arguments{ -\item{x}{Vector of numbers} - -\item{na.rm}{Should NA values be omitted?} -} -\value{ -The geometric mean -} -\description{ -Based on some posts in a thread on Stackoverflow -\url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in} -This function checks for negative values, removes NA values per default and -returns 0 if at least one element of the vector is 0. -} -\examples{ -geomean(c(1, 3, 9)) -geomean(c(1, 3, NA, 9)) -\dontrun{geomean(c(1, -3, 9)) # returns an error} -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/pfm_degradation.Rd b/pkg/man/pfm_degradation.Rd deleted file mode 100644 index 9ab1d0a..0000000 --- a/pkg/man/pfm_degradation.Rd +++ /dev/null @@ -1,35 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/pfm_degradation.R -\name{pfm_degradation} -\alias{pfm_degradation} -\title{Calculate a time course of relative concentrations based on an mkinmod model} -\usage{ -pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = - log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = - step_days)) -} -\arguments{ -\item{model}{The degradation model to be used. Either a parent only model like -'SFO' or 'FOMC', or an mkinmod object} - -\item{DT50}{The half-life. This is only used when simple exponential decline -is calculated (SFO model).} - -\item{parms}{The parameters used for the degradation model} - -\item{years}{For how many years should the degradation be predicted?} - -\item{step_days}{What step size in days should the output have?} - -\item{times}{The output times} -} -\description{ -Calculate a time course of relative concentrations based on an mkinmod model -} -\examples{ -head(pfm_degradation("SFO", DT50 = 10)) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/plot.TOXSWA_cwa.Rd b/pkg/man/plot.TOXSWA_cwa.Rd deleted file mode 100644 index b5f0163..0000000 --- a/pkg/man/plot.TOXSWA_cwa.Rd +++ /dev/null @@ -1,42 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/TOXSWA_cwa.R -\name{plot.TOXSWA_cwa} -\alias{plot.TOXSWA_cwa} -\title{Plot TOXSWA surface water concentrations} -\usage{ -\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t", "t_firstjan", - "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE, - total = FALSE, LC_TIME = "C", ...) -} -\arguments{ -\item{x}{The TOXSWA_cwa object to be plotted.} - -\item{time_column}{What should be used for the time axis. If "t_firstjan" is chosen, -the time is given in days relative to the first of January in the first year.} - -\item{xlab, ylab}{Labels for x and y axis.} - -\item{add}{Should we add to an existing plot?} - -\item{total}{Should the total concentration in water be plotted, including substance sorbed -to suspended matter?} - -\item{LC_TIME}{Specification of the locale used to format dates} - -\item{...}{Further arguments passed to \code{plot} if we are not adding to an existing plot} -} -\description{ -Plot TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body. -} -\examples{ -H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", - basedir = "SwashProjects/project_H_sw/TOXSWA", - zipfile = system.file("testdata/SwashProjects.zip", - package = "pfm")) -plot(H_sw_D4_pond) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/read.TOXSWA_cwa.Rd b/pkg/man/read.TOXSWA_cwa.Rd deleted file mode 100644 index 84ef3da..0000000 --- a/pkg/man/read.TOXSWA_cwa.Rd +++ /dev/null @@ -1,56 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/TOXSWA_cwa.R -\name{read.TOXSWA_cwa} -\alias{read.TOXSWA_cwa} -\title{Read TOXSWA surface water concentrations} -\usage{ -read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", - substance = "parent", total = FALSE, windows = NULL, - thresholds = NULL) -} -\arguments{ -\item{filename}{The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).} - -\item{basedir}{The path to the directory where the cwa file resides.} - -\item{zipfile}{Optional path to a zip file containing the cwa file.} - -\item{segment}{The segment for which the data should be read. Either "last", or -the segment number.} - -\item{substance}{For TOXSWA 4 .out files, the default value "parent" leads -to reading concentrations of the parent compound. Alternatively, the substance -of interested can be selected by its code name.} - -\item{total}{Set this to TRUE in order to read total concentrations as well. This is -only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -files. For .cwa files, the total concentration is always read as well.} - -\item{windows}{Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve.} - -\item{thresholds}{Numeric vector of threshold concentrations in µg/L for -generating event statistics.} -} -\value{ -An instance of an R6 object of class -\code{\link{TOXSWA_cwa}}. -} -\description{ -Read TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body. Per default, the data for the last -segment are imported. As TOXSWA 4 reports the values at the end of the hour -(ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay). -} -\examples{ -H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", - basedir = "SwashProjects/project_H_sw/TOXSWA", - zipfile = system.file("testdata/SwashProjects.zip", - package = "pfm")) -} -\author{ -Johannes Ranke -} - diff --git a/pkg/man/soil_scenario_data_EFSA_2015.Rd b/pkg/man/soil_scenario_data_EFSA_2015.Rd deleted file mode 100644 index b45af4a..0000000 --- a/pkg/man/soil_scenario_data_EFSA_2015.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/soil_scenario_data_EFSA_2015.R -\docType{data} -\name{soil_scenario_data_EFSA_2015} -\alias{soil_scenario_data_EFSA_2015} -\title{Properties of the predefined scenarios from the EFSA guidance from 2015} -\format{A data frame with one row for each scenario. Row names are the scenario codes, - e.g. CTN for the Northern scenario for the total concentration in soil. Columns are - mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.} -\source{ -EFSA (European Food Safety Authority) (2015) -EFSA guidance document for predicting environmental concentrations -of active substances of plant protection products and transformation products of these -active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093 -doi:10.2903/j.efsa.2015.4093 -} -\description{ -Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the -concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the -scenario and model adjustment factors from p. 15 and p. 17 are included. -} -\examples{ -\dontrun{ - # This is the code that was used to define the data - soil_scenario_data_EFSA_2015 <- data.frame( - Zone = rep(c("North", "Central", "South"), 2), - Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), - T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), - T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), - Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), - f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), - theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), - rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), - f_sce = c(3, 2, 2, 2, 1.5, 1.5), - f_mod = c(2, 2, 2, 4, 4, 4), - stringsAsFactors = FALSE, - row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") - ) - save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') -} - -# And this is the resulting dataframe -soil_scenario_data_EFSA_2015 -} -\keyword{datasets} - diff --git a/pkg/tests/testthat.R b/pkg/tests/testthat.R deleted file mode 100644 index d2df1cc..0000000 --- a/pkg/tests/testthat.R +++ /dev/null @@ -1,4 +0,0 @@ -library(testthat) -library(pfm) - -test_check("pfm") diff --git a/pkg/tests/testthat/EXSW2_R1_stream_printed.txt b/pkg/tests/testthat/EXSW2_R1_stream_printed.txt deleted file mode 100644 index 60bb5ac..0000000 --- a/pkg/tests/testthat/EXSW2_R1_stream_printed.txt +++ /dev/null @@ -1,10 +0,0 @@ - data from file 3.out segment 20 - datetime t t_firstjan t_rel_to_max cwa_mug_per_L -1 1978-10-01 00:00:00 0.000 273.0000 -55.083 0 -2 1978-10-01 01:00:00 0.042 273.0417 -55.041 0 -3 1978-10-01 02:00:00 0.083 273.0833 -55.000 0 -4 1978-10-01 03:00:00 0.125 273.1250 -54.958 0 -5 1978-10-01 04:00:00 0.167 273.1667 -54.916 0 -6 1978-10-01 05:00:00 0.208 273.2083 -54.875 0 -Moving window analysis -NULL diff --git a/pkg/tests/testthat/H_sw_D4_pond_printed.txt b/pkg/tests/testthat/H_sw_D4_pond_printed.txt deleted file mode 100644 index 5730be6..0000000 --- a/pkg/tests/testthat/H_sw_D4_pond_printed.txt +++ /dev/null @@ -1,10 +0,0 @@ - data from file 00001p_pa.cwa segment 1 - datetime t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L -1 1985-01-01 00:00:00 0.000 0.00000000 -396.167 0.00000000 0.00000000 -2 1985-01-01 01:00:00 0.042 0.04166667 -396.125 0.08323064 0.08323716 -3 1985-01-01 02:00:00 0.083 0.08333333 -396.084 0.16626900 0.16628210 -4 1985-01-01 03:00:00 0.125 0.12500000 -396.042 0.24911240 0.24913190 -5 1985-01-01 04:00:00 0.167 0.16666667 -396.000 0.33172050 0.33174650 -6 1985-01-01 05:00:00 0.208 0.20833333 -395.959 0.41401430 0.41404670 -Moving window analysis -NULL diff --git a/pkg/tests/testthat/H_sw_R1_stream_events.rds b/pkg/tests/testthat/H_sw_R1_stream_events.rds deleted file mode 100644 index ba6557b..0000000 Binary files a/pkg/tests/testthat/H_sw_R1_stream_events.rds and /dev/null differ diff --git a/pkg/tests/testthat/H_sw_R1_stream_printed.txt b/pkg/tests/testthat/H_sw_R1_stream_printed.txt deleted file mode 100644 index 572ad6d..0000000 --- a/pkg/tests/testthat/H_sw_R1_stream_printed.txt +++ /dev/null @@ -1,10 +0,0 @@ - data from file 00003s_pa.cwa segment 20 - datetime t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L -20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 0 -40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 0 -60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 0 -80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 0 -100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 0 -120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 0 -Moving window analysis -NULL diff --git a/pkg/tests/testthat/H_sw_R1_stream_windows.rds b/pkg/tests/testthat/H_sw_R1_stream_windows.rds deleted file mode 100644 index 2531189..0000000 Binary files a/pkg/tests/testthat/H_sw_R1_stream_windows.rds and /dev/null differ diff --git a/pkg/tests/testthat/test_PEC_sed.R b/pkg/tests/testthat/test_PEC_sed.R deleted file mode 100644 index 443f789..0000000 --- a/pkg/tests/testthat/test_PEC_sed.R +++ /dev/null @@ -1,9 +0,0 @@ -context("Simple PEC sediment calculations") - -test_that("PEC_sw_sed calculates correctly using the percentage method", { - # Application of 100 g/ha, 1 m spray drift distance (2.77% drift input), 50% in sediment, - # default assumptions of CRD spreadsheet (5 cm sediment depth, 1.3 kg/L sediment density) - # Reference value calculated with CRD spreadsheet - PEC_sw_100_1_m <- PEC_sw_drift(100, distances = 1) - expect_equivalent(round(PEC_sw_sed(PEC_sw_100_1_m, percentage = 50), 3), 2.131) -}) diff --git a/pkg/tests/testthat/test_PEC_soil.R b/pkg/tests/testthat/test_PEC_soil.R deleted file mode 100644 index 0661a52..0000000 --- a/pkg/tests/testthat/test_PEC_soil.R +++ /dev/null @@ -1,95 +0,0 @@ -library(pfm) -context("Simple PEC soil calculations") - -test_that("PEC_soil calculates correctly", { - # Application of 100 g/ha gives 0.133 mg/kg under default assumptions - expect_equal(as.numeric(PEC_soil(100)), 0.1 * 4/3) - - # or 0.1 mg/kg assuming 25% interception - expect_equal(as.numeric(PEC_soil(100, interception = 0.25)), 0.1) - - # Mixing depth of 1 cm gives five-fold PEC - expect_equal(as.numeric(PEC_soil(100, interception = 0.25, mixing_depth = 1)), 0.5) -}) - -test_that("Tier 1 PEC soil example for Pesticide A in EFSA guidance can be reproduced", { - # Calculate total soil concentrations for tier 1 scenarios - results_pfm <- PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") - - # From Table I.5, p. 80 - results_guidance <- matrix(c(22.0, 11.5, 9.1, 21.8, 11.4, 9.0), - ncol = 3, byrow = TRUE) - dimnames(results_guidance) <- list(t_avg = c(0, 21), - scenario = c("CTN", "CTC", "CTS")) - - - expect_equal(round(results_pfm, 1), results_guidance) - - # Calculate porewater soil concentrations for tier 1 scenarios - results_pfm_pw <- PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) - - # From Table I.5, p. 80 - results_guidance_pw <- matrix(c(0.76, 0.67, 0.91, 0.75, 0.66, 0.90), - ncol = 3, byrow = TRUE) - dimnames(results_guidance_pw) <- list(t_avg = c(0, 21), - scenario = c("CLN", "CLC", "CLS")) - - expect_equal(round(results_pfm_pw, 2), results_guidance_pw) -}) - -test_that("Tier 1 PEC soil example for Pesticide F in EFSA guidance can be reproduced", { - # Parent F - # Calculate total and porewater soil concentrations for tier 1 scenarios - results_pfm <- PEC_soil(1000, interval = 365, DT50 = 25, t_avg = c(0, 21), - scenarios = "EFSA_2015") - results_pfm_pw <- PEC_soil(1000, interval = 365, DT50 = 25, t_av = c(0, 21), - Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) - - # From Table I.14, p. 88 - results_guidance <- matrix(c(12.8, 7.7, 6.6, 11.8, 6.8, 5.7), - ncol = 3, byrow = TRUE) - results_guidance_pw <- matrix(c(0.50, 0.46, 0.71, 0.45, 0.41, 0.60), - ncol = 3, byrow = TRUE) - - # Skip checking dimnames by using expect_equivalent() - expect_equivalent(round(results_pfm, 1), results_guidance) - expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw) - - # Metabolite M1 - # Calculate total and porewater soil concentrations for tier 1 scenarios - # Relative molar mass is 200/300, formation fraction is 0.7 - results_pfm <- PEC_soil(200/300 * 0.7 * 1000, interval = 365, DT50 = 100, t_avg = c(0, 21), - scenarios = "EFSA_2015") - results_pfm_pw <- PEC_soil(200/300 * 0.7 * 1000, interval = 365, DT50 = 100, t_av = c(0, 21), - Kom = 10, scenarios = "EFSA_2015", porewater = TRUE) - - # From Table I.15, p. 88 - results_guidance <- matrix(c(7.27, 4.08, 3.38, 7.12, 3.97, 3.26), - ncol = 3, byrow = TRUE) - results_guidance_pw <- matrix(c(12.93, 10.42, 11.66, 12.58, 10.09, 11.15), - ncol = 3, byrow = TRUE) - - # Skip checking dimnames by using expect_equivalent() - expect_equivalent(round(results_pfm, 2), results_guidance) - expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw) - - # Metabolite M2 - # Calculate total and porewater soil concentrations for tier 1 scenarios - # Relative molar mass is 100/300, formation fraction is 0.7 * 1 - results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") - results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) - - # From Table I.16, p. 89 - results_guidance <- matrix(c(5.13, 2.69, 2.13, 5.08, 2.66, 2.10), - ncol = 3, byrow = TRUE) - results_guidance_pw <- matrix(c(1.61, 1.39, 1.80, 1.60, 1.37, 1.77), - ncol = 3, byrow = TRUE) - - # Skip checking dimnames by using expect_equivalent() - expect_equivalent(round(results_pfm, 2), results_guidance) - expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw) -}) diff --git a/pkg/tests/testthat/test_PEC_sw_drift.R b/pkg/tests/testthat/test_PEC_sw_drift.R deleted file mode 100644 index d09d578..0000000 --- a/pkg/tests/testthat/test_PEC_sw_drift.R +++ /dev/null @@ -1,15 +0,0 @@ -library(pfm) -context("Simple PEC surface water calculations with drift entry") - -test_that("PEC_sw_drift gives the same results as the CRD PEC calculator", { - # One application of 30 g/ha to field crops calculated with UK PEC calculator published by CRD - expect_equal(round(PEC_sw_drift(30), 3), - c('1 m' = 0.277, '5 m' = 0.057, '10 m' = 0.029, '20 m' = 0.015)) - - # 7 applications of 30 g/ha to field crops calculated with UK PEC calculator, initial PEC - expect_equal(round(PEC_sw_drift(30, 7), 3), - c('1 m' = 0.161, '5 m' = 0.033, '10 m' = 0.017, '20 m' = 0.008)) - - # 4 applications of 30 g/ha to late fruit crops calculated with UK PEC calculator published by CRD (uses different drift values from SANCO aquatic guidance) - #expect_equal(round(PEC_sw_drift(30, 4, crop = "Obstbau spät", distances = c(3, 20, 50)), 3), c('3 m' = 1.101, '20 m' = 0.080, '50 m' = 0.013)) -}) diff --git a/pkg/tests/testthat/test_SFO_actual_twa.R b/pkg/tests/testthat/test_SFO_actual_twa.R deleted file mode 100644 index b0a5537..0000000 --- a/pkg/tests/testthat/test_SFO_actual_twa.R +++ /dev/null @@ -1,13 +0,0 @@ -library(pfm) -context("Actual and time weighted average concentrations for SFO kinetics") - -test_that("SFO_actual_twa calculates correctly", { - test_times <- c(0, 1, 7, 21, 42) - # This was calculated with the CRD spreadsheet for multiple applications - reference <- data.frame( - actual = c(10, 9.330, 6.156, 2.333, 0.544), - twa = c(NaN, 9.661, 7.923, 5.267, 3.248), - row.names = test_times) - result <- round(10 * SFO_actual_twa(10, times = test_times), 3) - expect_equal(result, reference) -}) diff --git a/pkg/tests/testthat/test_TOXSWA_cwa.R b/pkg/tests/testthat/test_TOXSWA_cwa.R deleted file mode 100644 index 7c9a73c..0000000 --- a/pkg/tests/testthat/test_TOXSWA_cwa.R +++ /dev/null @@ -1,56 +0,0 @@ -library(pfm) -context("Read and analyse TOXSWA cwa files") - -zipfile_test = system.file("testdata/SwashProjects.zip", package = "pfm") -basedir_test = "SwashProjects/project_H_sw/TOXSWA" - -H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", - basedir = basedir_test, - zipfile = zipfile_test) - -H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", - basedir = basedir_test, - zipfile = zipfile_test) - -basedir_test_2 = "SwashProjects/Project_1/TOXSWA" - -EXSW2_R1_stream <- read.TOXSWA_cwa("3.out", - basedir = basedir_test_2, - zipfile = zipfile_test) - - - -test_that("TOXSWA cwa file is correctly read and printed", { - - # This was the setting when printing the output into text files - options(width = 100) - - # Most content of the R6 object is at least partially printed - - H_sw_D4_pond_printed <- capture.output(print(H_sw_D4_pond)) - - expect_equal(H_sw_D4_pond_printed, readLines("H_sw_D4_pond_printed.txt")) - - H_sw_R1_stream_printed <- capture.output(print(H_sw_R1_stream)) - expect_equal(H_sw_R1_stream_printed, readLines("H_sw_R1_stream_printed.txt")) - - # The basedir is not printed, therefore tested separately - expect_equal(H_sw_D4_pond$basedir, basedir_test) - - EXSW2_R1_stream_printed <- capture.output(print(EXSW2_R1_stream)) - expect_equal(EXSW2_R1_stream_printed, readLines("EXSW2_R1_stream_printed.txt")) - - # The basedir is not printed, therefore tested separately - expect_equal(H_sw_D4_pond$basedir, basedir_test) -}) - -test_that("Getting events and moving window analysis works", { - - # Event analysis with two different thresholds - H_sw_R1_stream$get_events(c(2, 10)) - expect_equal_to_reference(H_sw_R1_stream$events, file = "H_sw_R1_stream_events.rds") - - # Moving window analysis - H_sw_R1_stream$moving_windows(c(7, 21)) - expect_equal_to_reference(H_sw_R1_stream$windows, file = "H_sw_R1_stream_windows.rds") -}) diff --git a/pkg/tests/testthat/test_UK_drainage.R b/pkg/tests/testthat/test_UK_drainage.R deleted file mode 100644 index 859f145..0000000 --- a/pkg/tests/testthat/test_UK_drainage.R +++ /dev/null @@ -1,33 +0,0 @@ -library(pfm) -context("UK drainage PEC calculations") - -test_that("The mobility classification and the drained percentage are correct", { - # Expected results are from the CRD drainage calculator, retrieved 2015-06-11 - - expect_equivalent(SSLRC_mobility_classification(1), list("Very mobile", 1.9)) - expect_equivalent(SSLRC_mobility_classification(15), list("Mobile", 1.9)) - expect_equivalent(SSLRC_mobility_classification(30), list("Mobile", 1.9)) - expect_equivalent(SSLRC_mobility_classification(74.9), list("Mobile", 1.9)) - expect_equivalent(SSLRC_mobility_classification(75), list("Moderately mobile", 0.7)) - expect_equivalent(SSLRC_mobility_classification(100), list("Moderately mobile", 0.7)) - expect_equivalent(SSLRC_mobility_classification(800), list("Slightly mobile", 0.5)) - expect_equivalent(SSLRC_mobility_classification(2000), list("Slightly mobile", 0.02)) - expect_equivalent(SSLRC_mobility_classification(5000), list("Non mobile", 0.01)) -}) - -test_that("UK drainflow PECs are correct", { - # Expected results are from the CRD drainage calculator, retrieved 2015-06-11, except - # for the third example from the data requirements handbook - - # This is the first example calculation from the data requirements handbook, where they give - # 8.07 µg/L as the result (obviously a rounding error). - expect_equal(round(PEC_sw_drainage_UK(150, interception = 0, Koc = 100), 4), 8.0769) - - # This is the second example calculation from the data requirements handbook - expect_equal(round(PEC_sw_drainage_UK(90, interception = 0, Koc = 10), 4), 13.1538) - - # This is the third example calculation from the data requirements handbook, - expect_equal(round(PEC_sw_drainage_UK(60, interception = 0.5, Koc = 550, - latest_application = "01 July", - soil_DT50 = 200), 2), 0.84) -}) diff --git a/pkg/tests/testthat/test_geomean.R b/pkg/tests/testthat/test_geomean.R deleted file mode 100644 index 0cc3416..0000000 --- a/pkg/tests/testthat/test_geomean.R +++ /dev/null @@ -1,11 +0,0 @@ -library(pfm) -context("Geometric mean calculation") - -test_that("The geometric mean is correctly calculated", { - expect_equal(geomean(c(1, 3, 9)), 3) - expect_equal(geomean(c(0, 3, 9)), 0) - expect_error(geomean(c(1, 3, NA, 9), na.rm = FALSE), "NA") - expect_equal(geomean(c(1, 3, NA, 9), na.rm = TRUE), 3) - expect_error(geomean(c(1, -3, 9)), "positive") - expect_error(geomean(c(1, -3, NA, 9)), "positive") -}) diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..d2df1cc --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(pfm) + +test_check("pfm") diff --git a/tests/testthat/EXSW2_R1_stream_printed.txt b/tests/testthat/EXSW2_R1_stream_printed.txt new file mode 100644 index 0000000..60bb5ac --- /dev/null +++ b/tests/testthat/EXSW2_R1_stream_printed.txt @@ -0,0 +1,10 @@ + data from file 3.out segment 20 + datetime t t_firstjan t_rel_to_max cwa_mug_per_L +1 1978-10-01 00:00:00 0.000 273.0000 -55.083 0 +2 1978-10-01 01:00:00 0.042 273.0417 -55.041 0 +3 1978-10-01 02:00:00 0.083 273.0833 -55.000 0 +4 1978-10-01 03:00:00 0.125 273.1250 -54.958 0 +5 1978-10-01 04:00:00 0.167 273.1667 -54.916 0 +6 1978-10-01 05:00:00 0.208 273.2083 -54.875 0 +Moving window analysis +NULL diff --git a/tests/testthat/H_sw_D4_pond_printed.txt b/tests/testthat/H_sw_D4_pond_printed.txt new file mode 100644 index 0000000..5730be6 --- /dev/null +++ b/tests/testthat/H_sw_D4_pond_printed.txt @@ -0,0 +1,10 @@ + data from file 00001p_pa.cwa segment 1 + datetime t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L +1 1985-01-01 00:00:00 0.000 0.00000000 -396.167 0.00000000 0.00000000 +2 1985-01-01 01:00:00 0.042 0.04166667 -396.125 0.08323064 0.08323716 +3 1985-01-01 02:00:00 0.083 0.08333333 -396.084 0.16626900 0.16628210 +4 1985-01-01 03:00:00 0.125 0.12500000 -396.042 0.24911240 0.24913190 +5 1985-01-01 04:00:00 0.167 0.16666667 -396.000 0.33172050 0.33174650 +6 1985-01-01 05:00:00 0.208 0.20833333 -395.959 0.41401430 0.41404670 +Moving window analysis +NULL diff --git a/tests/testthat/H_sw_R1_stream_events.rds b/tests/testthat/H_sw_R1_stream_events.rds new file mode 100644 index 0000000..ba6557b Binary files /dev/null and b/tests/testthat/H_sw_R1_stream_events.rds differ diff --git a/tests/testthat/H_sw_R1_stream_printed.txt b/tests/testthat/H_sw_R1_stream_printed.txt new file mode 100644 index 0000000..572ad6d --- /dev/null +++ b/tests/testthat/H_sw_R1_stream_printed.txt @@ -0,0 +1,10 @@ + data from file 00003s_pa.cwa segment 20 + datetime t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L +20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 0 +40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 0 +60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 0 +80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 0 +100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 0 +120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 0 +Moving window analysis +NULL diff --git a/tests/testthat/H_sw_R1_stream_windows.rds b/tests/testthat/H_sw_R1_stream_windows.rds new file mode 100644 index 0000000..2531189 Binary files /dev/null and b/tests/testthat/H_sw_R1_stream_windows.rds differ diff --git a/tests/testthat/test_PEC_sed.R b/tests/testthat/test_PEC_sed.R new file mode 100644 index 0000000..443f789 --- /dev/null +++ b/tests/testthat/test_PEC_sed.R @@ -0,0 +1,9 @@ +context("Simple PEC sediment calculations") + +test_that("PEC_sw_sed calculates correctly using the percentage method", { + # Application of 100 g/ha, 1 m spray drift distance (2.77% drift input), 50% in sediment, + # default assumptions of CRD spreadsheet (5 cm sediment depth, 1.3 kg/L sediment density) + # Reference value calculated with CRD spreadsheet + PEC_sw_100_1_m <- PEC_sw_drift(100, distances = 1) + expect_equivalent(round(PEC_sw_sed(PEC_sw_100_1_m, percentage = 50), 3), 2.131) +}) diff --git a/tests/testthat/test_PEC_soil.R b/tests/testthat/test_PEC_soil.R new file mode 100644 index 0000000..0661a52 --- /dev/null +++ b/tests/testthat/test_PEC_soil.R @@ -0,0 +1,95 @@ +library(pfm) +context("Simple PEC soil calculations") + +test_that("PEC_soil calculates correctly", { + # Application of 100 g/ha gives 0.133 mg/kg under default assumptions + expect_equal(as.numeric(PEC_soil(100)), 0.1 * 4/3) + + # or 0.1 mg/kg assuming 25% interception + expect_equal(as.numeric(PEC_soil(100, interception = 0.25)), 0.1) + + # Mixing depth of 1 cm gives five-fold PEC + expect_equal(as.numeric(PEC_soil(100, interception = 0.25, mixing_depth = 1)), 0.5) +}) + +test_that("Tier 1 PEC soil example for Pesticide A in EFSA guidance can be reproduced", { + # Calculate total soil concentrations for tier 1 scenarios + results_pfm <- PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + scenarios = "EFSA_2015") + + # From Table I.5, p. 80 + results_guidance <- matrix(c(22.0, 11.5, 9.1, 21.8, 11.4, 9.0), + ncol = 3, byrow = TRUE) + dimnames(results_guidance) <- list(t_avg = c(0, 21), + scenario = c("CTN", "CTC", "CTS")) + + + expect_equal(round(results_pfm, 1), results_guidance) + + # Calculate porewater soil concentrations for tier 1 scenarios + results_pfm_pw <- PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) + + # From Table I.5, p. 80 + results_guidance_pw <- matrix(c(0.76, 0.67, 0.91, 0.75, 0.66, 0.90), + ncol = 3, byrow = TRUE) + dimnames(results_guidance_pw) <- list(t_avg = c(0, 21), + scenario = c("CLN", "CLC", "CLS")) + + expect_equal(round(results_pfm_pw, 2), results_guidance_pw) +}) + +test_that("Tier 1 PEC soil example for Pesticide F in EFSA guidance can be reproduced", { + # Parent F + # Calculate total and porewater soil concentrations for tier 1 scenarios + results_pfm <- PEC_soil(1000, interval = 365, DT50 = 25, t_avg = c(0, 21), + scenarios = "EFSA_2015") + results_pfm_pw <- PEC_soil(1000, interval = 365, DT50 = 25, t_av = c(0, 21), + Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) + + # From Table I.14, p. 88 + results_guidance <- matrix(c(12.8, 7.7, 6.6, 11.8, 6.8, 5.7), + ncol = 3, byrow = TRUE) + results_guidance_pw <- matrix(c(0.50, 0.46, 0.71, 0.45, 0.41, 0.60), + ncol = 3, byrow = TRUE) + + # Skip checking dimnames by using expect_equivalent() + expect_equivalent(round(results_pfm, 1), results_guidance) + expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw) + + # Metabolite M1 + # Calculate total and porewater soil concentrations for tier 1 scenarios + # Relative molar mass is 200/300, formation fraction is 0.7 + results_pfm <- PEC_soil(200/300 * 0.7 * 1000, interval = 365, DT50 = 100, t_avg = c(0, 21), + scenarios = "EFSA_2015") + results_pfm_pw <- PEC_soil(200/300 * 0.7 * 1000, interval = 365, DT50 = 100, t_av = c(0, 21), + Kom = 10, scenarios = "EFSA_2015", porewater = TRUE) + + # From Table I.15, p. 88 + results_guidance <- matrix(c(7.27, 4.08, 3.38, 7.12, 3.97, 3.26), + ncol = 3, byrow = TRUE) + results_guidance_pw <- matrix(c(12.93, 10.42, 11.66, 12.58, 10.09, 11.15), + ncol = 3, byrow = TRUE) + + # Skip checking dimnames by using expect_equivalent() + expect_equivalent(round(results_pfm, 2), results_guidance) + expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw) + + # Metabolite M2 + # Calculate total and porewater soil concentrations for tier 1 scenarios + # Relative molar mass is 100/300, formation fraction is 0.7 * 1 + results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + scenarios = "EFSA_2015") + results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) + + # From Table I.16, p. 89 + results_guidance <- matrix(c(5.13, 2.69, 2.13, 5.08, 2.66, 2.10), + ncol = 3, byrow = TRUE) + results_guidance_pw <- matrix(c(1.61, 1.39, 1.80, 1.60, 1.37, 1.77), + ncol = 3, byrow = TRUE) + + # Skip checking dimnames by using expect_equivalent() + expect_equivalent(round(results_pfm, 2), results_guidance) + expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw) +}) diff --git a/tests/testthat/test_PEC_sw_drift.R b/tests/testthat/test_PEC_sw_drift.R new file mode 100644 index 0000000..d09d578 --- /dev/null +++ b/tests/testthat/test_PEC_sw_drift.R @@ -0,0 +1,15 @@ +library(pfm) +context("Simple PEC surface water calculations with drift entry") + +test_that("PEC_sw_drift gives the same results as the CRD PEC calculator", { + # One application of 30 g/ha to field crops calculated with UK PEC calculator published by CRD + expect_equal(round(PEC_sw_drift(30), 3), + c('1 m' = 0.277, '5 m' = 0.057, '10 m' = 0.029, '20 m' = 0.015)) + + # 7 applications of 30 g/ha to field crops calculated with UK PEC calculator, initial PEC + expect_equal(round(PEC_sw_drift(30, 7), 3), + c('1 m' = 0.161, '5 m' = 0.033, '10 m' = 0.017, '20 m' = 0.008)) + + # 4 applications of 30 g/ha to late fruit crops calculated with UK PEC calculator published by CRD (uses different drift values from SANCO aquatic guidance) + #expect_equal(round(PEC_sw_drift(30, 4, crop = "Obstbau spät", distances = c(3, 20, 50)), 3), c('3 m' = 1.101, '20 m' = 0.080, '50 m' = 0.013)) +}) diff --git a/tests/testthat/test_SFO_actual_twa.R b/tests/testthat/test_SFO_actual_twa.R new file mode 100644 index 0000000..b0a5537 --- /dev/null +++ b/tests/testthat/test_SFO_actual_twa.R @@ -0,0 +1,13 @@ +library(pfm) +context("Actual and time weighted average concentrations for SFO kinetics") + +test_that("SFO_actual_twa calculates correctly", { + test_times <- c(0, 1, 7, 21, 42) + # This was calculated with the CRD spreadsheet for multiple applications + reference <- data.frame( + actual = c(10, 9.330, 6.156, 2.333, 0.544), + twa = c(NaN, 9.661, 7.923, 5.267, 3.248), + row.names = test_times) + result <- round(10 * SFO_actual_twa(10, times = test_times), 3) + expect_equal(result, reference) +}) diff --git a/tests/testthat/test_TOXSWA_cwa.R b/tests/testthat/test_TOXSWA_cwa.R new file mode 100644 index 0000000..7c9a73c --- /dev/null +++ b/tests/testthat/test_TOXSWA_cwa.R @@ -0,0 +1,56 @@ +library(pfm) +context("Read and analyse TOXSWA cwa files") + +zipfile_test = system.file("testdata/SwashProjects.zip", package = "pfm") +basedir_test = "SwashProjects/project_H_sw/TOXSWA" + +H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", + basedir = basedir_test, + zipfile = zipfile_test) + +H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", + basedir = basedir_test, + zipfile = zipfile_test) + +basedir_test_2 = "SwashProjects/Project_1/TOXSWA" + +EXSW2_R1_stream <- read.TOXSWA_cwa("3.out", + basedir = basedir_test_2, + zipfile = zipfile_test) + + + +test_that("TOXSWA cwa file is correctly read and printed", { + + # This was the setting when printing the output into text files + options(width = 100) + + # Most content of the R6 object is at least partially printed + + H_sw_D4_pond_printed <- capture.output(print(H_sw_D4_pond)) + + expect_equal(H_sw_D4_pond_printed, readLines("H_sw_D4_pond_printed.txt")) + + H_sw_R1_stream_printed <- capture.output(print(H_sw_R1_stream)) + expect_equal(H_sw_R1_stream_printed, readLines("H_sw_R1_stream_printed.txt")) + + # The basedir is not printed, therefore tested separately + expect_equal(H_sw_D4_pond$basedir, basedir_test) + + EXSW2_R1_stream_printed <- capture.output(print(EXSW2_R1_stream)) + expect_equal(EXSW2_R1_stream_printed, readLines("EXSW2_R1_stream_printed.txt")) + + # The basedir is not printed, therefore tested separately + expect_equal(H_sw_D4_pond$basedir, basedir_test) +}) + +test_that("Getting events and moving window analysis works", { + + # Event analysis with two different thresholds + H_sw_R1_stream$get_events(c(2, 10)) + expect_equal_to_reference(H_sw_R1_stream$events, file = "H_sw_R1_stream_events.rds") + + # Moving window analysis + H_sw_R1_stream$moving_windows(c(7, 21)) + expect_equal_to_reference(H_sw_R1_stream$windows, file = "H_sw_R1_stream_windows.rds") +}) diff --git a/tests/testthat/test_UK_drainage.R b/tests/testthat/test_UK_drainage.R new file mode 100644 index 0000000..859f145 --- /dev/null +++ b/tests/testthat/test_UK_drainage.R @@ -0,0 +1,33 @@ +library(pfm) +context("UK drainage PEC calculations") + +test_that("The mobility classification and the drained percentage are correct", { + # Expected results are from the CRD drainage calculator, retrieved 2015-06-11 + + expect_equivalent(SSLRC_mobility_classification(1), list("Very mobile", 1.9)) + expect_equivalent(SSLRC_mobility_classification(15), list("Mobile", 1.9)) + expect_equivalent(SSLRC_mobility_classification(30), list("Mobile", 1.9)) + expect_equivalent(SSLRC_mobility_classification(74.9), list("Mobile", 1.9)) + expect_equivalent(SSLRC_mobility_classification(75), list("Moderately mobile", 0.7)) + expect_equivalent(SSLRC_mobility_classification(100), list("Moderately mobile", 0.7)) + expect_equivalent(SSLRC_mobility_classification(800), list("Slightly mobile", 0.5)) + expect_equivalent(SSLRC_mobility_classification(2000), list("Slightly mobile", 0.02)) + expect_equivalent(SSLRC_mobility_classification(5000), list("Non mobile", 0.01)) +}) + +test_that("UK drainflow PECs are correct", { + # Expected results are from the CRD drainage calculator, retrieved 2015-06-11, except + # for the third example from the data requirements handbook + + # This is the first example calculation from the data requirements handbook, where they give + # 8.07 µg/L as the result (obviously a rounding error). + expect_equal(round(PEC_sw_drainage_UK(150, interception = 0, Koc = 100), 4), 8.0769) + + # This is the second example calculation from the data requirements handbook + expect_equal(round(PEC_sw_drainage_UK(90, interception = 0, Koc = 10), 4), 13.1538) + + # This is the third example calculation from the data requirements handbook, + expect_equal(round(PEC_sw_drainage_UK(60, interception = 0.5, Koc = 550, + latest_application = "01 July", + soil_DT50 = 200), 2), 0.84) +}) diff --git a/tests/testthat/test_geomean.R b/tests/testthat/test_geomean.R new file mode 100644 index 0000000..0cc3416 --- /dev/null +++ b/tests/testthat/test_geomean.R @@ -0,0 +1,11 @@ +library(pfm) +context("Geometric mean calculation") + +test_that("The geometric mean is correctly calculated", { + expect_equal(geomean(c(1, 3, 9)), 3) + expect_equal(geomean(c(0, 3, 9)), 0) + expect_error(geomean(c(1, 3, NA, 9), na.rm = FALSE), "NA") + expect_equal(geomean(c(1, 3, NA, 9), na.rm = TRUE), 3) + expect_error(geomean(c(1, -3, 9)), "positive") + expect_error(geomean(c(1, -3, NA, 9)), "positive") +}) -- cgit v1.2.1