From 6d8de73e68f2c0349e618af35ce4a8f095ca0ed5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Mar 2018 10:10:08 +0100 Subject: Rebuild static docs using current pkdown Process PELMO runs in example using 15 (hyperthreading) cores and show processor info. --- ChangeLog | 12 +++ DESCRIPTION | 2 +- R/PELMO_runs.R | 5 +- docs/authors.html | 18 ++++- docs/index.html | 22 ++++-- docs/pkgdown.css | 42 ++++++++++- docs/pkgdown.js | 88 +++++++++++++++++++++- docs/reference/FOCUS_GW_scenarios_2012.html | 16 +++- docs/reference/FOCUS_PELMO_crop_sze_names.html | 18 ++++- docs/reference/FOCUS_PELMO_crops.html | 19 ++++- docs/reference/FOCUS_PELMO_location_codes.html | 16 +++- docs/reference/FOCUS_Step_12_scenarios.html | 55 ++++++++------ docs/reference/GUS.html | 17 ++++- docs/reference/PEC_soil.html | 18 ++++- docs/reference/PEC_sw_drainage_UK.html | 16 +++- docs/reference/PEC_sw_drift.html | 17 ++++- docs/reference/PEC_sw_exposit_runoff.html | 18 ++++- docs/reference/PEC_sw_focus.html | 21 +++++- docs/reference/PEC_sw_sed.html | 19 ++++- docs/reference/PELMO_path.html | 15 +++- docs/reference/PELMO_runs.html | 33 ++++++-- docs/reference/SFO_actual_twa.html | 15 +++- docs/reference/SSLRC_mobility_classification.html | 16 +++- docs/reference/TOXSWA_cwa.html | 16 +++- docs/reference/chent_focus_sw.html | 15 +++- docs/reference/create_run_list.html | 15 +++- docs/reference/drift_data_JKI.html | 50 +++++++----- docs/reference/endpoint.html | 18 ++++- docs/reference/focus_80th.html | 18 ++++- docs/reference/geomean.html | 24 +++++- docs/reference/get_flux.html | 15 +++- docs/reference/get_interval.html | 15 +++- docs/reference/index.html | 14 +++- docs/reference/max_twa.html | 21 +++++- docs/reference/one_box-1.png | Bin 0 -> 15066 bytes docs/reference/one_box-2.png | Bin 5841 -> 14519 bytes docs/reference/one_box-3.png | Bin 0 -> 28566 bytes docs/reference/one_box.html | 25 ++++-- docs/reference/perc_runoff_exposit.html | 17 ++++- docs/reference/perc_runoff_reduction_exposit.html | 17 ++++- docs/reference/pesticide.txt | 4 + docs/reference/pfm_degradation.html | 15 +++- docs/reference/plot.TOXSWA_cwa-1.png | Bin 0 -> 20867 bytes docs/reference/plot.TOXSWA_cwa-2.png | Bin 7826 -> 20189 bytes docs/reference/plot.TOXSWA_cwa-3.png | Bin 0 -> 21221 bytes docs/reference/plot.TOXSWA_cwa-4.png | Bin 7575 -> 21595 bytes docs/reference/plot.TOXSWA_cwa-5.png | Bin 0 -> 14860 bytes docs/reference/plot.TOXSWA_cwa.html | 20 ++++- docs/reference/plot.one_box-1.png | Bin 0 -> 15342 bytes docs/reference/plot.one_box-2.png | Bin 5891 -> 31171 bytes docs/reference/plot.one_box-3.png | Bin 0 -> 35837 bytes docs/reference/plot.one_box.html | 19 ++++- docs/reference/read.TOXSWA_cwa.html | 19 ++++- docs/reference/sawtooth-1.png | Bin 0 -> 15868 bytes docs/reference/sawtooth-2.png | Bin 6217 -> 35837 bytes docs/reference/sawtooth.html | 23 +++++- docs/reference/soil_scenario_data_EFSA_2015.html | 54 ++++++++----- docs/reference/sum_periods.html | 15 +++- docs/reference/twa.html | 17 ++++- man/PELMO_runs.Rd | 5 +- 60 files changed, 855 insertions(+), 134 deletions(-) create mode 100644 docs/reference/one_box-1.png create mode 100644 docs/reference/one_box-3.png create mode 100644 docs/reference/plot.TOXSWA_cwa-1.png create mode 100644 docs/reference/plot.TOXSWA_cwa-3.png create mode 100644 docs/reference/plot.TOXSWA_cwa-5.png create mode 100644 docs/reference/plot.one_box-1.png create mode 100644 docs/reference/plot.one_box-3.png create mode 100644 docs/reference/sawtooth-1.png diff --git a/ChangeLog b/ChangeLog index 017af3a..ea7b134 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,15 @@ +commit ffeec05d913f2e987da362c05df2afc2a8a23965 +Author: Johannes Ranke +Date: 2018-01-29 10:11:27 +0100 + + Documentation fixes and updates + +commit 8423df9693c5cd2f2d36ee3131c7b6fcefa4d0ca +Author: Johannes Ranke +Date: 2018-01-29 10:11:27 +0100 + + Documentation fixes and updates + commit b9ce44748f2795ae1f35fe5a510e88635f247a7f Author: Johannes Ranke Date: 2018-01-29 09:22:42 +0100 diff --git a/DESCRIPTION b/DESCRIPTION index 35c29dc..deb08cc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.4-5 -Date: 2018-01-29 +Date: 2018-02-27 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R index 432231e..2768205 100644 --- a/R/PELMO_runs.R +++ b/R/PELMO_runs.R @@ -42,11 +42,14 @@ #' pot = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi"))) #' time_1 <- system.time( #' PECgw_1 <- PELMO_runs(runs_1, psm_dir = system.file("testdata", package = "pfm"), -#' cores = 6, overwrite = TRUE) +#' cores = 15, overwrite = TRUE) #' ) #' print(PECgw_1) #' # We get exactly the same PECgw values (on Linux, calling PELMO using Wine). #' print(time_1) +#' if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { +#' cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]])) +#' } #' #' # Demonstrate some results with metabolites. #' runs_2 <- list(list(psm = 'Pesticide_D_1_May_every_other_year_mets', diff --git a/docs/authors.html b/docs/authors.html index d2ef54f..d08c687 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -18,12 +18,16 @@ + + - + + + @@ -51,6 +55,12 @@
-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/index.html b/docs/index.html index 66f3304..5b977a6 100644 --- a/docs/index.html +++ b/docs/index.html @@ -8,8 +8,13 @@ Utilities for Pesticide Fate Modelling • pfm - - + + + + @@ -28,6 +33,12 @@

@@ -85,8 +96,7 @@ this program. If not, see <http://www.gnu.org/license

GPL

Developers

    -
  • Johannes Ranke
    Author, maintainer, copyright holder
    (0000-0003-4371-6538) -
    • +
  • Johannes Ranke
    Author, maintainer, copyright holder
@@ -97,7 +107,7 @@ this program. If not, see <http://www.gnu.org/license
-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 9c437c7..181fe63 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -34,6 +34,10 @@ img.icon { float: right; } +img { + max-width: 100%; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -96,6 +100,11 @@ a.anchor { margin-bottom: 0.5em; } +.orcid { + height: 16px; + vertical-align: middle; +} + /* Reference index & topics ----------------------------------------------- */ .ref-index th {font-weight: normal;} @@ -133,15 +142,30 @@ pre, code { color: #333; } -pre img { +pre code { + overflow: auto; + word-wrap: normal; + white-space: pre; +} + +pre .img { + margin: 5px 0; +} + +pre .img img { background-color: #fff; display: block; + height: auto; } code a, pre a { color: #375f84; } +a.sourceLine:hover { + text-decoration: none; +} + .fl {color: #1514b5;} .fu {color: #000000;} /* function */ .ch,.st {color: #036a07;} /* string */ @@ -152,3 +176,19 @@ code a, pre a { .error { color: orange; font-weight: bolder;} .warning { color: #6A0366; font-weight: bolder;} +/* Clipboard --------------------------*/ + +.hasCopyButton { + position: relative; +} + +.btn-copy-ex { + position: absolute; + right: 0; + top: 0; + visibility: hidden; +} + +.hasCopyButton:hover button.btn-copy-ex { + visibility: visible; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index c8b38c4..64b20df 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -1,8 +1,94 @@ $(function() { - $("#sidebar").stick_in_parent({offset_top: 40}); + + $("#sidebar") + .stick_in_parent({offset_top: 40}) + .on('sticky_kit:bottom', function(e) { + $(this).parent().css('position', 'static'); + }) + .on('sticky_kit:unbottom', function(e) { + $(this).parent().css('position', 'relative'); + }); + $('body').scrollspy({ target: '#sidebar', offset: 60 }); + var cur_path = paths(location.pathname); + $("#navbar ul li a").each(function(index, value) { + if (value.text == "Home") + return; + if (value.getAttribute("href") === "#") + return; + + var path = paths(value.pathname); + if (is_prefix(cur_path, path)) { + // Add class to parent
  • , and enclosing
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