path: root/ChangeLog

commit 46883a0c3a3c00127a563a7befa0af440573baaa
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-19 11:22:08 +0100

    Correct default y axis label for plot.one_box

commit 3947731a5a8c3598271b26f5201dea4bcb13ef6d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-19 10:47:09 +0100

    Fix one_box for ini = 1, use in sawtooth examples

commit dd30f0d0ff1d8d0cc46aaef6e0917c51fe798f52
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-19 10:36:19 +0100

    Move mkin::twa to pfm::max_twa.mkinfit
    
    - Add max_twa.mkinfit() recently introduced to mkin as mkin::twa() but
      never released with it
    - Add a test to check max_twa.one_box() against analytical solutions in
      max_twa.mkinfit().
    - Clean up R CMD check
    - Update docs

commit 3ead7acba845b4f2552f555dfb29da889ed0cda8
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-19 09:42:21 +0100

    Make max_twa() a bit safer

commit 74ed85b07f09ea99476208749cd274a476ba4536
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-19 09:27:36 +0100

    Documentation updates

commit a6d61c06d573574cf574ed893cc13808a9e8b785
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-19 09:20:22 +0100

    Fix order of arguments to one_box, correct docs

commit b8ac1393b9e1bef8c48b26b790cf5759ccd69fed
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-19 09:10:37 +0100

    Predict parent decline without fitting for non-SFO models

commit 3d4f6f8c582c19c38587ead305a1229ff069da63
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-19 08:24:44 +0100

    Switch sawtooth plotting example to FOMC
    
    as this it is claimed in the README that an mkinfit prediction is used.
    - Add another seealso link
    - Delete trailing whitespace

commit 9b5faa8b8475bdd7624c58b07d45d28d42a47a2e
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-18 23:02:14 +0100

    Point to the github.io documentation site

commit cff68edc1ac113ac9e159dfdf7cfcbb6721ff2a7
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-18 22:58:51 +0100

    Make README.md simple, and point to the reference

commit a76221d87485029444c8e684022ca606a0c7e68d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-18 22:41:01 +0100

    Update static docs using pkgdown
    
    - Add _pkgdown.yml for a structured function/data reference
    - Make seealso links active
    - Make mkinfit calls quiet
    - Use pkgdown branch from pull request hadley/pkgdown#229 to have topics
      ordered

commit a1d9f93138c2cfed92a683e37e72c737d52b7ad7
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-18 19:58:13 +0100

    One box time series and twa values
    
    - one_box() creates decline time series from mkinfit objects or simply
      from a half-life
    - sawtooth() generates sawtooth curves for arbitrary application
      patterns and decline models
    - twa() calculates moving window averages
    - max_twa() gives their maxima and
    - plot.one_box() can plot series generated by one_box() or sawtooth(),
      optionally adding a greay rectangle to illustrate the maximum moving
      window time weighted average

commit bba2cf3a70849ba86f37520d3e909cf1c706f416
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-12-22 11:06:57 +0100

    Fix reading in times from .out files
    
    The code from the previous commit was broken. Also, the time
    zone for the times that are read is now wet to 'UTC', in order to
    avoid setting different time zones due to daylight savings, which
    introduces artificial one-hour offsets on changeover days.

commit 0af7c7b8c34067fc4756929925239c329b28ed32
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-12-14 18:26:14 +0100

    Changelog update and roxygen run

commit 5a04ad3061c1484b45703e44149f49ec97cfbf15
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-12-14 16:52:14 +0100

    Set time correctly for 00:00 hours in .out file
    
    For ConLiqWatLayCur_xxxxx entries which are output at 00:00 (midnight),
    no time is listed in the .out file for this time. This commit introduces
    a workaround, setting the time to 00:00 when there is no time
    information.

commit e51e063564bffcb75dbb6ab7a364704c8d8e992e
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-12-12 21:24:24 +0100

    Fix reading .out for acronyms containing numbers

commit 9124e0f7d673c65584c1b2f838a3b944ea89c31d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-10-13 17:49:18 +0200

    Add drat target, remove unmaintained usage hints

commit 12a31f4c130c551f82232d9ef7dfb608bd52c53f
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-09-27 23:00:48 +0200

    Reorganise repository using standard package layout

commit 0d958ab6f84b569b5437f231c56004890c4ae23b
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-09-27 17:50:34 +0200

    Make the chents package optional

commit 399383adcdb37c4a3e32f1a2133a2fa3663618d0
Author: Johannes Ranke <jranke@uni-bremen.de>
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 <jranke@uni-bremen.de>
Date:   2016-09-23 18:16:51 +0200

    Slightly update the README

commit 2f618da8cfbeb0379f4d38af6f608a69c6d54bd5
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-07-30 11:29:09 +0200

    Update static documentation

commit 3b8730a58f7846b5261922ec90e582e0158a54c7
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-07-30 11:09:47 +0200

    Add 'methods' to dependecies

commit 3260b0e875b7af24f2aef7bc2464418525a192df
Author: Johannes Ranke <jranke@uni-bremen.de>
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 <jranke@uni-bremen.de>
Date:   2016-07-30 11:06:53 +0200

    Import 'is' from methods

commit 1ceb226d999d56276c9e361f359368287a0749c4
Author: Johannes Ranke <jranke@uni-bremen.de>
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 <jranke@uni-bremen.de>
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 <jranke@uni-bremen.de>
Date:   2016-06-08 08:36:48 +0200

    Clean up remainders of NL drift calculation function

commit 234a20018fe9fe9824bcfaae2c391e59d09f9871
Author: Johannes Ranke <jranke@uni-bremen.de>
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 <jranke@uni-bremen.de>
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 <jranke@uni-bremen.de>
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 <jranke@uni-bremen.de>
Date:   2016-03-10 05:17:45 +0100

    Add NL specific drift calculations

commit 1ab6d4c9f186fb7ea9bb8b968e47a9f1eab64583
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-03-02 17:51:21 +0100

    Fix the name of the Chateadun scenario

commit d14923ae1ac023c8f8f5ae8b5c0884f4247f764b
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2016-02-04 18:06:15 +0100

    Test reading .out files and close connections

commit 98a706373107188496a1df295697e739e51d6b06
Author: Johannes Ranke <johannes.ranke@jrwb.de>
Date:   2016-02-04 17:45:02 +0100

    Improve reading spead for new TOXSWA format

commit 057ba40426d49e09c06db26fb7d4072741b4cb8d
Author: Johannes Ranke <johannes.ranke@jrwb.de>
Date:   2016-02-04 12:21:02 +0100

    Read cwa data from TOXSWA 4.4.2 .out files

commit e7f8a0e82b24d28b74681dafc97f1cf8a4662b51
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-12-27 12:30:20 +0100

    Fix rounding of endpoint retrieval functions

commit f9373e361dde232b08fe7431e85bf367a1cfc269
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-12-27 12:29:37 +0100

    Another useless variant to avoid warnings in staticdoc plots

commit 3a579d87820ccbec514f1be5eb090e874fd87eec
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-12-22 19:32:54 +0100

    EFSA 2015 tier 1 PEC soil, clean up, add static docs

commit 9851a97ec915ddbfc8357f1a7e2cabae56c89f7d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-12-18 14:45:24 +0100

    Documentation fixes, chents is currently a hard dependency

commit 6b4e342b240baaf18150360986d15895fc80a937
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-10-15 14:41:26 +0200

    Add endpoint and GUS functions, roxygenize

commit c43b4947007b3c26bc56260499af51c41b8cd702
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-10-01 14:42:14 +0200

    Add some soil data for FOCUS groundwater scenarios

commit 697e0554bf89a63f23b9ab5548e31f218bc483e9
Author: Johannes Ranke <jranke@uni-bremen.de>
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 <jranke@uni-bremen.de>
Date:   2015-09-10 16:18:17 +0200

    Add PEC soil for product with serveral ais

commit 1ec3ee4a03d4e47fdd3be1bcbe754e478353410b
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-08-22 12:10:06 +0200

    Updates of DESCRIPTION and NAMESPACE

commit 51aa1a77c9b9b9a6becdb2a5a85213946719b051
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-08-22 12:06:37 +0200

    Add README.html for cgit on jrwb.de

commit 83c8575e2abde12208584b9c80935d4a873689fd
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-08-22 12:01:57 +0200

    Small documentation updates

commit 5038ba57fef6cc386566ec30f3d5dd67e62decff
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-08-21 15:10:42 +0200

    Adapt the description to R CMD check requirements

commit 4477e69b46e88c196f354463190753650157ea0d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-08-21 15:01:10 +0200

    Updates to pass checks and tests

commit ad4cd5d9a1f8c3976d08048a441129b1fb49a62b
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-07-02 16:05:59 +0200

    Changes to pass R CMD check --as-cran, roxygen run

commit fef0bb7fe916f91dcff089c17aa3290c0ea1ab1f
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-12 02:19:38 +0200

    Add sediment PEC calculations using the percentage method

commit 5b32c30549bfa3cb42ffde7e13f75608b98c79c2
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-12 02:19:01 +0200

    Make UK drainage with non-SFO soil degradation work

commit 9b8e5cb80ba4a89578d979bee134f8342ca0a527
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 17:38:01 +0200

    Now we pass R CMD check

commit dd803b191062925eda830543236836e7822fd884
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 16:57:43 +0200

    Add UK tier 1 drainage PEC calculations

commit 09cf970942706cfab43753d298b42e8d85216d80
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 15:25:22 +0200

    Now there is enough content to warrant 0.2-x

commit 3aa5fb86772c28402047c7ebd07841061dbcdbba
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 15:23:22 +0200

    Add facilities to calculate decline curves

commit d3daa7b73fa5d0508ff51a843247d126c2a11691
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 13:17:13 +0200

    Generate README.md with current pfm version

commit cb0d72e2c2d431bd32ffb129b62ea1a522cbdfeb
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 13:09:10 +0200

    Rename PEC_sw_drift() to PEC_sw_drift_ini()

commit ea9b75183bcf41fcdd6f61ec6060e94c4bc321a2
Author: Johannes Ranke <jranke@uni-bremen.de>
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 <jranke@uni-bremen.de>
Date:   2015-06-11 12:12:40 +0200

    Use devtools for roxygenizing, improve logging

commit 6e4a152925011528c21937f12bc53042a53f72de
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 10:13:18 +0200

    JKI drift percentage data for field crops and pome/stone fruit

commit 53099978c971ee8e5c94e67bf972f51629d67fd3
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 10:04:22 +0200

    and the incomplete documentation

commit 372ab2f2f59f0baaee759ce966a705f9f754cf6d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 10:03:32 +0200

    Intermediate stage for pfm_chent

commit 586b248f5d249f4ebaad2175c9f78fcae8646636
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-06-11 09:54:57 +0200

    Formatting

commit fd1609aafd2f40266c1e29d8dfdf5e08e8838d35
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-05-24 03:52:28 +0200

    Start of a pfm_chent data object

commit e2b1d510e921f7721647b0df6602c2618937c1da
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-05-08 08:47:11 +0200

    Update the Figure in the README

commit 8021c7cb9aac06e961227a3c0e0b013ec2d2d501
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-05-07 16:15:23 +0200

    Bugfix: Reset maximum event concentration for each event

commit 508d883f7689d617d15915dbd26a27f1613bb857
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-05-07 12:04:28 +0200

    Make quarterly labels for plot.TOXSWA_cwa

commit c6e57ab29170266b3038b01c54bf161ab361d440
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-04-24 02:22:21 +0200

    Do not test the path to the zip file

commit 7d2096855edcc196629c1c7a9983a56ec6addd1e
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-04-24 02:21:04 +0200

    Add a geometric mean function

commit bcfe0af7970efe36c3aa661e89953fbe3689c310
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-04-24 02:20:21 +0200

    Clean the Makefile a bit

commit 768a043848dd84b9e699916657d0a23b2f3b9e83
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-04-22 13:48:42 +0200

    Fix header formatting

commit 04502ca0c658a6c929debd61aee87be8c7eceb04
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-04-22 13:46:32 +0200

    Update markdown version of README

commit ec79637749d300ab4ca170805c673905e52d67dd
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-04-22 13:42:10 +0200

    Add simplest PEC soil calcs, use testthat

commit 8ffbc49b3f01deac6f9e83aaa6d318d4e2f8552b
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-01-23 16:44:04 +0100

    Add option to plot relative to maximum

commit 8975dc148d0a6f222174980eb60314054be9b6cf
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-01-13 14:54:58 +0100

    Fix warning in README

commit 891af5d0f1ee8d45cd4403af43293463d23ba96b
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-01-13 14:05:31 +0100

    README.rmd with example, fix reading unzipped files

commit 4d74570f1ca4a94d894c6c5169684a8246d0a51c
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-01-13 12:58:26 +0100

    Correctly initialize R6 fields, read from zip files

commit ee070c11f7c7faff2f573d27cf32aafab78971a8
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2015-01-07 23:56:54 +0100

    Pass ... parameters to added cwa lines

commit 92d97ba99d7b90d95a67796cb5e68f28f752b70b
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2014-12-17 21:39:42 +0100

    Initial commit: R6 class for TOXSWA cwa files