commit 80b451ddb4e749041c2b216603274a012dc83d59
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-30 14:28:23 +0100
PELMO summary files for testing
commit 826cf9a2687ff1d7ca5b568882f5686f76f82074
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-30 14:11:34 +0100
Use relative tolerance of 1e-6 for flux test
to pass test also for more extreme situations as in the current test data.
commit eea72720956dc8358fac98b29c9a627a9363cbd2
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-30 13:12:24 +0100
Better documentation of PELMO_runs().
commit d78d2effd517ab3c27412ae6f4ae701c456ae590
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-30 12:46:57 +0100
pfm for windows in my drat
commit eaf3b558747ff8228e87ded727a6c0e91a6579f8
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-30 12:01:14 +0100
More extreme parameters for metabolites for testing
commit a6c13f70f6c6669a8088827a602ac475fdf9b624
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-29 16:58:53 +0100
Setting up PELMO runs, execution and evaluation
It all works!
commit bc97a35a32c4f47e29364488a3601f94c6e68d45
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-27 18:33:45 +0100
Really use all scenarios in test data
Maize, that was used in the last commit, is not parameterised for
Jokioinen
commit a4081ddfea726283874968c0b62a7f46e4fd1232
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-27 18:23:35 +0100
Use all scenarios in the test data
commit 3c82d26206e2f2e74600acd71a49c70eaed555c4
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-27 08:17:08 +0100
Also test run with metabolites
commit 8fd050e57b7babfbdb1ccfabb468a0398396d466
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-27 07:54:53 +0100
Include a run with metabolites in PELMO test data
commit b38055278d4a801598ece9d2c93716a9bf67134a
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-27 01:00:07 +0100
Set up FOCUS PELMO runs and run them in parallel
- This works on Linux using wine
- PELMO runs (including pelmo.inp files) are correctly generated
- The PLM files for FOCUS Pesticide_D in the test data archive are
correctly reproduced
- The data files (including FOCUS groundwater scenario data) are now
created and documented in R files
commit 40c2f387775a168df1be699813807586cf098648
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-26 10:30:32 +0100
Improved test data with 'irrigation'
commit 228ab628b407af4812a48f20693a9a3a6bba8af4
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-25 16:45:24 +0100
More variable selection of test data
commit bf6634b7d9a5033a217f04060f77e0c7d5b3046a
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-25 15:27:05 +0100
Use tar.bz2 to correctly transfer file names
commit 476d556cb6a490b138e47d487dd732f298aa6c3d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-25 14:29:41 +0100
Add FOCUS PELMO 5.5.3 output for dummy pesticide D
commit 9f16be247e851c948edb30ac756550d89ba0af52
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-19 11:44:22 +0100
Another correction of the docs
commit 2ab822d51c4c7e29d62076336d7a3f02a46e41a5
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-19 11:41:19 +0100
Corrections in the documentation
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
