path: root/ChangeLog

commit 020bce41dd821b5949f824eaa3a2998584a14585
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-10-15 11:27:59 +0200

    Residue processing for depth profiles over time

commit a2ca8be6f5593f0afd833ea73b62149055ee84f9
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-10-10 14:56:35 +0200

    Do not mess with zero values at time zero

commit a071d46f698397a6c8247e19eceb0fcd5f139056
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-10-10 12:25:42 +0200

    Fix set_nd for metabolites, handle zero at time zero

commit a5503d3e26408f7308a7bf4da617205b93d17422
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-10-10 09:21:46 +0200

    Fix documentation for set_nd

commit a5e458ecb33ae87e46b2237174a194f6252a97cf
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-10-10 08:53:30 +0200

    Finish documentation of set_nd and test it

commit 63df3871a442de4bf47e4d9de1449e7f6ed65b2f
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-10-09 19:17:07 +0200

    Function to set non-detects in residue series

commit 9f848a9518aabf162723271bafba244221ee83ed
Author: Johannes Ranke <johannes.ranke@jrwb.de>
Date:   2019-09-27 12:55:03 +0200

    Built windows binary for drat

commit 435e07a6f7fd2599d783fd306ee6d9e08acc0c6b
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-09-27 10:00:15 +0200

    Fix for UK drainage, some EFSA interception and washoff
    
    - PEC_sw_drainage_UK() gave results that were a little bit too high
    for the substances with the highest Koc (>4000), as I used 0.01% instead
    of 0.008% for them. This must have come from an old vesion of the UK
    data requirements handbook, at least I do not have another explanation
    
    - Add EFSA interception (from 2014 DegT50 guidance) and tier 1
    crop wash-off factors (from 2017 PEC soil guidance) for some major
    arable crops
    
    - Update docs

commit 803fe13e505960fddccdbd4dcb524715f5eb068d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-09-18 18:18:40 +0200

    Add url: tag to _pkgdown.yml, typo, update docs

commit 8deaa29a659630a40e8b11df1fa3ebbbd9ca9e68
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-07-01 08:04:40 +0200

    Typo

commit 37a1513d73201dbacc71af3c33a2a2a4e798583c
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-06-12 18:15:46 +0200

    Update of static docs

commit 5c9dd5c269acc4a6e6e32a7e599afb8f98d8ca36
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-06-12 18:14:46 +0200

    Documentation fix

commit 069824057caf8e57507852b858a7ecfd8e13e49a
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-05-14 12:41:16 +0200

    Version bump and doc update

commit 41f3c867008c24b69a9bb0e5c7c084969d46bebd
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-05-14 12:33:21 +0200

    Add Exposit version 3.01a2 for runoff calculations
    
    At the request of Muris Korkaric (Agroscope). This is for 3 m buffer
    only and provides consistency with earlier calculations

commit 7b11b5d0da29447df026002af3ae5283510fdae9
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-04-29 13:03:00 +0200

    Additional runoff data used by Agroscope

commit 67cd9e04caaf18a40231262c9033fb24e8bb2a66
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-04-26 13:45:44 +0200

    Formatting improvement for the online docs

commit 45f540ef19fd2a2a80e3f3f72950933ed6396f0c
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-04-26 13:33:27 +0200

    Another take on completing the drift data
    
    The R script I used yesterday got lost because I used the .Rd file
    that got overwritten by roxygen later.

commit 451b332c8888bac8279340b086abb3b714ac3ae1
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-04-25 11:50:35 +0200

    Add more drift data, especially 3 m field crop data
    
    To support Agroscope in doing lots of PEC calculations for Switzerland

commit 3bb842b93107dd6207610de1fe5b44be66779e4d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-04-25 10:25:56 +0200

    Remove leftover docs from earlier version
    
    Docs now live in docs/

commit 77f63efa62b6530fbe2accdacc866e34626fe4e3
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-21 16:01:38 +0100

    Update docs

commit 5086e2b87eaec90a02b4744d1321c6949d0b8982
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-21 15:59:22 +0100

    Use codecov

commit e21ec96873bf60072414369bc96e4c076a450235
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-19 17:13:55 +0100

    Add grImport to Suggests:
    
    Because chent which in turn suggests grImport is loaded from github
    which obviously does not pull grImport

commit 4e99ae029638a3720eba97b28bd7de3129a727ce
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-19 15:22:26 +0100

    Update README.html

commit 31eca93dadf58d47b3f3dd7aa485f89023090440
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-19 14:54:26 +0100

    Add Remotes: field for travis

commit 70b85fd2a11da1e20cd4978c717540021af34be8
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-19 14:35:15 +0100

    Test on Travis

commit 17755babc3a517f4c7cec1c04e3e1f32b7ffb5d9
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-19 14:27:03 +0100

    Add another test for Exposit drainage
    
    to test overriding the mobility group derived from Koc

commit 138638976f792684483520fe7837ded0a27938e4
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-19 12:35:19 +0100

    Stop endless appending to pesticide.txt example

commit 72c56f4246966c1bea627f601cf3cc457734f023
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-19 12:27:00 +0100

    Add German drainage calculations using Exposit 3.02

commit e5a077e28153f6494c99d6945b8b1bd239464609
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-02-08 15:25:19 +0100

    Make SSLRC and PEC drainage UK accept NA for Koc

commit b935273d651301b271e0cb66bf36c2bbc1d15b32
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-01-31 01:40:24 +0100

    Separate out PELMO utilities into rPELMO

commit 1611dd58df6b2b2e6ad01af6573664da8ce8b6b9
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2019-01-30 23:58:55 +0100

    Convenience function for metabolite PEC soil

commit eab95c62479d732cbd531ad67ea458d2744af420
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-09-27 18:58:32 +0200

    Create valid Step 1 files with fewer arguments

commit 8452daa2015aa645dcc1eca3ec2bba5726603e4e
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-09-22 09:54:59 +0200

    Add test and update docs

commit ff7e67a4d3415419dd3f712ef1af7467ebf65508
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-09-21 19:39:44 +0200

    Support FOMC in PEC_soil

commit 03c3035ca01c66b6a1352f7e509753fe2d057af2
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-07-11 03:41:43 +0200

    Improve PELMO tests

commit 22b36c824fe5e1561868a649216fe079c6fbfb85
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-07-10 18:06:29 +0200

    Update static docs

commit cb3695dd434b3a3273217fb22c5ffb86065ae96d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-07-10 17:57:33 +0200

    EFSA PEC soil guidance from 2017
    
    - Implement the new guidance as well as possible
    - Maintenance work addressing CRAN checks

commit c4c3ca282c6aadca82e392692ae4100fec1dd834
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-07-10 16:46:47 +0200

    .out file from TOXSWA 5.5.3 for testing

commit a736ecc357889107b6e93f14cdf0c1ea4587817f
Author: Johannes Ranke <johannes.ranke@jrwb.de>
Date:   2018-07-10 16:08:52 +0200

    Adapt path to package on windows

commit 8989a484b9b2d23463c95e0a3927e307ec0a5e64
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-07-04 10:59:47 +0200

    Some documentation updates
    
    Document that TOXSWA 5.5.3 is supported in the help files

commit 6ca8bdb8636141fac592688a6794ae092f0bc85a
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-06-20 14:58:44 +0200

    Advertise drat repo

commit 6acfd0dfb2670e3eeab6144c90586f28105583a8
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-06-20 14:53:02 +0200

    Update static docs

commit cac29c8c1cc0f6004ef0cd63229cfb993a24496c
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-06-11 16:27:22 +0200

    Adapt to TOXSWA 5.5.3

commit bd15236d5dedb4067bd29e58e655c5352aca1db4
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-06-08 16:20:40 +0200

    Enable PEC porewater for the default scenario
    
    The default scenario uses soil parameters from the REACH guidance R.16,
    Table R.16-9.

commit ec2052d68950745380c2724757b3ba8b116605fc
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-06-08 14:54:40 +0200

    Add actual/twa calcs for FOMC, typo

commit edc3462fb4fa9f0eb604fc18ec62bb48997b5627
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-06-08 14:53:58 +0200

    Pending stuff from the doc update

commit 197606de234a936751ac3c1db2e4feb3fa117a92
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-06-06 02:48:44 +0200

    Rebuild docs with pkgdown 1.1.0

commit 282820693c62b958e12104f4bb6229c04803f098
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-03-01 10:32:08 +0100

    Add a README.html for cgit.jrwb.de

commit 6d8de73e68f2c0349e618af35ce4a8f095ca0ed5
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-03-01 10:10:08 +0100

    Rebuild static docs using current pkdown
    
    Process PELMO runs in example using 15 (hyperthreading) cores and show
    processor info.

commit ffeec05d913f2e987da362c05df2afc2a8a23965
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-01-29 10:11:27 +0100

    Documentation fixes and updates

commit 8423df9693c5cd2f2d36ee3131c7b6fcefa4d0ca
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-01-29 10:11:27 +0100

    Documentation fixes and updates

commit b9ce44748f2795ae1f35fe5a510e88635f247a7f
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2018-01-29 09:22:42 +0100

    Correction of return value documentation for PEC_sw_exposit_runoff
    
    Rebuild pkgdown documentation

commit 87d63e649da5e12409c50cb06d3d2a01e9880759
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-12-15 17:25:21 +0100

    Improve handling of µ in y axis for plot.TOXSWA_cwa

commit 4944d7ade227f1dd54c94b6a02c3c849dc1fb8ab
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-12-14 10:19:43 +0100

    Update copyright date

commit 0e1d517d4d6351f2d43ab8636363e73d8b8cf677
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-11-04 11:48:08 +0100

    Option to thin low TOXSWA PECsw data for plotting
    
    to reduce the file size of plots e.g. as PDF files

commit eb4465035dd44907eae3ea0340221316b7cfca12
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-11-03 11:18:10 +0100

    Also return runoff percentages

commit 06b528f0c19ca9f7a311612c0e9ae80c0d0c1d3f
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-10-27 18:15:29 +0200

    Exposit runoff calculations for surface water

commit 2cd464455a22791c0450ada45a0e0128c637fade
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-10-23 15:19:03 +0200

    Typos, rebuild static docs

commit 6f6575701d9b028af4b3b1b4b61c36d4989e2812
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-10-10 14:03:20 +0200

    Add ORCID

commit a33f1bbbf6f6121e8ad40284690a463733a00bc2
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-10-09 08:48:39 +0200

    Write Step 2 input files on windows

commit 311c4fbcc51ad727551da41569d64e6bc290c2b2
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-10-06 09:30:21 +0200

    Update docs, small bugfix

commit 72d7358581bca88af8c507b6c80791100aaafafc
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-08-24 10:30:11 +0200

    Build for windows using roxygen from master
    
    Now that roxygen can handle UTF8 characters in function
    arguments thanks to Hadley Wickham and Jim Hester

commit a8a2a9d57f40ec7a4fc70df3dc470d88cd10c525
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-07-24 16:31:07 +0200

    Improve Makefile

commit 89fc0926722fbfd6420297194c8b18f5b8a9447d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-07-24 16:26:51 +0200

    Version bump as I had 0.4.3 in my drat already

commit 762880a78620e50814351248c02d012a7b030fb8
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-07-24 16:23:22 +0200

    Avoid warning about possibly mis-spelled word

commit a2e24495c01f837474b69263a9861a89050cbfd1
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-07-21 11:15:41 +0200

    New Option for Step 1, fix example, update docs
    
    Also add the reference file for testing Step12 input file generation

commit dffa31a5ad5026d4d67327da622f45c00be40584
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-06-22 08:23:13 +0200

    Add scenario, region and season to run name

commit 0607a619d92d582ba40f9c0c3b32a1d0a8791655
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-06-20 16:40:21 +0200

    Possibility to turn off formation in water
    
    This makes it possible to compare the Step 1 output with earlier
    versions of the Steps 12 tool.

commit 0d60c88ba7e0693a832056ea3db5cc0eaf3b0819
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-06-20 14:16:14 +0200

    Fix line endings and allow all interception classes

commit dc1e49c8bb27cac81268719055bc4336843c0506
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-06-20 06:16:19 +0200

    Keep dos format for pesticide.txt test data

commit fd40f74907e89077bd81af5d779ae93e1434d8c6
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-06-20 06:11:12 +0200

    Now the errors in PELMO output are gone - not reproducible

commit 88044fd98c5b95d3f3f9bbef7416af66552189c1
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-06-20 06:04:14 +0200

    Tests for Step 1 and 2 (input file only) pass, PELMO fails
    
    There are spurious errors in the output PELMO generates. Two examples
    are in the test.log

commit 34d4915297faf6236479f0e6474f8aa6b8d4b416
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-06-20 04:30:52 +0200

    Fix generation of input files
    
    - Write header only if not appending
    - Write max_soil and max_ws for metabolites
    - Formatting

commit 7233eed00b799e08c31ae971f997b4b3c14eaea2
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-06-19 20:10:21 +0200

    Single line of generated Step12  input file partially validated

commit c9bcd8e68db61515080ff377c6a04fa807337258
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-06-17 16:36:13 +0200

    Start with the generation of an input file

commit e6f968cf97ed6ca9268e6098d86ba63ff2c6d2b0
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-24 16:07:35 +0200

    Fix for the sawtooth function for repeated applications
    
    For n > 2, the second application was made at 2 * i instead of i.

commit 4835e20d1d08203657ab616600286ad9dfd71344
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-24 15:46:44 +0200

    Re-enable PELMO examples and tests
    
    - Add .gitattributes to make sure CRLF line endings are kept for PELMO
    .psm files
    - Update static docs

commit 539ea37b45ddc41b36dd199f06ffe5936ab13f21
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-17 12:23:38 +0200

    Documentation fix

commit 62bffd4873bc53fa9cd81336efa716b220c83e0a
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-17 09:36:22 +0200

    Simplify tests where possible

commit d60bb9c0b52c8e0452bfbe507e60d5f651589cc8
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-16 18:57:16 +0200

    Update static documentation

commit 14fa47b1ea1651fc2cb7bbf0086741a8004d35ee
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-16 18:54:34 +0200

    Remove external data also from git as their licence is unclear

commit 608c4f89a2656f67ba915aab17633d41acc789a7
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-16 18:44:22 +0200

    Add build and test logs to the git repo

commit 3e26a8ab76a434c3465ea1db1b4a2a2ff3ea8ec8
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-16 18:40:25 +0200

    Add TWA concentrations for days > 1, fix link
    
    Now we have seven test calculations for the Step 1 calculator, all
    perfectly passing. This provides confidence that this is a
    correct reimplementation of the Step 1 part of the Step 1/2 calculator.

commit 36036b5901223591e7e21e8b73d8cd1fb034f4cb
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-16 15:43:50 +0200

    Finish the Step 1 calculator including tests
    
    Some cleaning up. PELMO facilities do not currently work at my end,
    as I have no working wine installation on this computer

commit d042f8f06b313e8595087587455daac73d84f17b
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-05-15 20:01:28 +0200

    Start of an Steps 1/2 calculator in R

commit b052bf8d1e090e07bf0853f0aa8b895db8f41a2a
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-03-29 19:24:37 +0200

    Make it possible to use expressions in axis labels

commit d69fda8d8f854b735394ecdaec9d59fb18c42b00
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-03-28 10:09:45 +0200

    Update Changelog

commit 90e5ff0a9fdadd65e179c04c7d43b4db6e301984
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-03-06 17:59:16 +0100

    Move static docs to pkdown.jrwb.de, update them

commit 68e36eb0a5f1b611588d47f77e0ef7c3d9ba0beb
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-03-01 11:37:31 +0100

    The package is not in subdir `pkg` any more

commit f67ea0c4aeb68631e9f93c95e86c14364718477a
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-31 07:33:21 +0100

    Small documentation fix

commit 4e696997516543e29119e94d67283f513be4484d
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-30 18:08:50 +0100

    Regenerate static documentation

commit 03bda75d343402dad99df2aad55611e11279b833
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-30 18:04:53 +0100

    Correct psm file in the example with metabolites

commit 39d202b0a0f833c756bc98fb4961483de1b15353
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-30 16:14:15 +0100

    Ignore windows binary builds in git and in R package

commit e6bb9654679f43af6958d6e28cb5206abb91d574
Author: Johannes Ranke <jranke@uni-bremen.de>
Date:   2017-01-30 16:10:30 +0100

    Test reproducing the FOCUS Summary information
    
    generated from the FOCUS PELMO GUI, as copied into the text files
    in the testdata directory.

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