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2022-11-10set_nd_nq is now in mkin, fix Steps12 bugJohannes Ranke1-86/+0
If a scenario with a slash "/" was selected in PEC_sw_focus(), the Step 2 file generated giving an error (path not found) in the Steps12 calculator, because the scenario name is part of the "compound" name in this implementation, in order to show it in the list that the calculator presents.
2020-07-23PEC_sw_drift: Rautmann formula (1 app, Ackerbau)Johannes Ranke1-4/+19
This makes it possible to calculate drift PECsw for other distances than present in the JKI data or the Rautmann paper.
2020-07-07Remove copyright headers, update TOXSWA_cwa testJohannes Ranke5-3/+3
- The window column of the windows component of a TOXSWA_cwa object is not a factor any more, but a character vector. - testthat::expect_equal_to_reference is replaced by testthat::expect_known_output, so we can have git diff show what has changed
2020-04-16Make na.rm = FALSE the default for geomean()Johannes Ranke1-2/+2
This makes more sense and is in line with mean() from base R. Adapt tests and update docs.
2019-10-15Residue processing for depth profiles over timeJohannes Ranke1-11/+53
2019-10-10Fix set_nd for metabolites, handle zero at time zeroJohannes Ranke1-0/+2
2019-10-10Finish documentation of set_nd and test itJohannes Ranke1-0/+42
2019-09-27Fix for UK drainage, some EFSA interception and washoffJohannes Ranke1-2/+5
- 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
2019-02-19Add another test for Exposit drainageJohannes Ranke1-0/+8
to test overriding the mobility group derived from Koc
2019-02-19Add German drainage calculations using Exposit 3.02Johannes Ranke2-19/+75
2019-01-31Separate out PELMO utilities into rPELMOJohannes Ranke1-201/+0
2018-09-22Add test and update docsJohannes Ranke1-0/+20
2018-07-11Improve PELMO testsJohannes Ranke1-19/+15
2018-07-10EFSA PEC soil guidance from 2017Johannes Ranke3-36/+91
- Implement the new guidance as well as possible - Maintenance work addressing CRAN checks
2017-10-27Exposit runoff calculations for surface waterJohannes Ranke1-0/+25
2017-06-22Add scenario, region and season to run nameJohannes Ranke1-19/+23
2017-06-20Tests for Step 1 and 2 (input file only) pass, PELMO failsJohannes Ranke1-28/+88
There are spurious errors in the output PELMO generates. Two examples are in the test.log
2017-06-19Single line of generated Step12 input file partially validatedJohannes Ranke1-68/+104
2017-06-17Start with the generation of an input fileJohannes Ranke1-2/+13
2017-05-24Re-enable PELMO examples and testsJohannes Ranke1-6/+20
- Add .gitattributes to make sure CRLF line endings are kept for PELMO .psm files - Update static docs
2017-05-17Simplify tests where possibleJohannes Ranke1-11/+6
2017-05-16Add TWA concentrations for days > 1, fix linkJohannes Ranke1-14/+14
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.
2017-05-16Finish the Step 1 calculator including testsJohannes Ranke2-16/+88
Some cleaning up. PELMO facilities do not currently work at my end, as I have no working wine installation on this computer
2017-05-15Start of an Steps 1/2 calculator in RJohannes Ranke1-0/+52
2017-01-30Test reproducing the FOCUS Summary informationJohannes Ranke1-1/+35
generated from the FOCUS PELMO GUI, as copied into the text files in the testdata directory.
2017-01-30Use relative tolerance of 1e-6 for flux testJohannes Ranke1-1/+3
to pass test also for more extreme situations as in the current test data.
2017-01-29Setting up PELMO runs, execution and evaluationJohannes Ranke1-18/+56
It all works!
2017-01-27Also test run with metabolitesJohannes Ranke1-30/+33
2017-01-27Set up FOCUS PELMO runs and run them in parallelJohannes Ranke2-0/+101
- 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
2017-01-19Move mkin::twa to pfm::max_twa.mkinfitJohannes Ranke1-0/+11
- 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
2016-09-27Reorganise repository using standard package layoutJohannes Ranke13-0/+266

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