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2017-07-21New Option for Step 1, fix example, update docsJohannes Ranke1-1/+2
Also add the reference file for testing Step12 input file generation
2017-06-22Merge branch 'master' of kolab:pfmJohannes Ranke1-2/+11
2017-06-22Add scenario, region and season to run nameJohannes Ranke1-4/+11
2017-06-20Possibility to turn off formation in waterJohannes Ranke1-2/+11
This makes it possible to compare the Step 1 output with earlier versions of the Steps 12 tool.
2017-06-20Fix line endings and allow all interception classesJohannes Ranke1-2/+4
2017-06-20Fix generation of input filesJohannes Ranke1-18/+21
- Write header only if not appending - Write max_soil and max_ws for metabolites - Formatting
2017-06-19Single line of generated Step12 input file partially validatedJohannes Ranke1-39/+122
2017-06-17Start with the generation of an input fileJohannes Ranke1-3/+56
2017-05-24Fix for the sawtooth function for repeated applicationsJohannes Ranke1-1/+1
For n > 2, the second application was made at 2 * i instead of i.
2017-05-24Re-enable PELMO examples and testsJohannes Ranke1-3/+0
- Add .gitattributes to make sure CRLF line endings are kept for PELMO .psm files - Update static docs
2017-05-17Documentation fixJohannes Ranke1-2/+2
2017-05-16Add TWA concentrations for days > 1, fix linkJohannes Ranke2-8/+25
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 Ranke4-27/+113
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 Ranke2-0/+146
2017-03-29Make it possible to use expressions in axis labelsJohannes Ranke1-2/+2
2017-01-31Small documentation fixJohannes Ranke1-1/+1
2017-01-30Correct psm file in the example with metabolitesJohannes Ranke1-4/+26
2017-01-30Test reproducing the FOCUS Summary informationJohannes Ranke1-26/+56
generated from the FOCUS PELMO GUI, as copied into the text files in the testdata directory.
2017-01-30Better documentation of PELMO_runs().Johannes Ranke1-4/+6
2017-01-29Setting up PELMO runs, execution and evaluationJohannes Ranke2-29/+148
It all works!
2017-01-27Also test run with metabolitesJohannes Ranke1-2/+3
2017-01-27Set up FOCUS PELMO runs and run them in parallelJohannes Ranke3-2/+446
- 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
2017-01-19Another correction of the docsJohannes Ranke1-5/+5
2017-01-19Corrections in the documentationJohannes Ranke1-10/+16
2017-01-19Correct default y axis label for plot.one_boxJohannes Ranke1-1/+1
2017-01-19Fix one_box for ini = 1, use in sawtooth examplesJohannes Ranke1-6/+5
2017-01-19Move mkin::twa to pfm::max_twa.mkinfitJohannes Ranke1-7/+81
- 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
2017-01-19Make max_twa() a bit saferJohannes Ranke1-3/+13
2017-01-19Documentation updatesJohannes Ranke1-4/+3
2017-01-19Fix order of arguments to one_box, correct docsJohannes Ranke1-7/+8
2017-01-19Predict parent decline without fitting for non-SFO modelsJohannes Ranke1-3/+37
2017-01-19Switch sawtooth plotting example to FOMCJohannes Ranke1-8/+11
as this it is claimed in the README that an mkinfit prediction is used. - Add another seealso link - Delete trailing whitespace
2017-01-18Update static docs using pkgdownJohannes Ranke1-5/+5
- 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
2017-01-18One box time series and twa valuesJohannes Ranke1-0/+220
- 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
2016-12-22Fix reading in times from .out filesJohannes Ranke1-7/+10
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.
2016-12-14Set time correctly for 00:00 hours in .out fileJohannes Ranke1-5/+10
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.
2016-12-12Fix reading .out for acronyms containing numbersJohannes Ranke1-1/+1
2016-09-27Reorganise repository using standard package layoutJohannes Ranke14-0/+1242

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