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2017-01-27Merge branch 'master' of jrwb.de:pfmJohannes Ranke1-0/+0
2017-01-27Include a run with metabolites in PELMO test dataJohannes Ranke1-0/+0
2017-01-27Set up FOCUS PELMO runs and run them in parallelJohannes Ranke17-6/+778
- 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
2017-01-26Improved test data with 'irrigation'Johannes Ranke1-0/+0
2017-01-25More variable selection of test dataJohannes Ranke1-0/+0
2017-01-25Use tar.bz2 to correctly transfer file namesJohannes Ranke2-0/+0
2017-01-25Add FOCUS PELMO 5.5.3 output for dummy pesticide DJohannes Ranke1-0/+0
2017-01-19Another correction of the docsJohannes Ranke3-15/+15
2017-01-19Corrections in the documentationJohannes Ranke4-23/+60
2017-01-19Correct default y axis label for plot.one_boxJohannes Ranke11-3/+3
2017-01-19Fix one_box for ini = 1, use in sawtooth examplesJohannes Ranke10-14/+26
2017-01-19Move mkin::twa to pfm::max_twa.mkinfitJohannes Ranke14-19/+182
- 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 Ranke3-4/+30
2017-01-19Documentation updatesJohannes Ranke6-16/+14
2017-01-19Fix order of arguments to one_box, correct docsJohannes Ranke8-21/+81
2017-01-19Predict parent decline without fitting for non-SFO modelsJohannes Ranke9-10/+63
2017-01-19Switch sawtooth plotting example to FOMCJohannes Ranke6-13/+29
as this it is claimed in the README that an mkinfit prediction is used. - Add another seealso link - Delete trailing whitespace
2017-01-18Point to the github.io documentation siteJohannes Ranke2-4/+4
2017-01-18Make README.md simple, and point to the referenceJohannes Ranke7-175803/+12
2017-01-18Update static docs using pkgdownJohannes Ranke73-10450/+3840
- 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 Ranke9-3/+423
- 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
2016-12-22Merge branch 'master' of ssh://jrwb.de/pfmJohannes Ranke17-26/+12
2016-12-22Fix reading in times from .out filesJohannes Ranke3-8/+28
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.
2016-12-14Changelog update and roxygen runJohannes Ranke18-27/+19
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 Ranke5-5/+17
2016-10-13Add drat target, remove unmaintained usage hintsJohannes Ranke1-10/+3
2016-09-27Reorganise repository using standard package layoutJohannes Ranke121-29/+10927
2016-09-27Make the chents package optionalJohannes Ranke3-8/+7
2016-09-23Keep the graph for the markdown fileJohannes Ranke2-1/+0
The markdown file is not self-contained as the html file...
2016-09-23Slightly update the READMEJohannes Ranke6-29/+175503
2016-07-30Update static documentationJohannes Ranke17-41/+55
2016-07-30Add 'methods' to dependeciesJohannes Ranke1-1/+2
2016-07-30Fix the TOXSWA reading testJohannes Ranke2-8/+13
Since a recent commit we are reading the concentrations at the end of each hour, so the test needed to be updated accordingly
2016-07-30Import 'is' from methodsJohannes Ranke2-0/+2
2016-07-30Read cwas from .out files with metabolitesJohannes Ranke2-7/+29
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.
2016-07-15Fix calculation of t_firstjanJohannes Ranke2-2/+8
There is an inconsistency in (some?) output files, so the first datetime needs to be fixed before reading it into a data frame
2016-06-08Clean up remainders of NL drift calculation functionJohannes Ranke2-38/+0
2016-06-08Merge branch 'master' of https://github.com/jranke/pfmJohannes Ranke0-0/+0
2016-06-08Use the concentration at the end of the hourJohannes Ranke3-6/+10
This is also what TOXSWA presents in the summary files
2016-06-08Use the concentration at the end of the hourJohannes Ranke2-4/+8
This is also what TOXSWA presents in the summary files
2016-03-10Merge the NL drift calculations based on percentages into PEC_sw_driftJohannes Ranke5-54/+56
2016-03-10Add NL specific drift calculationsJohannes Ranke2-2/+51
2016-03-02Fix the name of the Chateadun scenarioJohannes Ranke2-2/+2
2016-02-04Test reading .out files and close connectionsJohannes Ranke5-5/+27
2016-02-04Improve reading spead for new TOXSWA formatJohannes Ranke7-16/+28
2016-02-04Read cwa data from TOXSWA 4.4.2 .out filesJohannes Ranke2-40/+93
2015-12-27Fix rounding of endpoint retrieval functionsJohannes Ranke3-3/+7
2015-12-27Another useless variant to avoid warnings in staticdoc plotsJohannes Ranke1-0/+2
2015-12-22EFSA 2015 tier 1 PEC soil, clean up, add static docsJohannes Ranke75-175780/+11589

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