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2023-04-15Increase test coverageJohannes Ranke1-2/+14
Also, using mkin analytical solutions for more than one observed variable is not supported (but could be if out_values would be reordered).
2023-04-15Make predefined symbols saferJohannes Ranke1-4/+20
We still need to create a parallel processing cluster _after_ creating a compiled model that is moved to a user defined location, at least I did not find another way to make it work. This is not a problem with parallel processing without a cluster, which is not available on Windows.
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke1-0/+0
2023-01-03Neutral names for code chunks in the templateJohannes Ranke1-5/+4
2023-01-03Improve template text, use neutral name for dll_dirJohannes Ranke1-6/+6
2023-01-03Improved skeleton for hierarchical fitsJohannes Ranke1-15/+166
Now with working pathway fits using SFORB-SFO2 (only two parallel metabolites instead of three) as the data for compound Ia was not sufficient for a reliable fit.
2022-12-22Improve code formatting in template skeletonJohannes Ranke1-1/+3
2022-12-19Rename template folder, create formatJohannes Ranke3-34/+11
Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of.
2022-12-19Template and spreadsheet for hierarchical kineticsJohannes Ranke3-0/+189
The template only shows parent data evaluation without covariate models for now. The spreadsheet will also be useful for unit testing of the read_spreadsheet function.
2022-11-18Make mixed model test data permanent to ensure reproducibilityJohannes Ranke1-0/+105
To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package.
2021-09-15Correction of the dimethenamid datasetJohannes Ranke1-16/+8
The data given in previous mkin versions for "Borstel 2" (Staudenmaier 2013) are in fact a subset of the "Borstel 1" data, with the "Borstel 2" data simply being further analysed for isomer composition by Staudenmaier (2013). While correcting this, the URL of the RAR published by EFSA was updated, as the EFSA Register of Questions was replaced by the Open EFSA portal. This also affects the recent publication in "Environments" [1], where these two datasets were pooled. However, the influence on the final results can be expected to be minimal. Out of the 16 observations for the Borstel soil, five were erroneously duplicated which just changes the weight of the different sampling points and modifies the variance. The conclusions of the publication are qualitative and are not considered to be affected. [1] https://doi.org/10.3390/environments8080071
2020-12-19Dimethenamid data, normalisation optionsJohannes Ranke2-1/+156
2020-11-13Fixes for f_time_norm_focus, still very fragile...Johannes Ranke1-6/+8
2020-11-12Use preprocessed data for 2,4-D, update docsJohannes Ranke1-27/+27
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke2-0/+82
- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU assessment as mkindsg object with metadata - f_time_norm_focus() to do time-step normalisation using the FOCUS method - focus_soil_moisture data with default moisture contents at pF1, pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance - Dataset generation scripts in inst/dataset_generation - Depend on R >= 2.15.1 in order to facilitate the use of utils::globalVariables()
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-0/+219
2019-07-08Support summarizing older fitsJohannes Ranke1-0/+0
generated with mkin < 0.9.49.5
2019-05-02Prepare for CRAN releaseJohannes Ranke1-0/+0
- Skip long running tests on CRAN as well to avoid timeout on winbuilder - Don't install benchmark results in the package, they are only needed in the git repository - Don't run example in man/add_err.Rd as it takes > 10 s on winbuilder - Rebuild docs
2019-05-02Better initials for error model parametersJohannes Ranke1-0/+0
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-0/+0
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-01-31Restore NAMESPACEJohannes Ranke1-1/+0
which was accidentally overwritten by pkgdown -> roxygen
2016-11-17Satisfy CRAN checks, also on R-develJohannes Ranke1-63/+0
- Use https for canonical R URLs - Update CAKE URL to one giving a valid SSL certificate
2016-10-06Remove staticdocs from old locationJohannes Ranke70-17199/+0
2016-09-10Static documentation rebuilt with current staticdocsJohannes Ranke10-66/+66
Using hadley/staticdocs commit #8c1069d from 8 days ago
2016-09-10Static documentation rebuilt by staticdocs::build_site()Johannes Ranke43-189/+206
2016-06-28Bump version for new release, rebuild static docsJohannes Ranke42-159/+159
The test test_FOMC_ill-defined leads to errors on several architectures/distributions, as apparent from CRAN checks, so we need a new release. Static documentation rebuilt by staticdocs::build_site()
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke43-169/+169
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke10-66/+66
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke10-68/+68
2016-06-28Avoid multicore fits in vignettes for passing CRAN checksJohannes Ranke50-551/+1331
Also a small fix to the FOCUS Z vignette, and an update of the static documentation generated by staticdocs.
2016-03-24Static documentation rebuilt by staticdocs::build_site()v0.9.42Johannes Ranke42-223/+230
2016-03-24Address feedback from CRAN submissionJohannes Ranke36-104/+104
- Put the CRAN URL that the badge points to into canonical form. I had missed the requirement to use the canonical form before, as the R CMD check message complained about a (possibily) invalid URL, so I overlooked the explanation later in the check log. Thanks to Uwe for his patience. Fix checked with winbuilder. - Slightly reduced the build time for the compiled_models vignette by skipping the warm-up. 3 repetitions are necessary for the autoplot method to work
2016-03-23Static documentation rebuilt by staticdocs::build_site()Johannes Ranke10-45/+45
2016-03-23Added 'from_max_mean' to 'mkinfit'.Johannes Ranke42-162/+170
- Now it is easier to do decline kinetics from the maximum occurrence - Static documentation rebuilt by staticdocs::build_site() - Fixed an URL in the README, thanks to the win-builder check with R-devel
2015-12-09Static documentation rebuilt by staticdocs::build_site()Johannes Ranke12-72/+56
2015-11-13Add plots to compiled_models vignette, rebuild staticdocsJohannes Ranke42-147/+158
2015-11-09Update staticdocsv0.9-41Johannes Ranke10-89/+62
2015-11-09Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke11-28/+191
r-forge
2015-11-09Rebuild vignettes and static documentationJohannes Ranke61-0/+16319
2015-10-19Add the R6 class mkindsJohannes Ranke1-0/+1
2015-06-24Staticdocs site_path argument in build_site() now worksJohannes Ranke1-2/+0
This long-standing issue finally got fixed in 2f56137fc9ba60bfea54e575d233f4e696bb8a5a
2015-05-19Typo in dummy fileJohannes Ranke1-1/+1
2015-05-14Start of migration from RUnit to testthatJohannes Ranke4-390/+0
2014-08-25Bug fix and unit tests for mkinerrminJohannes Ranke2-37/+63
See NEWS.md for details
2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke1-47/+16
2014-06-26Calculate additional DT50 values for non-SFO modelsJohannes Ranke1-12/+12
2014-05-08Support building static documentation, build itJohannes Ranke1-0/+2
2014-05-07Fork the GUI into package gmkin. See ChangeLog for detailsJohannes Ranke3-930/+0
2014-05-05Update initials selection, separate out handler functionJohannes Ranke1-4/+10
- Write a separate handler function for the Configure button for easier debugging - Update the selection combobox for initial values after pressing the Keep fit button
2014-05-02More polishing, update plot options in fit selectorJohannes Ranke1-14/+28

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