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2023-02-17Fix path, build target for prebuilt pdf vignettesJohannes Ranke1-0/+3
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke1-5/+2
2022-12-19Rename template folder, create formatJohannes Ranke1-2/+2
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 Ranke1-1/+3
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.
2022-12-02Avoid error message at testthat terminationJohannes Ranke1-2/+6
https://github.com/r-lib/processx/issues/236
2022-11-14Automatic starting parameters for saem.mmkinJohannes Ranke1-1/+1
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions
2022-09-16Improve multistart documentation, bugfixJohannes Ranke1-1/+1
- Split out llhist and parhist documentation - Add example code for multistart - Create a multistart vignette, because the example code fails when run by pkgdown - Fix multistart for the case of mkin transformations in the saem fit
2022-07-22Update MakefileJohannes Ranke1-2/+1
2022-07-22Move logs into own directory to clean rootJohannes Ranke1-9/+9
2022-07-01Add R version to data in benchmark vignetteJohannes Ranke1-1/+1
2022-03-03More work to try to pass tests on R-devel winbuilderJohannes Ranke1-1/+4
2022-02-28Update travis config and _pkgdown.ymlJohannes Ranke1-1/+1
2022-02-10GNUMakefile: Convince testthat to give dynamic outputJohannes Ranke1-5/+4
This means that we still get the \r in the test logs so so the postprocessing with sed works unmodified
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke1-0/+1
2022-02-08Merge branch 'nlmixr'Johannes Ranke1-1/+1
2021-11-18Updates after changing the default branch to mainJohannes Ranke1-1/+1
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke1-3/+0
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-07-23Rerun tests, use current vdiffr on travisJohannes Ranke1-3/+0
2021-02-15Fully rebuild docs, rerun tests and checkJohannes Ranke1-1/+1
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-1/+1
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
2020-12-08Test plots on R-release and cache packages againJohannes Ranke1-1/+1
2020-11-12Use preprocessed data for 2,4-D, update docsJohannes Ranke1-1/+1
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke1-1/+2
- 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()
2020-10-08Fix another URL, add devcheck targetv0.9.50.3Johannes Ranke1-0/+3
2020-10-08Fix issues for releaseJohannes Ranke1-1/+1
2020-07-15Improve testsJohannes Ranke1-2/+6
- Reduce significant digits for the objective function output in mkinfit(..., quiet = FALSE) as R and R-devel gave different output on my system - Add makefile target 'devtest' for testing with R-devel, in order to fix problems showing up with R-devel on Travis
2020-06-15Test plots on r-devel onlyJohannes Ranke1-1/+2
following the arguments of Xavier Robin https://github.com/r-lib/vdiffr/issues/86#issuecomment-636447231
2020-05-13Further formatting improvement of benchmark vignetteJohannes Ranke1-5/+5
Also, use .rmd extension instead of .Rmd for vignettes.
2020-05-12Update vignettes and docsJohannes Ranke1-0/+4
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-0/+2
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke1-1/+0
2020-02-14Update local r-forge path in MakefileJohannes Ranke1-1/+1
2019-10-28Parallel computation for confidence intervalsJohannes Ranke1-1/+1
Only on Linux at the moment. Some more examples in the help page. Remove the distribution argument for the quadratic method
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-3/+6
2019-10-22Improved visual testingJohannes Ranke1-1/+3
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-0/+4
mkinfit objects now include an ll() function to calculate the log-likelihood. Part of the code was refactored, hopefully making it easier to read and maintain. IRLS is currently the default algorithm for the error model "obs", for no particular reason. This may be subject to change when I get around to investigate. Slow tests are now in a separate subdirectory and will probably only be run by my own Makefile target. Formatting of test logs is improved. Roundtripping error model parameters works with a precision of 10% when we use lots of replicates in the synthetic data (see slow tests). This is not new in this commit, but as I think it is reasonable this closes #7.
2019-10-21Improve test log formattingJohannes Ranke1-0/+1
2019-09-19Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Further corrections of the twa vignetteJohannes Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-05-14Don't use remote CRAN incoming checksJohannes Ranke1-1/+1
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-0/+7
Static documentation rebuilt by pkgdown
2018-09-14Skip some more tests on CRANJohannes Ranke1-2/+2
Static documentation rebuilt by pkgdown
2018-09-14Remove two vignettes from the package but not from docsJohannes Ranke1-1/+7
- Rebuild static documentation - Adapt test to new approach to two component error model where the model is inadequate
2018-09-14Exclude more example code from CRAN checksJohannes Ranke1-1/+1
to avoid NOTES about long execution times. Static documentation rebuilt by pkgdown with run_dont_run = TRUE
2018-09-13Merge branch 'master' of jrwb.de:mkinJohannes Ranke1-1/+0
2018-09-13Add targets for windows binariesJohannes Ranke1-0/+12
2018-09-13Enable new error model in gmkinJohannes Ranke1-1/+0
Also improve the irls fitting of the error model and add a test for FOCUS_2006_C where the second component of the error model is zero
2018-06-06Articles are built as well in pd targetJohannes Ranke1-6/+1
2018-03-11Static docs rebuilt again, with current pkgdownJohannes Ranke1-3/+2
2018-03-03Change location of mkin.tar for syncing with r-forgeJohannes Ranke1-2/+2

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