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2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke25-2157/+1952
Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel mailing list and for the suggestion on how to fix it. See the current benchmark vignette for the new data on mkin 1.1.1 with R 4.2.1, with unprecedented performance.
2022-07-01Sensitivity of AIC values in DMTA vignette to BLAS versionJohannes Ranke17-147/+2399
2022-07-01Rerun benchmarks with R 4.2.1 and openblas-serialJohannes Ranke2-11/+11
After confirming that lapack versus atlas versus openblas results are quite similar, and therefore not responsible for the differences between R 4.1.3 and R 4.2.1
2022-07-01Update benchmark article in online docsJohannes Ranke3-65/+65
2022-07-01Add benchmarks on laptop with R 4.1.3 and 4.2.1Johannes Ranke3-46/+75
2022-07-01Add R version to data in benchmark vignetteJohannes Ranke18-279/+2777
2022-06-30Merge branch 'dmta_vignette'Johannes Ranke13-25/+36
2022-06-30Remove stray sentence from vignette, update docsJohannes Ranke20-29/+33
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke143-5054/+1061
This also adds the first benchmark results obtained on my laptop system
2022-04-13More control of y axes in plot.mkinfit, updatesJohannes Ranke9-22/+30
Documentation and test results were updated, the latter with regard to the previous work on plot.mixed.mmkin.
2022-04-12Fix using defaults for log rate constantsJohannes Ranke1-1/+3
2022-04-11Update static docsJohannes Ranke16-12/+34
2022-04-09Improvements to mean_degparms() and plot.mixed.mmkin()Johannes Ranke8-15/+53
- New argument 'default_log_parms' for mean_degparms() - 'plot.mixed.mmkin': Pass the frame argument also to residual plots, take the 'default_log_parms' argument for 'mean_degparms' used for constructing approximate population curves, plot population curve last to avoid that it is covered by data
2022-03-19Test saemix without special analytical solutionsJohannes Ranke4-28/+50
Also increase the performance a bit (from about 210 s to about 140 s in the case of DFOP with four chains and 300, 100 iterations).
2022-03-19Improvements to CAKE_export()Johannes Ranke7-45/+45
2022-03-16Use saemix in help page, typo in vignetteJohannes Ranke18-136/+239
2022-03-14Release date of mkin 1.1.0Johannes Ranke1-1/+1
2022-03-14Reduce check time for CRAN, releasev1.1.0Johannes Ranke19-63/+83
2022-03-09Fix link to saem.mmkin from READMEJohannes Ranke4-4/+8
Thanks to Uwe Ligges for spotting this inmidst of a lot of ambiguous URL check results.
2022-03-08Avoid using multiple processes on CRAN check machinesJohannes Ranke4-10/+10
2022-03-07Update maintainer e-mail addressJohannes Ranke1-1/+1
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke124-4983/+3230
I am postponing my attempts to get the nlmixr interface to CRAN, given some problems with nlmixr using R-devel under Windows, see https://github.com/nlmixrdevelopment/nlmixr/issues/596 and https://github.com/r-hub/rhub/issues/512, which is fixed by the removal of nlmixr from the testsuite. For the tests to be more platform independent, the biphasic mixed effects models test dataset was defined in a way that fitting should be more robust (less ill-defined).
2022-03-03Reintroduce the skipped test, with a workaroundJohannes Ranke1-8/+15
2022-03-03Add R-devel to travis configJohannes Ranke1-0/+1
2022-03-03Skip a test that assigns to the global environmentJohannes Ranke1-0/+1
2022-03-03R-devel with openblasJohannes Ranke2-54/+27
2022-03-03Update link to 2,4-D dataJohannes Ranke5-4/+4
2022-03-03More work to try to pass tests on R-devel winbuilderJohannes Ranke9-91/+107
2022-03-02Skip some tests on CRAN to reduce loadJohannes Ranke1-0/+2
In the hope that winbuilder will cope better then
2022-03-02Make tests more platform independent, update docsJohannes Ranke241-16887/+32692
2022-03-02Fix nlmixr fits with parallel metabolitesJohannes Ranke4-17/+80
2022-03-02Add a test for tffm0()Johannes Ranke4-23/+41
2022-03-01Avoid using cat() for default output, testsJohannes Ranke5-21/+29
2022-03-01Let travis wait for covrJohannes Ranke1-1/+1
as the last build timed out after not receiving output for 10 min in this step.
2022-03-01Use current R in travisJohannes Ranke1-1/+1
2022-03-01Add some more testsJohannes Ranke10-47/+83
2022-03-01Some more tests for nlmixr.mmkinJohannes Ranke4-0/+80
2022-03-01Add a test for the DMTA dataJohannes Ranke1-39/+41
comparing nlme and saemix. This test shows a reasonable evaluation of the DMTA data with nlme and saemix, which was missing, as the data used in the paper are flawed.
2022-03-01Make it possible to fix parameters in saem.mmkinJohannes Ranke1-2/+3
By actually passing dot arguments (that can include fixed.estim) to saemixModel, as advertised in the docs.
2022-03-01Make it possible to specify a vector of fixed effectsJohannes Ranke1-1/+1
as obtained by mean_degparms(..., random = FALSE), instead of the list obtained by mean_degparms(, ... random = TRUE) that is passed by nlme.mmkin to nlme by default.
2022-02-28Add test for summary.nlmixr.mmkinJohannes Ranke3-0/+118
2022-02-28Relax a test for travisJohannes Ranke2-27/+27
2022-02-28Improve tests, skip some on TravisJohannes Ranke7-26/+73
Respect digits argument when printing correlations in summaries
2022-02-28Update travis config and _pkgdown.ymlJohannes Ranke3-7/+5
2022-02-28Update docsJohannes Ranke58-17943/+18865
2022-02-28Add nlmixr tests, reorganize, test intervals()Johannes Ranke6-176/+236
2022-02-28With saemix 3.0 on CRAN there's no need to check for it in testsJohannes Ranke5-126/+79
2022-02-28Improve dimethenamid vignetteJohannes Ranke3-241/+126
2022-02-28Improve algorithm summary for saemix fitsJohannes Ranke1-1/+3
2022-02-10GNUMakefile: Convince testthat to give dynamic outputJohannes Ranke2-161/+11
This means that we still get the \r in the test logs so so the postprocessing with sed works unmodified

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