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2023-04-20Merge branch 'v1.2.3_pkgdown'Johannes Ranke8-41/+87
2023-04-20Fix and rebuild documentation, see NEWSJohannes Ranke7-40/+42
I had to fix the two pathway vignettes, as they did not work with the released version any more. So they and the multistart vignette which got some small fixes as well were rebuilt. Complete rebuild of the online docs with the released version. The documentation of the 'hierarchial_kinetics' format had to be fixed as well.
2023-04-20Small changes to the multistart vignetteJohannes Ranke1-16/+11
- Fix legend positions and y axis scaling - Include two more variants in the model comparison at the end, and fix the logic of the discussion
2023-04-17Post release changes to the docsJohannes Ranke2-14/+49
The cyantraniliprole and dmta pathway vignettes were not working any more with the latest changes in deSolve and mkin. All docs need a rebuild.
2023-04-17Improve docs of multistart methodJohannes Ranke2-47/+36
2023-04-16Complete rebuild of static docsJohannes Ranke2-0/+0
2023-02-17Update online docs, fix bug that surfacedJohannes Ranke2-0/+0
2023-02-17Update benchmark results for 7950XJohannes Ranke10-123/+208
2023-02-17Rethink versioning and remove 7950X benchmarksJohannes Ranke2-0/+0
I will add benchmark data for 1.2.0, 1.2.2 and 1.2.3 for better comparison
2023-02-17Finish adapting to upcoming deSolveJohannes Ranke7-149/+217
2023-02-17Commit prebuilt vignettes from desktopJohannes Ranke3-0/+0
2023-02-17Merge remote-tracking branch 'origin/main' into faster_lsodaJohannes Ranke1-1/+1
2023-02-17Fix path, build target for prebuilt pdf vignettesJohannes Ranke1-1/+1
2023-02-13WIP adapting to new deSolve with faster lsodaJohannes Ranke2-16/+83
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke27-566/+3259
2023-01-28Update saem benchmark with new CPUJohannes Ranke1-0/+0
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke26-499/+3293
2022-12-06Some parplot improvementsJohannes Ranke2-67/+53
llquant argument, improved legend text, tests
2022-11-24Start online docs of the development versionJohannes Ranke2-0/+0
2022-11-17Complete update of online docs for v1.2.0Johannes Ranke2-0/+0
2022-11-16Update online docsJohannes Ranke1-0/+0
2022-11-16We get about 25% performance gainJohannes Ranke5-15/+137
with the custom lsoda call, avoiding repeated getNativeSymbolInfo calls. It's just that we should not be calling foreign functions from different packages, because the may change without notice. Using getNativeSymbolInfo for "call_lsoda" avoids the CRAN note, and a similar call could probably be used for "unlock_solver", avoiding the NOTE in checks for cran, but we should not do this in a CRAN package.
2022-11-15Import saemix for easier profiling, update online docsJohannes Ranke6-134/+13
2022-11-14Update online docsJohannes Ranke2-0/+0
2022-11-14Start benchmark vignette for saem fitsJohannes Ranke4-0/+2281
2022-11-14Comment on an errorJohannes Ranke1-1/+1
I will not correct the error in order to keep the benchmarks consistent
2022-11-01Update online docsJohannes Ranke1-0/+0
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke1-3/+3
That parhist name was not the brightest idea, as it does not show histograms.
2022-10-26Really test anova output, test covariatesJohannes Ranke1-36/+0
2022-10-26Update multistart example code and vignetteJohannes Ranke3-22/+97
2022-09-28Update vignette and static docsJohannes Ranke3-2/+2
2022-09-28Fix handling of multistart fits with failuresJohannes Ranke3-26/+0
2022-09-19Improve parhist and llhistJohannes Ranke3-11/+15
In particular, adapt the display of parameter boxplots for saem fits using mkin transformations to the way used for saem fits using saemix transformations, i.e. always show parameters on the natural scale, and normalised them by dividing by the median from the multiple runs.
2022-09-16Add llhist to the multistart vignetteJohannes Ranke2-0/+14
2022-09-16Improve multistart documentation, bugfixJohannes Ranke3-0/+512
- 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
2022-09-16Improve docs and update pkgdownJohannes Ranke1-0/+0
2022-09-16Diagnostic plots for multistart methodJohannes Ranke1-72/+79
2022-08-10Change dev branch used for docs, update static docsJohannes Ranke1-0/+0
2022-07-22Update static docsJohannes Ranke1-0/+0
2022-07-14Improve readability of benchmark code shown in vignetteJohannes Ranke3-29/+44
2022-07-12Tests before releasev1.1.1Johannes Ranke1-112/+0
2022-07-12Rerun benchmarks on desktop computerJohannes Ranke4-13/+162
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke6-314/+83
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 Ranke9-2/+2209
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 Ranke1-0/+0
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 Ranke5-15/+2342
2022-06-30Merge branch 'dmta_vignette'Johannes Ranke1-1/+1
2022-06-30Remove stray sentence from vignette, update docsJohannes Ranke1-1/+1

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