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2023-11-16Update pkgdown docs to bootstrap 5 with searchJohannes Ranke37-935/+596
2023-11-02Benchmarks on new CPU with current versionsJohannes Ranke2-2/+66
2023-10-30Update static docsRanke Johannes37-110/+285
2023-05-19Prepare release of v1.2.4v1.2.4Johannes Ranke23-180/+242
- Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release
2023-04-20Fix and rebuild documentation, see NEWSJohannes Ranke44-308/+1137
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.
2022-11-17Complete update of online docs for v1.2.0Johannes Ranke26-1036/+1734
2022-10-29Merge branch 'update_online_docs_v1.1.1'Johannes Ranke1-56/+62
2022-10-29Rebuild vignette with rbenchmark installedJohannes Ranke1-56/+62
2022-07-22Update static docsJohannes Ranke1-22/+57
2022-07-12Rerun benchmarks on desktop computerJohannes Ranke1-1/+30
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke2-47/+78
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 Ranke7-144/+189
2022-07-01Update benchmark article in online docsJohannes Ranke1-64/+64
2022-07-01Add R version to data in benchmark vignetteJohannes Ranke1-125/+283
2022-06-30Merge branch 'dmta_vignette'Johannes Ranke1-8/+8
2022-06-30Remove stray sentence from vignette, update docsJohannes Ranke1-7/+7
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke19-216/+256
This also adds the first benchmark results obtained on my laptop system
2022-03-16Use saemix in help page, typo in vignetteJohannes Ranke1-2/+2
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke2-131/+92
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).
2022-03-02Make tests more platform independent, update docsJohannes Ranke48-989/+1581
2021-03-31Bug fix in plot.mkinfitJohannes Ranke33-9/+65
In residual plots, use xlab and xlim if appropriate
2021-02-15Correct grant numbers in README, update docsJohannes Ranke1-11/+11
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke39-144/+246
Also bump version to 1.0.3.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke31-363/+399
- 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
2020-10-15Update online docs for release versionJohannes Ranke31-551/+784
2020-05-27Add docs generated using released version 0.9.52Johannes Ranke10-365/+265
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke4-28/+37
2020-05-13Further formatting improvement of benchmark vignetteJohannes Ranke1-85/+61
Also, use .rmd extension instead of .Rmd for vignettes.
2020-05-12Update pkgdownJohannes Ranke1-30/+165
2020-05-12Update vignettes and docsJohannes Ranke16-495/+432
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-145/+103
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-04-04Static documentation rebuilt by pkgdownJohannes Ranke1-6/+6
2020-04-03Compiled models article, reduce distractionsJohannes Ranke1-108/+63
- Added a section with platform specific notes on getting compiled models to work to the compiled models article - Don't return empty SFORB parameter list from endpoints() if there is no SFORB model - Avoid warnings when using standardized = TRUE in plot.mmkin()
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke14-62/+37
2019-09-19Static documentation rebuilt by pkgdownJohannes Ranke4-20/+20
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Static documentation rebuilt by pkgdownJohannes Ranke2-15/+15
to check if the link to the pfm package is correctly generated by pkgdown after preparing the pfm package docs accordingly
2019-09-18Add url: tag to _pkgdown.ymlJohannes Ranke2-16/+16
Static documentation rebuilt by pkgdown
2019-09-18Further corrections of the twa vignetteJohannes Ranke2-16/+16
Static documentation rebuilt by pkgdown
2019-09-18Correct and rebuild docsJohannes Ranke4-111/+131
- Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown
2019-07-09Adaptations for gmkinJohannes Ranke20-459/+623
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke20-627/+463
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke4-20/+20
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke4-20/+20
Static documentation rebuilt by pkgdown
2019-06-05Add error model algorithm to outputJohannes Ranke4-20/+20
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke31-131/+138
The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets.
2019-05-08Add functionality to plot the error modelJohannes Ranke4-20/+20
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2019-05-07Fix hessian calculationsJohannes Ranke5-509/+435
Static documentation rebuilt by pkgdown
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke5-445/+519
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke12-201/+206
Now we have a three stage fitting process for nonconstant error models: - Unweighted least squares - Only optimize the error model - Optimize both Static documentation rebuilt by pkgdown
2019-05-02Remove reference to archived kinfit packageJohannes Ranke2-16/+16
from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown

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