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2022-10-29Rebuild vignette with rbenchmark installedJohannes Ranke1-56/+62
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2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke19-216/+256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
2019-05-02Prepare for CRAN releaseJohannes Ranke2-18/+18
- 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 Ranke26-136/+132
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke20-374/+818
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-03-04Make some example output more reproducibleJohannes Ranke2-12/+12
In order to avoid some unnecessary documentation rebuilds
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke3-377/+416
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke3-5/+14
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke18-5/+938
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke2-7/+7

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