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2023-05-19Prepare release of v1.2.4v1.2.4Johannes Ranke114-598/+605
- 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 Ranke161-1139/+3207
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.
2022-11-18Update docsJohannes Ranke7-10/+260
2022-11-17Complete update of online docs for v1.2.0Johannes Ranke121-2781/+5705
2022-08-10Update docsJohannes Ranke2-261/+347
2022-08-10Update static docsJohannes Ranke8-267/+639
2022-07-22Update static docsJohannes Ranke5-20/+568
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke1-1/+1
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.
2022-07-01Add R version to data in benchmark vignetteJohannes Ranke3-21/+33
2022-06-30Merge branch 'dmta_vignette'Johannes Ranke10-15/+26
2022-06-30Remove stray sentence from vignette, update docsJohannes Ranke15-19/+22
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke102-568/+570
This also adds the first benchmark results obtained on my laptop system
2022-04-11Update static docsJohannes Ranke14-10/+28
2022-03-16Use saemix in help page, typo in vignetteJohannes Ranke8-58/+145
2022-03-14Reduce check time for CRAN, releasev1.1.0Johannes Ranke6-16/+20
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke82-670/+692
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).
2022-03-03Update link to 2,4-D dataJohannes Ranke2-1/+1
2022-03-02Make tests more platform independent, update docsJohannes Ranke144-12575/+28110
2021-10-01Update online docs to 1.0.5Johannes Ranke9-35/+32
2021-07-29Add publication to README, update docsJohannes Ranke1-2/+2
2021-07-27Publication date for 1.0.4 in NEWS, update docsJohannes Ranke21-4/+4
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke14-4/+5
2021-03-31Bug fix in plot.mkinfitJohannes Ranke65-53/+53
In residual plots, use xlab and xlim if appropriate
2021-02-24Rebuild docsJohannes Ranke7-3/+3
2021-02-15Correct grant numbers in README, update docsJohannes Ranke2-0/+0
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke111-304/+298
Also bump version to 1.0.3.
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke7-3/+3
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke14-116/+148
The errors in the example code were in the \dontrun sections, so they were not caught by CRAN checks. In addition, the static help files generated with pkgdown were cached, so I noticed the errors only after completely regenerating the documentation for version 1.0.0.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke125-1124/+4265
- 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 Ranke86-1479/+1596
2020-05-27Add docs generated using released version 0.9.52Johannes Ranke39-855/+308
2020-05-26Use all cores per default, confint toleranceJohannes Ranke7-104/+77
Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.
2020-05-25First working version of saemix helper functionsJohannes Ranke11-23/+520
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-15Use markdown links in mkinfit documentationJohannes Ranke1-46/+48
2020-05-14Update version number, better example formattingJohannes Ranke2-16/+8
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-3/+80
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke2-11/+14
2020-05-12Another documentation updateJohannes Ranke1-22/+22
2020-05-12Add a link to the benchmark vignette to the docsJohannes Ranke1-0/+3
2020-05-12Update vignettes and docsJohannes Ranke67-777/+882
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke8-103/+88
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke49-870/+906
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke2-4/+14
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke13-270/+398
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-07Another overhaul of analytical solutionsJohannes Ranke12-118/+347
Still in preparation for analytical solutions of coupled models
2020-05-07Merge parent solutions to one fileJohannes Ranke6-6/+46
- Combine R/*.solution.R into R/parent_solutions.R - Create a roxygen family of related functions - Reduce redundancy by using the inherit tag - Change the parent.0 argument to parent_0 to match the corresponding parameter name used in mkinfit
2020-05-07Static documentation rebuilt by pkgdownJohannes Ranke14-581/+582
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke3-27/+21
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke3-6/+188
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke2-10/+48

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