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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2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke26-328/+360
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 Ranke7-162/+123
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 Ranke65-1935/+2501
2021-10-01Update online docs to 1.0.5Johannes Ranke1-1/+1
2021-03-31Bug fix in plot.mkinfitJohannes Ranke53-54/+158
In residual plots, use xlab and xlim if appropriate
2021-02-24Rebuild docsJohannes Ranke1-1/+1
2021-02-15Correct grant numbers in README, update docsJohannes Ranke3-30/+30
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke61-250/+469
Also bump version to 1.0.3.
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-1/+1
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-1/+1
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 Ranke46-538/+571
- 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 Ranke48-786/+1070
2020-05-27Add docs generated using released version 0.9.52Johannes Ranke18-462/+347
2020-05-14Update version number, better example formattingJohannes Ranke1-1/+1
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke8-60/+81
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
2020-05-12Add a link to the benchmark vignette to the docsJohannes Ranke1-0/+3
2020-05-12Update vignettes and docsJohannes Ranke22-695/+653
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke2-5/+5
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-1/+1
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 Ranke6-263/+208
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 Ranke1-1/+1
Still in preparation for analytical solutions of coupled models
2020-05-07Static documentation rebuilt by pkgdownJohannes Ranke3-62/+86
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke1-1/+1
2020-04-10Improve nlme function docsJohannes Ranke1-1/+1
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()
2020-01-09Remove unused FME package from DESCRIPTION textJohannes Ranke1-1/+1
2019-11-01Make the 'quadratic' the default for 'confint'Johannes Ranke1-1/+1
Also the documentation was improved here and there
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke39-802/+103
2019-10-25Static documentation rebuilt by pkgdownJohannes Ranke2-1/+2
2019-10-21Static documentation rebuilt by pkgdownJohannes Ranke1-1/+4
2019-09-19Static documentation rebuilt by pkgdownJohannes Ranke8-47/+47
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Static documentation rebuilt by pkgdownJohannes Ranke5-40/+40
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 Ranke4-40/+40
Static documentation rebuilt by pkgdown
2019-09-18Further corrections of the twa vignetteJohannes Ranke5-41/+41
Static documentation rebuilt by pkgdown
2019-09-18Correct and rebuild docsJohannes Ranke9-208/+264
- 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 Ranke27-695/+912
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke28-928/+719
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke8-46/+46
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke8-49/+49
Static documentation rebuilt by pkgdown
2019-06-05Add error model algorithm to outputJohannes Ranke8-63/+71
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke48-176/+183
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 Ranke8-48/+48
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 Ranke8-681/+640
Static documentation rebuilt by pkgdown
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke10-654/+695
- Fix the respective error in the code - Static documentation rebuilt by pkgdown

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