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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
2022-08-10Change 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 Ranke3-11/+152
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke4-276/+41
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 Ranke4-14/+2341
2022-06-30Merge branch 'dmta_vignette'Johannes Ranke1-1/+1
2022-06-30Remove stray sentence from vignette, update docsJohannes Ranke1-1/+1
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke4-4006/+3
This also adds the first benchmark results obtained on my laptop system
2022-03-16Use saemix in help page, typo in vignetteJohannes Ranke1-1/+1
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke2-267/+134
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 Ranke1-0/+0
2022-02-28Improve dimethenamid vignetteJohannes Ranke3-241/+126
2022-01-11Update the dimethenamid vignette with current saemixJohannes Ranke14-162/+153
Convergence is faster with this version (@ecomets mentioned that there was a bugfix lately that could lead to faster convergence). However, if I use too many iterations (i.e. 10 000 as in the last version of this vignette), I get an error in solving omega.teta during later iterations, apparently due to overparameterisation of the DFOP model in this case.
2021-09-27intervals() methods, more DFOP/tc variantsJohannes Ranke15-180/+327
2021-09-17Put the AIC comparison in a subsubsectionJohannes Ranke2-15/+28
2021-09-16Adapt and improve the dimethenamid vignetteJohannes Ranke20-230/+384
Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs
2021-08-04Improve AIC table in vignetteJohannes Ranke1-1/+3
2021-07-27Fix dimethenamid vignette problems and update docsJohannes Ranke2-38/+128
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke1-66/+0
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-07-23Some example evaluations of dimethenamid dataJohannes Ranke20-0/+2304
Evaluations with nlme, saemix and nlmixr are included
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-0/+0
In residual plots, use xlab and xlim if appropriate
2021-02-15Correct grant numbers in README, update docsJohannes Ranke1-0/+0
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke7-205/+359
Also bump version to 1.0.3.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-0/+0
- 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
2020-11-30Complete rebuild of static docs of dev versionJohannes Ranke1-0/+0
2020-11-19Depend on parallel, doc improvementsJohannes Ranke1-0/+0
By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9.
2020-11-06Update benchmarks for dev versionJohannes Ranke1-0/+0
2020-10-15Update online docs for release versionJohannes Ranke1-0/+0
2020-10-08Fix issues for releaseJohannes Ranke3-314/+317
2020-05-27Change dev version label to info colorJohannes Ranke1-0/+0
instead of the orange danger color.
2020-05-27Create up to date pkgdown docs in development modeJohannes Ranke1-0/+0
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke1-0/+0
2020-05-13Further formatting improvement of benchmark vignetteJohannes Ranke6-237/+220
Also, use .rmd extension instead of .Rmd for vignettes.
2020-05-12Update pkgdownJohannes Ranke1-0/+0
2020-05-12Improve formatting of benchmark vignetteJohannes Ranke3-39/+182
2020-05-12Update vignettes and docsJohannes Ranke5-186/+225
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-11/+11
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-10Default to analytical for coupled models if availableJohannes Ranke2-137/+120
This revealed that transforming rates is necessary for fitting the analytical solution of the SFO-SFO model to the FOCUS D dataset. Benchmarks show that fitting coupled models with deSolve got a bit slower through the latest changes
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke2-176/+0
2020-04-03Compiled models article, reduce distractionsJohannes Ranke5-208/+542
- 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()
2019-05-02Prepare for CRAN releaseJohannes Ranke3-29/+35
- 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
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke3-0/+4312
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit

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