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2022-09-16Diagnostic plots for multistart methodJohannes Ranke1-72/+79
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 Ranke4-13/+162
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke6-314/+83
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 Ranke5-15/+2342
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2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke6-4088/+80
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 Ranke6-27/+28
2022-02-28Improve dimethenamid vignetteJohannes Ranke3-241/+126
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke4-25/+25
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.
2021-12-08PD in Freiburg statt BremenJohannes Ranke1-1/+1
2021-11-17Update required saemix version, update testsJohannes Ranke2-30/+30
2021-10-06Replace outdated JSS article URL by doiJohannes Ranke1-1/+1
Thanks to the hint of Achim Zeileis from the CRAN team
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 Ranke25-274/+438
Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke3-33/+12
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 Ranke5-151/+95
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-07-23Rerun tests, use current vdiffr on travisJohannes Ranke3-56/+48
2021-07-23Some example evaluations of dimethenamid dataJohannes Ranke21-4/+2323
Evaluations with nlme, saemix and nlmixr are included
2021-04-21Merge branch 'master' into saemixJohannes Ranke3-121/+73
2021-03-31Bug fix in plot.mkinfitJohannes Ranke3-123/+75
In residual plots, use xlab and xlim if appropriate
2021-02-18Merge branch 'master' into saemixJohannes Ranke1-0/+0
2021-02-15Correct grant numbers in README, update docsJohannes Ranke1-0/+0
2021-02-15Fully rebuild docs, rerun tests and checkJohannes Ranke3-18/+18
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke16-485/+619
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
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke1-2/+2
Depends on inline >= 0.16.2 (including the bug fixes from eddelbuettel/inline#18), which provides 'moveDLL' to store the DLL for a compiled function in a safe place in case the argument 'dll_dir' is specified in the call to 'mkinmod'. Huge thanks to Dirk @eddelbuettel for his review and support for the work on the inline package.
2020-11-24Support storing mkinmod compiled code as CFunc objectsJohannes Ranke1-4/+43
With automatic reloading in mkinfit and mkinpredict in case the DLL is not loaded and the original DLL path has been cleaned up. Depends on jranke/inline@974bdea04fcedfafaab231e6f359c88270b56cb9 See inline#13
2020-11-19Depend on parallel, doc improvementsJohannes Ranke3-96/+171
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
2020-10-15Reintroduce saemix helper functionsJohannes Ranke3-42/+69
2020-10-08Fix issues for releaseJohannes Ranke9-410/+420
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

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