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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2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke6-4088/+80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
2020-05-26Use all cores per default, confint toleranceJohannes Ranke4-227/+259
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.
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke1-0/+0
2020-05-13Further formatting improvement of benchmark vignetteJohannes Ranke10-581/+564
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

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