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2022-08-10Merge branch 'v1.1.2'Johannes Ranke75-4158/+5580
2022-08-10Remove codemeta file to avoid the maintenanceJohannes Ranke1-322/+0
2022-08-10Change dev branch used for docs, update static docsJohannes Ranke75-4158/+5580
2022-08-10Update docsJohannes Ranke4-263/+354
2022-08-10Naming of random effects for reduced parameter modelsJohannes Ranke4-6/+81
2022-08-10Increase test coverage, require saemix version 3.1Johannes Ranke7-6/+35
2022-08-10Update static docsJohannes Ranke16-282/+664
2022-08-10Batch processing for hierarchical fitsJohannes Ranke14-24/+460
- 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel. - 'R/saem.R': 'logLik' and 'update' methods for 'saem.mmkin' objects. - 'R/illparms.R': Add methods for 'saem.mmkin' and 'mhmkin' objects. tests: Use 2 cores on travis, should work according to docs
2022-08-09Update docs for saemJohannes Ranke1-3/+3
2022-08-08Error on unsupported saemix transformationsJohannes Ranke4-13/+26
Also, support FOMC with saemix transformations
2022-08-08Fix fitting HS with saemix transformationsJohannes Ranke4-27/+39
2022-07-26Import parallel instead of depending on itJohannes Ranke3-6/+7
This cleans up the startup message. Loading parallel is not that important, users wanting to use it will know what to do. Also, add codemeta.json to .Rbuildignore
2022-07-23r-universe badge, release date of v1.1.1 in NEWSJohannes Ranke4-12/+11
Also skip complete log directory in .Rbuildignore and reorganize that file to improve readability
2022-07-22Update MakefileJohannes Ranke1-2/+1
2022-07-22Add codemeta file as created by R package codemetaJohannes Ranke1-0/+322
2022-07-22Remove TODO file as I hardly ever look at itJohannes Ranke1-7/+0
2022-07-22Move logs into own directory to clean rootJohannes Ranke8-15/+10
2022-07-22Update static docsJohannes Ranke15-50/+651
2022-07-21Try to tell covr that Travis is not CRANJohannes Ranke1-1/+1
2022-07-21Try coverage from r-ci, re-add badgesJohannes Ranke2-4/+6
2022-07-21Remove platform sensitive convergence testsJohannes Ranke4-40/+20
2022-07-21Try to explicitly install nlme from CRANJohannes Ranke1-0/+1
to get the current version
2022-07-21Try the r2u variantJohannes Ranke1-5/+4
2022-07-21Don't use BSPM as it fails due to low nlme versionJohannes Ranke1-3/+4
2022-07-21Try Travis with Dirks run.sh from eddelbuettel/r-ciJohannes Ranke3-5/+36
2022-07-21Remove travis config as R seems to be unmaintained thereJohannes Ranke3-29/+7
See https://travis-ci.community/t/please-update-the-r-version-used-for-r-release-to-r-4-1-0/11886 and the Pull request referenced there, and the message by Gabor which I found today: https://travis-ci.community/t/about-the-r-category/748/2
2022-07-21Update Travis configJohannes Ranke1-1/+3
- Use current R release - Add system libraries used by textshaping, pulled in by pkgdown
2022-07-21Summary method for mmkin objectsJohannes Ranke21-5117/+1574
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-07-21Updates to summary.mkinfitJohannes Ranke1-2/+2
2022-07-14Improve readability of benchmark code shown in vignetteJohannes Ranke3-29/+44
2022-07-12Tests before releasev1.1.1Johannes Ranke5-132/+3906
2022-07-12Avoid spawning multiple cores in tests on CRANJohannes Ranke1-2/+2
2022-07-12Rerun benchmarks on desktop computerJohannes Ranke6-15/+193
2022-07-08Use inherits() instead of comparing class to stringJohannes Ranke1-1/+1
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke25-2157/+1952
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 Ranke17-147/+2399
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 Ranke3-65/+65
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 Ranke18-279/+2777
2022-06-30Merge branch 'dmta_vignette'Johannes Ranke13-25/+36
2022-06-30Remove stray sentence from vignette, update docsJohannes Ranke20-29/+33
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke143-5054/+1061
This also adds the first benchmark results obtained on my laptop system
2022-04-13More control of y axes in plot.mkinfit, updatesJohannes Ranke9-22/+30
Documentation and test results were updated, the latter with regard to the previous work on plot.mixed.mmkin.
2022-04-12Fix using defaults for log rate constantsJohannes Ranke1-1/+3
2022-04-11Update static docsJohannes Ranke16-12/+34
2022-04-09Improvements to mean_degparms() and plot.mixed.mmkin()Johannes Ranke8-15/+53
- New argument 'default_log_parms' for mean_degparms() - 'plot.mixed.mmkin': Pass the frame argument also to residual plots, take the 'default_log_parms' argument for 'mean_degparms' used for constructing approximate population curves, plot population curve last to avoid that it is covered by data
2022-03-19Test saemix without special analytical solutionsJohannes Ranke4-28/+50
Also increase the performance a bit (from about 210 s to about 140 s in the case of DFOP with four chains and 300, 100 iterations).
2022-03-19Improvements to CAKE_export()Johannes Ranke7-45/+45
2022-03-16Use saemix in help page, typo in vignetteJohannes Ranke18-136/+239

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