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2023-04-20Fix and rebuild documentation, see NEWSJohannes Ranke1-0/+4
I had to fix the two pathway vignettes, as they did not work with the released version any more. So they and the multistart vignette which got some small fixes as well were rebuilt. Complete rebuild of the online docs with the released version. The documentation of the 'hierarchial_kinetics' format had to be fixed as well.
2023-04-15Update description and newsJohannes Ranke1-2/+6
2023-04-02Deal with covariates in summary for saem.mmkin objectsJohannes Ranke1-2/+2
2023-04-01Update tests on 5950xJohannes Ranke1-1/+1
Update platform dependent test plots
2023-03-23Support covariates in endpoints()Johannes Ranke1-1/+3
2023-03-22Fix typo in mkinerrminJohannes Ranke1-0/+2
Thanks to Sebastian Meyer for spotting it.
2023-02-17Rethink versioning and remove 7950X benchmarksJohannes Ranke1-1/+1
I will add benchmark data for 1.2.0, 1.2.2 and 1.2.3 for better comparison
2023-02-17Mention deSolve development in NEWSJohannes Ranke1-2/+6
2022-12-19Rename template folder, create formatJohannes Ranke1-0/+4
Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of.
2022-12-15List random effects correlations in output if anyJohannes Ranke1-1/+3
Update docs
2022-12-07Fix parplot for the case of failed multistart runsJohannes Ranke1-0/+2
2022-12-07Check slopes in saemix covariate modelsJohannes Ranke1-0/+2
2022-12-06Some parplot improvementsJohannes Ranke1-0/+2
llquant argument, improved legend text, tests
2022-12-02Avoid redundant warnings in summariesJohannes Ranke1-1/+1
2022-12-01Possibility to manually specify no_random_effects in mhmkinJohannes Ranke1-1/+1
2022-11-29Complete starting values in summary for saem.mmkin fitsJohannes Ranke1-1/+3
Also update tests to the changes in mhmkin (see NEWS)
2022-11-25mhmkin: Easy specification of ill-defined parmsJohannes Ranke1-1/+1
The argument 'no_random_effect' now accepts an illparms.mhmkin object
2022-11-22Start new development versionJohannes Ranke1-1/+5
2022-11-18Use cluster with two cores to reduce windows check timeJohannes Ranke1-0/+2
2022-11-18Round parameters with signif() before printingJohannes Ranke1-1/+3
This will hopefully make the test pass on all relevant platforms.
2022-11-18Update NEWSJohannes Ranke1-0/+10
2022-11-17Complete update of online docs for v1.2.0Johannes Ranke1-1/+1
2022-11-16Update DESCRIPTION and NEWS, check and testJohannes Ranke1-6/+6
2022-11-14Automatic starting parameters for saem.mmkinJohannes Ranke1-0/+2
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions
2022-11-01Add tex_listing()Johannes Ranke1-0/+4
2022-10-31Add anova.mhmkin methodJohannes Ranke1-0/+2
2022-10-29Next version will be 1.2.0, complete NEWSJohannes Ranke1-7/+7
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke1-2/+2
That parhist name was not the brightest idea, as it does not show histograms.
2022-09-16Diagnostic plots for multistart methodJohannes Ranke1-1/+1
2022-08-11Start a multistart methodJohannes Ranke1-0/+2
2022-08-10Batch processing for hierarchical fitsJohannes Ranke1-2/+6
- '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
2022-08-08Error on unsupported saemix transformationsJohannes Ranke1-1/+1
Also, support FOMC with saemix transformations
2022-08-08Fix fitting HS with saemix transformationsJohannes Ranke1-0/+2
2022-07-23r-universe badge, release date of v1.1.1 in NEWSJohannes Ranke1-1/+1
Also skip complete log directory in .Rbuildignore and reorganize that file to improve readability
2022-07-21Summary method for mmkin objectsJohannes Ranke1-0/+8
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke1-0/+2
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.
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke1-0/+4
This also adds the first benchmark results obtained on my laptop system
2022-04-13More control of y axes in plot.mkinfit, updatesJohannes Ranke1-0/+2
Documentation and test results were updated, the latter with regard to the previous work on plot.mixed.mmkin.
2022-04-09Improvements to mean_degparms() and plot.mixed.mmkin()Johannes Ranke1-0/+4
- 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 Ranke1-0/+2
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 Ranke1-0/+2
2022-03-16Use saemix in help page, typo in vignetteJohannes Ranke1-1/+5
2022-03-14Release date of mkin 1.1.0Johannes Ranke1-1/+1
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-3/+1
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).
2022-02-28Update docsJohannes Ranke1-1/+1
2021-09-27intervals() methods, more DFOP/tc variantsJohannes Ranke1-0/+2
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke1-1/+5
2021-09-15Fix Open EFSA URL, changelog for 1.0.5v1.0.5Johannes Ranke1-0/+4
The EFSA URL failed on winbuilder because some cookie sets a different domain, so I am now using \href{} with the full link as link text instead of \url{}
2021-07-29Go back to 1.0.x version, update docsJohannes Ranke1-0/+2
2021-07-27Publication date for 1.0.4 in NEWS, update docsJohannes Ranke1-1/+1

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