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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2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke1-0/+4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
2021-06-11Finished 'summary.nlmixr.mmkin', checks, docsJohannes Ranke1-1/+1
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke1-10/+4
- All degradation models are specified as ODE models. This appears to be fast enough - Error models are being translated to nlmixr as close to the mkin error model as possible. When using the 'saem' backend, it appears not to be possible to use the same error model for more than one observed variable - No support yet for models with parallel formation of metabolites, where the ilr transformation is used in mkin per default - There is a bug in nlmixr which appears to be triggered if the data are not balanced, see nlmixrdevelopment/nlmixr#530 - There is a print and a plot method, the summary method is not finished
2021-04-21Merge branch 'master' into saemixJohannes Ranke1-3/+5
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-0/+2
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-2/+2
In residual plots, use xlab and xlim if appropriate
2021-03-19test_log_parms for plot.mixed.mmkin, roxygen runJohannes Ranke1-1/+3
2021-03-09Some improvements for borderline casesJohannes Ranke1-0/+2
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-24Clarify version status in NEWSJohannes Ranke1-1/+1
2021-02-24Merge branch 'master' into saemixJohannes Ranke1-1/+7
2021-02-24Rebuild docsJohannes Ranke1-0/+6
2021-02-18Merge branch 'master' into saemixJohannes Ranke1-4/+4
2021-02-15Don't let pkgdown add release datesJohannes Ranke1-4/+4
It didn't pick up the release of 1.0.3, and most of the other release dates were duplicated.
2021-02-15Merge branch 'master' into saemixJohannes Ranke1-1/+5
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-0/+4
Also bump version to 1.0.3.
2021-02-13Structure NEWS entryJohannes Ranke1-0/+4
2021-02-13Merge branch 'master' into saemixJohannes Ranke1-1/+5
Run make testcheck to regenerate logs with merge conflicts
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-0/+4
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Reintroduce interface to saemixJohannes Ranke1-0/+10
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-06Increase test tolerance for parameter comparisonsv1.0.1Johannes Ranke1-0/+2
Platform dependence also revealed after upgrade to bullseye
2021-02-06Address issue revealed by additional tests on CRANJohannes Ranke1-0/+2
Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset, as this is platform dependent. After the upgrade, the fit converges on this system as well, although neither ATLAS is used, nor R was configured disabling long doubles (these were the conditions under which the tests failed on CRAN).
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-0/+8
The errors in the example code were in the \dontrun sections, so they were not caught by CRAN checks. In addition, the static help files generated with pkgdown were cached, so I noticed the errors only after completely regenerating the documentation for version 1.0.0.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-12/+3
- 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
2021-01-25Some more plotting improvementsJohannes Ranke1-2/+2
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke1-0/+5
See NEWS.md. Closes #12

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