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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
2023-02-17Finish adapting to upcoming deSolveJohannes Ranke1-1/+1
2023-02-13WIP adapting to new deSolve with faster lsodaJohannes Ranke1-1/+1
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke1-9/+9
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke1-1/+1
2023-01-03Improved skeleton for hierarchical fitsJohannes Ranke1-7/+7
Now with working pathway fits using SFORB-SFO2 (only two parallel metabolites instead of three) as the data for compound Ia was not sufficient for a reliable fit.
2022-11-24Start online docs of the development versionJohannes Ranke1-1/+1
2022-11-22Start new development versionJohannes Ranke1-2/+2
2022-11-18Prepare follow-up release to fix CRAN checksJohannes Ranke1-2/+2
2022-11-16Update DESCRIPTION and NEWS, check and testJohannes Ranke1-1/+1
2022-11-16We get about 25% performance gainJohannes Ranke1-4/+4
with the custom lsoda call, avoiding repeated getNativeSymbolInfo calls. It's just that we should not be calling foreign functions from different packages, because the may change without notice. Using getNativeSymbolInfo for "call_lsoda" avoids the CRAN note, and a similar call could probably be used for "unlock_solver", avoiding the NOTE in checks for cran, but we should not do this in a CRAN package.
2022-11-01Add tex_listing()Johannes Ranke1-1/+1
2022-11-01Add read_spreadsheetJohannes Ranke1-1/+1
2022-10-29Next version will be 1.2.0, complete NEWSJohannes Ranke1-1/+1
2022-10-26We don't use KernSmooth any moreJohannes Ranke1-2/+1
2022-09-16Diagnostic plots for multistart methodJohannes Ranke1-2/+3
2022-09-14Remove purrr dependencyJohannes Ranke1-2/+2
We now directly import from rlang and vctrs, which were indirect dependencies anyways. purrr::map_dfr is deprecated in the upcoming purrr 1.0, and depends on dplyr (since when?) which is only suggested by purrr. This would lead new installations of mkin to fail if dplyr is not installed as well.
2022-08-10Increase test coverage, require saemix version 3.1Johannes Ranke1-1/+1
2022-07-26Import parallel instead of depending on itJohannes Ranke1-4/+4
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
2022-07-21Summary method for mmkin objectsJohannes Ranke1-2/+2
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 Ranke1-2/+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 Ranke1-1/+1
This also adds the first benchmark results obtained on my laptop system
2022-04-09Improvements to mean_degparms() and plot.mixed.mmkin()Johannes Ranke1-1/+1
- 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
2022-03-07Update maintainer e-mail addressJohannes Ranke1-1/+1
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-2/+2
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).
2022-03-03More work to try to pass tests on R-devel winbuilderJohannes Ranke1-1/+1
2022-03-02Make tests more platform independent, update docsJohannes Ranke1-1/+1
2022-02-28Update docsJohannes Ranke1-1/+1
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke1-2/+2
2021-10-01Bump date to update online dev docsJohannes Ranke1-1/+1
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke1-3/+3
2021-09-15Update test result to corrected data, version bumpJohannes Ranke1-3/+3
2021-07-29Add citations to the DESCRIPTIONJohannes Ranke1-3/+8
2021-07-29Go back to 1.0.x version, update docsJohannes Ranke1-2/+2
2021-07-23Some example evaluations of dimethenamid dataJohannes Ranke1-2/+2
Evaluations with nlme, saemix and nlmixr are included
2021-06-12Small cosmeticsJohannes Ranke1-1/+1
2021-06-11Finished 'summary.nlmixr.mmkin', checks, docsJohannes Ranke1-1/+1
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke1-5/+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 Ranke1-1/+1
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-1/+1
2021-02-24Merge branch 'master' into saemixJohannes Ranke1-2/+2
2021-02-24Rebuild docsJohannes Ranke1-2/+2
2021-02-15Merge branch 'master' into saemixJohannes Ranke1-2/+2
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-2/+2
Also bump version to 1.0.3.
2021-02-13Merge branch 'master' into saemixJohannes Ranke1-2/+2
Run make testcheck to regenerate logs with merge conflicts
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-2/+2
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Reintroduce interface to saemixJohannes Ranke1-2/+3
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-06Address issue revealed by additional tests on CRANJohannes Ranke1-1/+1
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 Ranke1-2/+2
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 Ranke1-10/+10
- 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

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