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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2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke1-1/+1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
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke1-3/+4
Address release critical check and test issues
2020-12-10nlme with varConstProp is releasedJohannes Ranke1-2/+2
Also fix incompatibility with saem fits from earlier mkin versions
2020-12-07Updates after inline 0.3.17 has been releasedJohannes Ranke1-1/+1
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke1-1/+1
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 Ranke1-1/+1
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 Ranke1-3/+3
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.
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke1-1/+2
- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU assessment as mkindsg object with metadata - f_time_norm_focus() to do time-step normalisation using the FOCUS method - focus_soil_moisture data with default moisture contents at pF1, pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance - Dataset generation scripts in inst/dataset_generation - Depend on R >= 2.15.1 in order to facilitate the use of utils::globalVariables()
2020-10-22Improve interface to experimental version of nlmeJohannes Ranke1-1/+1
The experimental nlme version in my drat repository contains the variance function structure varConstProp which makes it possible to use the two-component error model in generalized nonlinear models using nlme::gnls() and in mixed effects models using nlme::nlme().
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-3/+3
2020-10-08Fix another URL, add devcheck targetv0.9.50.3Johannes Ranke1-1/+1
2020-10-08Fix issues for releaseJohannes Ranke1-2/+2
2020-10-08Avoid dep on dev version of saemix for releaseJohannes Ranke1-2/+2
2020-09-10Regenerate docs with current roxygenJohannes Ranke1-1/+1
2020-07-20Require upcoming nlme version, remove anova.nlme.mmkinJohannes Ranke1-1/+1
The method is no longer necessary, now that Bug 17761 is fixed upstream https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
2020-07-15Bump date to trigger Travis build after clearing cacheJohannes Ranke1-1/+1
2020-05-25Tell travis where to find the required saemix versionJohannes Ranke1-2/+2
2020-05-25First working version of saemix helper functionsJohannes Ranke1-1/+1
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-14Update version number, better example formattingJohannes Ranke1-2/+2

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