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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
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-2/+3
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke1-0/+1
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-2/+2
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-2/+2
Still in preparation for analytical solutions of coupled models
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-1/+1
Preparing for symbolic solutions for more than one compound
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke1-2/+2
2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke1-2/+2
2020-04-14Keep order of datasets in nlme_data, add a plotJohannes Ranke1-1/+1
2020-04-10Trigger rebuild after deleting caches on travisJohannes Ranke1-1/+1
According to the hint of @jimhester received in the Travis Forum - thanks!
2020-04-07Add some tests for the nlme convenience functionsJohannes Ranke1-2/+2
2020-04-03Merge branch 'master' into mxkinJohannes Ranke1-2/+2
Merge DESCRIPTION manually to combine dependencies and rerun check to update check.log

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