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2022-08-14Basic multistart method for saem.mmkin objectsJohannes Ranke3-9/+55
2022-08-10Update docsJohannes Ranke1-1/+6
2022-08-10Batch processing for hierarchical fitsJohannes Ranke3-7/+112
- '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
2022-07-26Import parallel instead of depending on itJohannes Ranke1-2/+2
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 Ranke4-1/+122
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke2-12/+12
This also adds the first benchmark results obtained on my laptop system
2022-04-13More control of y axes in plot.mkinfit, updatesJohannes Ranke1-1/+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 Ranke3-4/+22
- 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
2022-03-19Improvements to CAKE_export()Johannes Ranke1-2/+2
2022-03-16Use saemix in help page, typo in vignetteJohannes Ranke1-35/+36
2022-03-14Reduce check time for CRAN, releasev1.1.0Johannes Ranke3-5/+6
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke6-426/+3
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).
2022-03-03Update link to 2,4-D dataJohannes Ranke1-1/+1
2022-03-02Make tests more platform independent, update docsJohannes Ranke1-2/+1
2022-03-02Fix nlmixr fits with parallel metabolitesJohannes Ranke1-0/+24
2022-03-02Add a test for tffm0()Johannes Ranke1-8/+12
2022-03-01Add some more testsJohannes Ranke1-0/+1
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke2-0/+4
2021-10-05Update docsJohannes Ranke1-3/+5
2021-09-29Reduce noise in nlmixr.mmkin output in examplesJohannes Ranke1-14/+25
2021-09-27intervals() methods, more DFOP/tc variantsJohannes Ranke4-4/+54
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke1-5/+2
2021-09-15Fix Open EFSA URL, changelog for 1.0.5v1.0.5Johannes Ranke1-1/+1
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{}
2021-09-15Update test result to corrected data, version bumpJohannes Ranke1-2/+2
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke4-17/+28
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-06-17Let backtransform_odeparms handle nlmixr formation fractionsJohannes Ranke3-4/+89
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
2021-06-11Finished 'summary.nlmixr.mmkin', checks, docsJohannes Ranke6-28/+48
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke7-29/+334
- 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 Ranke1-2/+3
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-2/+3
2021-03-19test_log_parms for plot.mixed.mmkin, roxygen runJohannes Ranke3-3/+19
2021-03-09Some improvements for borderline casesJohannes Ranke2-4/+26
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-15Merge branch 'master' into saemixJohannes Ranke1-0/+4
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-0/+4
Also bump version to 1.0.3.
2021-02-06Reintroduce interface to saemixJohannes Ranke4-5/+269
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke7-50/+44
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 Ranke4-270/+6
- 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
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke2-1/+4
See NEWS.md. Closes #12
2021-01-22We do not need to suppress saemix plots any moreJohannes Ranke1-4/+0
This makes fitting with saem within parallel::mclapply much faster and, surprisingly, much less hungry for RAM.
2021-01-11Rebuild docsJohannes Ranke4-7/+7
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke3-5/+7
Address release critical check and test issues
2020-12-21plot.mixed: Possibility to overlay predictionsJohannes Ranke2-1/+17
2020-12-19Dimethenamid data, normalisation optionsJohannes Ranke2-2/+39
2020-12-16And add the second candidate modelJohannes Ranke1-0/+4
2020-12-16and update docsJohannes Ranke1-1/+1
2020-12-16Add printout of d24 model and update docsJohannes Ranke2-2/+1
2020-12-09Make saem using mkinpredict work againJohannes Ranke1-13/+17
I threw out mclapply as it did not play well with the linear algebra routines used in the saemix code. Most of the change is actually indentation in the code creating the model function. But there is an important fix in mkinpredict which I had broken.
2020-12-08mixed.mmkin and test coverageJohannes Ranke4-7/+94
2020-12-02Possibility to specify random effects structuresJohannes Ranke1-4/+5
The default is pdDiag again, as we often have a small number of datasets in degradation kinetics.
2020-11-30Complete rebuild of static docs of dev versionJohannes Ranke1-2/+4

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