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2022-10-31Fix R CMD checkJohannes Ranke3-3/+14
2022-10-29Update multistart docsJohannes Ranke1-2/+2
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke3-11/+14
That parhist name was not the brightest idea, as it does not show histograms.
2022-10-28Export status method for mhmkin, move to status.RJohannes Ranke1-0/+6
2022-10-28Rename 'convergence' method to 'status'Johannes Ranke3-40/+39
The reason is that it is misleading in the case of saem.mmkin objects, because convergence is not really checked there.
2022-10-26Update multistart example code and vignetteJohannes Ranke1-9/+2
2022-10-26Remove kernel density estimate from llhistJohannes Ranke1-3/+2
2022-10-25Complete documentation and fix a bugJohannes Ranke3-4/+19
The bug was introduced by the changes in summary.saem.mmkin.R and surfaced in the tests when using saemix transformations.
2022-10-21Add a simple anova method for model comparisonJohannes Ranke4-1/+57
Update docs
2022-10-14Select best fit from multistart, use in parhistJohannes Ranke2-4/+32
- Add 'best' and 'which.best' generics with methods for multistart objects - Per default, scale the parameters in parhist plots using the fit with the highest log likelihood.
2022-10-05Simplify the removal of random effectsJohannes Ranke1-0/+12
This is achieved by introducing the argument 'no_random_effect' to the saem function.
2022-09-29Add set_nd_nq previously in pfmJohannes Ranke1-0/+103
pfm depends on mkin anyways, so reexporting set_nd_nq and set_nd_nq_focus in pfm should provide reasonable continuity.
2022-09-28Fix handling of multistart fits with failuresJohannes Ranke2-4/+7
2022-09-19Make the multistart method work on WindowsJohannes Ranke1-7/+19
2022-09-19Improve parhist and llhistJohannes Ranke1-7/+3
In particular, adapt the display of parameter boxplots for saem fits using mkin transformations to the way used for saem fits using saemix transformations, i.e. always show parameters on the natural scale, and normalised them by dividing by the median from the multiple runs.
2022-09-16Improve multistart documentation, bugfixJohannes Ranke3-14/+94
- Split out llhist and parhist documentation - Add example code for multistart - Create a multistart vignette, because the example code fails when run by pkgdown - Fix multistart for the case of mkin transformations in the saem fit
2022-09-16Improve docs and update pkgdownJohannes Ranke2-15/+16
2022-09-16Diagnostic plots for multistart methodJohannes Ranke3-4/+25
2022-09-13More work on multistartJohannes Ranke3-2/+14
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

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