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2022-09-29Adapt to new format of failed saem.mmkin fitsJohannes Ranke2-8/+13
2022-09-28Fix handling of multistart fits with failuresJohannes Ranke6-60/+147
2022-09-26Make BIC.mhmkin work with failed fitsJohannes Ranke1-1/+4
2022-09-19Make the multistart method work on WindowsJohannes Ranke1-10/+24
2022-09-19Improve parhist and llhistJohannes Ranke3-23/+46
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 Ranke3-55/+118
- 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 Ranke2-14/+13
2022-09-16Diagnostic plots for multistart methodJohannes Ranke3-13/+90
2022-09-14Remove purrr dependencyJohannes Ranke4-5/+8
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.
2022-09-13More work on multistartJohannes Ranke1-0/+1
2022-08-31Some more work on multistartJohannes Ranke2-5/+33
2022-08-14Basic multistart method for saem.mmkin objectsJohannes Ranke2-14/+42
2022-08-11Start a multistart methodJohannes Ranke1-0/+24
2022-08-10Naming of random effects for reduced parameter modelsJohannes Ranke2-6/+12
2022-08-10Batch processing for hierarchical fitsJohannes Ranke3-3/+285
- '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
2022-08-09Update docs for saemJohannes Ranke1-3/+3
2022-08-08Error on unsupported saemix transformationsJohannes Ranke1-2/+13
Also, support FOMC with saemix transformations
2022-08-08Fix fitting HS with saemix transformationsJohannes Ranke1-8/+19
2022-07-21Summary method for mmkin objectsJohannes Ranke4-41/+199
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-07-21Updates to summary.mkinfitJohannes Ranke1-2/+2
2022-07-08Use inherits() instead of comparing class to stringJohannes Ranke1-1/+1
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke2-3/+4
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.
2022-04-13More control of y axes in plot.mkinfit, updatesJohannes Ranke1-6/+11
Documentation and test results were updated, the latter with regard to the previous work on plot.mixed.mmkin.
2022-04-12Fix using defaults for log rate constantsJohannes Ranke1-1/+3
2022-04-09Improvements to mean_degparms() and plot.mixed.mmkin()Johannes Ranke3-10/+26
- 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
2022-03-19Test saemix without special analytical solutionsJohannes Ranke1-12/+20
Also increase the performance a bit (from about 210 s to about 140 s in the case of DFOP with four chains and 300, 100 iterations).
2022-03-19Improvements to CAKE_export()Johannes Ranke1-3/+8
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 Ranke7-977/+5
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 Ranke1-1/+29
2022-03-02Add a test for tffm0()Johannes Ranke1-8/+11
2022-03-01Avoid using cat() for default output, testsJohannes Ranke2-4/+3
2022-03-01Add some more testsJohannes Ranke1-1/+2
2022-03-01Make it possible to fix parameters in saem.mmkinJohannes Ranke1-2/+3
By actually passing dot arguments (that can include fixed.estim) to saemixModel, as advertised in the docs.
2022-03-01Make it possible to specify a vector of fixed effectsJohannes Ranke1-1/+1
as obtained by mean_degparms(..., random = FALSE), instead of the list obtained by mean_degparms(, ... random = TRUE) that is passed by nlme.mmkin to nlme by default.
2022-02-28Improve tests, skip some on TravisJohannes Ranke3-3/+3
Respect digits argument when printing correlations in summaries
2022-02-28Improve algorithm summary for saemix fitsJohannes Ranke1-1/+3
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke3-3/+13
2021-11-17Update required saemix version, update testsJohannes Ranke1-3/+2
2021-10-08Round initial population values for nlmixrJohannes Ranke1-3/+3
This avoids numerical instabilities that sometimes occur with the FOCEI algorithm in nlmixr when the initial values are very close to the optimum values
2021-10-05Fix nlmixr for logit transformed parametersJohannes Ranke1-4/+11
2021-09-29Reduce noise in nlmixr.mmkin output in examplesJohannes Ranke1-14/+25
2021-09-27intervals() methods, more DFOP/tc variantsJohannes Ranke2-2/+181
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{}
2021-09-15Correction of the dimethenamid datasetJohannes Ranke1-2/+2
The data given in previous mkin versions for "Borstel 2" (Staudenmaier 2013) are in fact a subset of the "Borstel 1" data, with the "Borstel 2" data simply being further analysed for isomer composition by Staudenmaier (2013). While correcting this, the URL of the RAR published by EFSA was updated, as the EFSA Register of Questions was replaced by the Open EFSA portal. This also affects the recent publication in "Environments" [1], where these two datasets were pooled. However, the influence on the final results can be expected to be minimal. Out of the 16 observations for the Borstel soil, five were erroneously duplicated which just changes the weight of the different sampling points and modifies the variance. The conclusions of the publication are qualitative and are not considered to be affected. [1] https://doi.org/10.3390/environments8080071
2021-07-23Some example evaluations of dimethenamid dataJohannes Ranke2-14/+24
Evaluations with nlme, saemix and nlmixr are included

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