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2022-10-25Revert accidental changeJohannes Ranke1-21/+27
2022-10-21Explain chisq tests in anovaJohannes Ranke1-1/+2
Now that I understand how anova.lmer from which I ported the code produces mostly meaningful likelihood ratio tests in the table.
2022-10-21Adapt summary.saem.mmkin to covariate modelsJohannes Ranke1-7/+6
Dissipation times are calculated for covariate values of zero currently, which will usually not be very useful.
2022-10-21Add a simple anova method for model comparisonJohannes Ranke7-5/+175
Update docs
2022-10-21Make update.saem.mmkin work with objects from multistartJohannes Ranke1-6/+10
In particular, objects selected using best.multistart can now be updated, as the starting parameters are inserted into the call, without reference to 'start_parms' which will not be available outside the multistart method.
2022-10-20First working version setting up covariate modelsJohannes Ranke1-4/+53
2022-10-18Don't fail if one of the Hessians can't be computedJohannes Ranke1-1/+8
2022-10-17Fix selecting by log likelihood in parhistJohannes Ranke1-8/+21
2022-10-17SFORB in saem, update for mhmkin and multistartJohannes Ranke6-9/+94
2022-10-14update method for mhmkin objects, clarify commentJohannes Ranke2-2/+25
2022-10-14Select best fit from multistart, use in parhistJohannes Ranke6-31/+117
- 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.
2022-10-13Cope with failed FIM inversionsJohannes Ranke3-10/+29
2022-10-05Simplify the removal of random effectsJohannes Ranke5-29/+94
This is achieved by introducing the argument 'no_random_effect' to the saem function.
2022-10-04Add set_nd_nq to pkgdown topicsJohannes Ranke1-0/+1
2022-09-30Test the package with saemix development versionJohannes Ranke1-43/+12
2022-09-30Install development version of saemix on travisJohannes Ranke1-0/+1
I need this version for the parhist.multistart method, otherwise results for the two-component error model parameters can switch between positive and negative values.
2022-09-30r2u is now the default for r-ciJohannes Ranke1-1/+1
2022-09-29Add set_nd_nq previously in pfmJohannes Ranke7-18/+405
pfm depends on mkin anyways, so reexporting set_nd_nq and set_nd_nq_focus in pfm should provide reasonable continuity.
2022-09-29More adaptations to deal with failed saem fitsJohannes Ranke1-2/+8
2022-09-29Adapt to new format of failed saem.mmkin fitsJohannes Ranke2-8/+13
2022-09-28Update vignette and static docsJohannes Ranke8-21/+46
2022-09-28Fix handling of multistart fits with failuresJohannes Ranke13-104/+159
2022-09-26Make BIC.mhmkin work with failed fitsJohannes Ranke1-1/+4
2022-09-19Make the multistart method work on WindowsJohannes Ranke2-17/+43
2022-09-19Improve parhist and llhistJohannes Ranke13-59/+77
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.
2022-09-16Add llhist to the multistart vignetteJohannes Ranke5-1/+23
2022-09-16Improve multistart documentation, bugfixJohannes Ranke26-101/+1319
- 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
2022-09-16Tell travis to wait for coverage reportJohannes Ranke1-1/+1
2022-09-16Rerun test with saemix 3.1 from CRANJohannes Ranke3-14/+14
Apparently, the change I introduced into saemix saemixdevelopment/saemixextension#34 to fix error model parameters to positive values slightly influences the results. So this is now with the CRAN version to keep test results in sync with Travis
2022-09-16Improve docs and update pkgdownJohannes Ranke22-445/+560
2022-09-16Diagnostic plots for multistart methodJohannes Ranke13-111/+223
2022-09-14Remove purrr dependencyJohannes Ranke6-8/+11
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 Ranke5-2/+18
2022-08-31Some more work on multistartJohannes Ranke2-5/+33
2022-08-14Basic multistart method for saem.mmkin objectsJohannes Ranke6-23/+99
2022-08-11Start a multistart methodJohannes Ranke2-0/+26
2022-08-10Update dev docsJohannes Ranke2-2/+2
2022-08-10Merge branch 'v1.1.2'Johannes Ranke75-4158/+5580
2022-08-10Remove codemeta file to avoid the maintenanceJohannes Ranke1-322/+0
2022-08-10Change dev branch used for docs, update static docsJohannes Ranke75-4158/+5580
2022-08-10Update docsJohannes Ranke4-263/+354
2022-08-10Naming of random effects for reduced parameter modelsJohannes Ranke4-6/+81
2022-08-10Increase test coverage, require saemix version 3.1Johannes Ranke7-6/+35
2022-08-10Update static docsJohannes Ranke16-282/+664
2022-08-10Batch processing for hierarchical fitsJohannes Ranke14-24/+460
- '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 Ranke4-13/+26
Also, support FOMC with saemix transformations
2022-08-08Fix fitting HS with saemix transformationsJohannes Ranke4-27/+39
2022-07-26Import parallel instead of depending on itJohannes Ranke3-6/+7
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
2022-07-23r-universe badge, release date of v1.1.1 in NEWSJohannes Ranke4-12/+11
Also skip complete log directory in .Rbuildignore and reorganize that file to improve readability

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