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2023-04-02Deal with covariates in summary for saem.mmkin objectsJohannes Ranke1-1/+16
2023-03-23Support covariates in endpoints()Johannes Ranke6-15/+43
2023-03-22Fix typo in mkinerrminJohannes Ranke2-4/+4
Thanks to Sebastian Meyer for spotting it.
2023-02-26Improve documentation of the formatJohannes Ranke1-1/+19
2023-02-17Finish adapting to upcoming deSolveJohannes Ranke2-11/+8
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke11-37/+164
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke4-23/+29
2022-12-19Rename template folder, create formatJohannes Ranke1-0/+29
Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of.
2022-12-15List random effects correlations in output if anyJohannes Ranke1-1/+12
Update docs
2022-12-07Check slopes in saemix covariate modelsJohannes Ranke1-1/+12
2022-12-06Some parplot improvementsJohannes Ranke1-1/+6
llquant argument, improved legend text, tests
2022-12-01Possibility to manually specify no_random_effects in mhmkinJohannes Ranke1-6/+44
2022-11-25mhmkin: Easy specification of ill-defined parmsJohannes Ranke1-9/+7
The argument 'no_random_effect' now accepts an illparms.mhmkin object
2022-11-18Make mixed model test data permanent to ensure reproducibilityJohannes Ranke1-0/+24
To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package.
2022-11-18Pass error.init to saemix_model, show in parplotJohannes Ranke2-1/+6
Due to an oversight, error.init was not really passed to saemix_model in saem.mmkin. The new initial values were reverted to c(1, 1), in order to avoid changing the test results. Initial values for error model parameters are now shown in parplot.multistart.
2022-11-16Update docsJohannes Ranke1-1/+1
2022-11-16We get about 25% performance gainJohannes Ranke3-16/+19
with the custom lsoda call, avoiding repeated getNativeSymbolInfo calls. It's just that we should not be calling foreign functions from different packages, because the may change without notice. Using getNativeSymbolInfo for "call_lsoda" avoids the CRAN note, and a similar call could probably be used for "unlock_solver", avoiding the NOTE in checks for cran, but we should not do this in a CRAN package.
2022-11-14Automatic starting parameters for saem.mmkinJohannes Ranke1-1/+15
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions
2022-11-08Show DFOP g equivalent of SFORB in summary, testJohannes Ranke1-2/+3
2022-11-08Simplify SFORB also in the endpoint functionJohannes Ranke1-9/+8
2022-11-08Simplify SFORB analytical solution, whitespaceJohannes Ranke2-4/+4
I do not know why the formulae for b1 and b2 on page 64 of FOCUS kinetics (2014) were not simplified. Clearly, the term k12 * k21 - (k12 + k1output) * k21) can be simplified to - k1output * k21 The test for equivalence of DFOP and SFORB fits verifies that the change is OK. I also removed trailing whitespaces, substituted tab characters by two whitespaces and removed indenting of text in paragraphs describing parameters in roxygen comments to unify formatting.
2022-11-04Attempt at automatic setting of random effectsJohannes Ranke1-3/+15
Based on parameters in the separate fits that fail the t-test.
2022-11-04Make it easy to override maxsteps for lsodaJohannes Ranke1-15/+18
The hope was to be more successful in saemix fits, but I did not notice an improvement (e.g. for a failing likelihood calculation with importance sampling, where the error message suggested to increase maxsteps).
2022-11-04Never fail with errors in saem.mmkinJohannes Ranke1-4/+0
I think it is always preferable to be able to investigate the saemix object returned.
2022-11-03Update docsJohannes Ranke1-1/+2
2022-11-01Add tex_listing()Johannes Ranke1-0/+20
2022-11-01Add read_spreadsheetJohannes Ranke1-0/+55
2022-11-01Fix plotting saem fits with covariatesJohannes Ranke2-0/+11
2022-11-01Fix illparms testsJohannes Ranke1-1/+1
2022-11-01Improved printing for illparms()Johannes Ranke1-2/+5
For the case of single fits and no ill-defined parameters found
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

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