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6 daysAxis legend formatting, update vignettesJohannes Ranke1-2/+2
6 daysUpdate docsJohannes Ranke1-5/+1
6 daysMerge branch 'devel'Johannes Ranke2-1/+5
6 daysUpdate wordlist, bump date and simplify DESCRIPTIONJohannes Ranke2-3/+3
Also, the R-Universe URL that the badge points to is updated
2024-12-19Skip small symbols in plot.mixed()Ranke Johannes1-1/+1
2024-12-19Support observed data as tibbleRanke Johannes2-3/+4
Closes #14
2023-11-26Deal with 'saem' fits failing when updating an 'mhmkin' objectJohannes Ranke1-0/+14
2023-11-23Bump version, fix test from last commit, check and testJohannes Ranke1-1/+5
2023-08-08Update docs, check and test on RStudio serverRanke Johannes1-2/+2
2023-05-19Prepare release of v1.2.4v1.2.4Johannes Ranke2-2/+2
- Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release
2023-04-20Merge branch 'v1.2.3_pkgdown'Johannes Ranke1-1/+3
2023-04-20Fix and rebuild documentation, see NEWSJohannes Ranke1-1/+3
I had to fix the two pathway vignettes, as they did not work with the released version any more. So they and the multistart vignette which got some small fixes as well were rebuilt. Complete rebuild of the online docs with the released version. The documentation of the 'hierarchial_kinetics' format had to be fixed as well.
2023-04-17Improve docs of multistart methodJohannes Ranke1-4/+3
2023-04-15Make predefined symbols saferJohannes Ranke1-0/+4
We still need to create a parallel processing cluster _after_ creating a compiled model that is moved to a user defined location, at least I did not find another way to make it work. This is not a problem with parallel processing without a cluster, which is not available on Windows.
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

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