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2025-09-12Facilitate centering covariatesJohannes Ranke1-3/+11
The motivation for this is to obtain confidence intervals for covariate dependent parameters that are valid for a median/mean value of the covariate. Implementation by adding an argument to the 'saem' function, and adapting the relevant functions working with 'saem' objects. Vignettes, the template and tests were updated to use the new functionality.
2025-03-28Make parent model selection more robustdevJohannes Ranke1-1/+1
In case one of the fits failed, the corresponding entry in `aic_parent` is `NA`, so we need to tell the `min()` function to ignore `NA` values instead of returning and empty result.
2023-10-09Fix an error in the templateJohannes Ranke2-1/+1
Thanks to Janina Wöltjen for pointing it out
2023-04-17Improve docs of multistart methodJohannes Ranke1-0/+0
2023-04-16Make the template work on Windows (with RStudio)Johannes Ranke1-4/+8
It seems that we cannot use stored DLLs (for pathway fits) on clusters when using Windows, where we use PSOCK clusters. Although it works on winbuilder in the tests in tests/testthat/test_compiled.R. Maybe it is something RStudio specific.
2023-04-15Increase test coverageJohannes Ranke1-2/+14
Also, using mkin analytical solutions for more than one observed variable is not supported (but could be if out_values would be reordered).
2023-04-15Make predefined symbols saferJohannes Ranke1-4/+20
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.
2023-01-03Neutral names for code chunks in the templateJohannes Ranke1-5/+4
2023-01-03Improve template text, use neutral name for dll_dirJohannes Ranke1-6/+6
2023-01-03Improved skeleton for hierarchical fitsJohannes Ranke1-15/+166
Now with working pathway fits using SFORB-SFO2 (only two parallel metabolites instead of three) as the data for compound Ia was not sufficient for a reliable fit.
2022-12-22Improve code formatting in template skeletonJohannes Ranke1-1/+3
2022-12-19Rename template folder, create formatJohannes Ranke3-0/+166
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.

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