mkin/inst/rmarkdown, branch v1.2.6 Fitting kinetic models to chemical degradation data (also on github) https://cgit.jrwb.de/mkin/atom?h=v1.2.6 2023-10-09T19:29:05Z Fix an error in the template 2023-10-09T19:29:05Z Johannes Ranke jranke@uni-bremen.de 2023-10-09T19:29:05Z urn:sha1:39dc3545f0ff6f561ba6193a96daa99cf06472a1 Thanks to Janina Wöltjen for pointing it out Improve docs of multistart method 2023-04-17T17:39:09Z Johannes Ranke jranke@uni-bremen.de 2023-04-17T17:39:09Z urn:sha1:004fce2520d6889d82226e21bc443426e81d93f2 Make the template work on Windows (with RStudio) 2023-04-16T11:31:14Z Johannes Ranke jranke@uni-bremen.de 2023-04-16T11:31:14Z urn:sha1:c99a12f1ccb03b46264c536bc9ded5d5de9f85df 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. Increase test coverage 2023-04-15T18:00:00Z Johannes Ranke jranke@uni-bremen.de 2023-04-15T18:00:00Z urn:sha1:f215080efba4097ccdaa2d1208edd36c26d7978a Also, using mkin analytical solutions for more than one observed variable is not supported (but could be if out_values would be reordered). Make predefined symbols safer 2023-04-15T13:35:06Z Johannes Ranke jranke@uni-bremen.de 2023-04-15T13:35:06Z urn:sha1:b0b710ee9f9bb9bbe9708676d0c5822465e02203 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. Neutral names for code chunks in the template 2023-01-03T16:52:39Z Johannes Ranke jranke@uni-bremen.de 2023-01-03T16:52:39Z urn:sha1:fc692554ecdaff66548cc3e6d666e44b7aaaa9af Improve template text, use neutral name for dll_dir 2023-01-03T16:31:47Z Johannes Ranke jranke@uni-bremen.de 2023-01-03T16:31:47Z urn:sha1:18a18ef46391c4b9fa3e5e1cb06937d90a83ba05 Improved skeleton for hierarchical fits 2023-01-03T08:31:48Z Johannes Ranke jranke@uni-bremen.de 2023-01-03T08:31:48Z urn:sha1:ed2ab7bba07e3cb036782227fe27943f4b5583fa 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. Improve code formatting in template skeleton 2022-12-22T11:59:18Z Johannes Ranke jranke@uni-bremen.de 2022-12-22T11:57:24Z urn:sha1:9a066c13e2f6324920910a238e3b40261854e21a Rename template folder, create format 2022-12-19T11:38:07Z Johannes Ranke jranke@uni-bremen.de 2022-12-19T11:31:56Z urn:sha1:886c9ef013124aa954d960c655b349b5340ff154 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.