mkin/inst, branch v1.2.6Fitting kinetic models to chemical degradation data (also on github)https://erac.jrwb.de/mkin/atom?h=v1.2.62023-10-09T19:29:05ZFix an error in the template2023-10-09T19:29:05ZJohannes Rankejranke@uni-bremen.de2023-10-09T19:29:05Zurn:sha1:39dc3545f0ff6f561ba6193a96daa99cf06472a1
Thanks to Janina Wöltjen for pointing it out
Mesotrione data and vignette2023-08-04T11:27:41ZJohannes Rankejranke@uni-bremen.de2023-08-04T11:27:41Zurn:sha1:804a5cb47fcdc823d41c585729ace151b283ca65
The vignette illustrates pH dependent degradation (covariate modelling)
with some detail for the parent compound.
Also, a bug in the saem method of the illparms function was fixed, which
prevented to find ill-defined parameters in cases where e.g. slopes of
covariate models have a negative estimate.
Improve docs of multistart method2023-04-17T17:39:09ZJohannes Rankejranke@uni-bremen.de2023-04-17T17:39:09Zurn:sha1:004fce2520d6889d82226e21bc443426e81d93f2Make the template work on Windows (with RStudio)2023-04-16T11:31:14ZJohannes Rankejranke@uni-bremen.de2023-04-16T11:31:14Zurn: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 coverage2023-04-15T18:00:00ZJohannes Rankejranke@uni-bremen.de2023-04-15T18:00:00Zurn: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 safer2023-04-15T13:35:06ZJohannes Rankejranke@uni-bremen.de2023-04-15T13:35:06Zurn: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.
Prebuilt PDF vignettes, summary_listing2023-01-09T05:22:04ZJohannes Rankejranke@uni-bremen.de2023-01-09T05:22:04Zurn:sha1:24eb77216700cf8b2f2bde3abad84c1f83f9e32aNeutral names for code chunks in the template2023-01-03T16:52:39ZJohannes Rankejranke@uni-bremen.de2023-01-03T16:52:39Zurn:sha1:fc692554ecdaff66548cc3e6d666e44b7aaaa9afImprove template text, use neutral name for dll_dir2023-01-03T16:31:47ZJohannes Rankejranke@uni-bremen.de2023-01-03T16:31:47Zurn:sha1:18a18ef46391c4b9fa3e5e1cb06937d90a83ba05Improved skeleton for hierarchical fits2023-01-03T08:31:48ZJohannes Rankejranke@uni-bremen.de2023-01-03T08:31:48Zurn: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.