mkin/R, branch v1.2.1 Fitting kinetic models to chemical degradation data (also on github) https://cgit.jrwb.de/mkin/atom?h=v1.2.1 2022-11-18T18:14:47Z Make mixed model test data permanent to ensure reproducibility 2022-11-18T18:14:47Z Johannes Ranke jranke@uni-bremen.de 2022-11-18T18:14:47Z urn:sha1:5364f037a72863ef5ba81e14ba4417f68fd389f9 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. Pass error.init to saemix_model, show in parplot 2022-11-18T07:37:40Z Johannes Ranke jranke@uni-bremen.de 2022-11-18T07:37:40Z urn:sha1:df0cff4b829f1abf62f037591a24a8019174dd0a 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. Improve logLik.mkinfit to attach nobs attribute 2022-11-18T04:59:02Z Johannes Ranke jranke@uni-bremen.de 2022-11-18T04:56:25Z urn:sha1:9db8338d3a9240ed4685fcdd7aab9692031d5a04 The lack of that attribute lead to a failure to calculate the BIC in test_AIC.R on R-devel from yesterday. Read in all data per default 2022-11-16T13:50:12Z Johannes Ranke jranke@uni-bremen.de 2022-11-16T13:50:12Z urn:sha1:80ae27dcc4186f03e17164be74158454651474e7 Import saemix for easier profiling, update online docs 2022-11-15T07:01:52Z Johannes Ranke jranke@uni-bremen.de 2022-11-15T07:01:52Z urn:sha1:679cf716192cdfd91dfd232578cbd4e30d7eac12 Automatic starting parameters for saem.mmkin 2022-11-14T19:03:42Z Johannes Ranke jranke@uni-bremen.de 2022-11-14T19:03:42Z urn:sha1:21ad91256dc29423bd905de5c298fd23862b1f3b For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions Same SFORB simplification for saem.mmkin fits 2022-11-08T14:44:39Z Johannes Ranke jranke@uni-bremen.de 2022-11-08T14:44:39Z urn:sha1:c3c0007bd76292d976bd7624bf72aa75e168128c Show DFOP g equivalent of SFORB in summary, test 2022-11-08T07:46:57Z Johannes Ranke jranke@uni-bremen.de 2022-11-08T07:46:57Z urn:sha1:56415f3c0638725aaa77db2c02eeaf9d4983452b Simplify SFORB also in the endpoint function 2022-11-08T06:56:50Z Johannes Ranke jranke@uni-bremen.de 2022-11-08T06:56:50Z urn:sha1:7186006740aca909660e42dce8d92eb4735af533 Simplify SFORB analytical solution, whitespace 2022-11-08T06:33:39Z Johannes Ranke jranke@uni-bremen.de 2022-11-08T06:26:57Z urn:sha1:f9343a9f401dce52188fceec456865ba4f2eb95f 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.