mkin/R, branch v1.2.0Fitting kinetic models to chemical degradation data (also on github)https://erac.jrwb.de/mkin/atom?h=v1.2.02022-11-16T13:50:12ZRead in all data per default2022-11-16T13:50:12ZJohannes Rankejranke@uni-bremen.de2022-11-16T13:50:12Zurn:sha1:80ae27dcc4186f03e17164be74158454651474e7Import saemix for easier profiling, update online docs2022-11-15T07:01:52ZJohannes Rankejranke@uni-bremen.de2022-11-15T07:01:52Zurn:sha1:679cf716192cdfd91dfd232578cbd4e30d7eac12Automatic starting parameters for saem.mmkin2022-11-14T19:03:42ZJohannes Rankejranke@uni-bremen.de2022-11-14T19:03:42Zurn: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 fits2022-11-08T14:44:39ZJohannes Rankejranke@uni-bremen.de2022-11-08T14:44:39Zurn:sha1:c3c0007bd76292d976bd7624bf72aa75e168128cShow DFOP g equivalent of SFORB in summary, test2022-11-08T07:46:57ZJohannes Rankejranke@uni-bremen.de2022-11-08T07:46:57Zurn:sha1:56415f3c0638725aaa77db2c02eeaf9d4983452bSimplify SFORB also in the endpoint function2022-11-08T06:56:50ZJohannes Rankejranke@uni-bremen.de2022-11-08T06:56:50Zurn:sha1:7186006740aca909660e42dce8d92eb4735af533Simplify SFORB analytical solution, whitespace2022-11-08T06:33:39ZJohannes Rankejranke@uni-bremen.de2022-11-08T06:26:57Zurn: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.
Make print and summary for saem.mmkin more robust2022-11-07T04:58:50ZJohannes Rankejranke@uni-bremen.de2022-11-07T04:58:50Zurn:sha1:b9b3c72cf076ce0393aa53a4d723a195b856c99c
If the likelihood computed by importance sampling, these methods failed.
Now they report "Not available" or NA, respectively.
Further improvement of robustness of anova method2022-11-04T19:45:52ZJohannes Rankejranke@uni-bremen.de2022-11-04T19:45:52Zurn:sha1:7ec1454c0a0c89987644bbe1981716595d4f1f4bFix anova.saem.mmkin for unavailable likelihoods2022-11-04T18:06:27ZJohannes Rankejranke@uni-bremen.de2022-11-04T18:06:27Zurn:sha1:ba737d366f62460b7ff4702cc6702322ef850027