mkin/man, branch v1.2.1Fitting kinetic models to chemical degradation data (also on github)https://cgit.jrwb.de/mkin/atom?h=v1.2.12022-11-18T18:14:47ZMake mixed model test data permanent to ensure reproducibility2022-11-18T18:14:47ZJohannes Rankejranke@uni-bremen.de2022-11-18T18:14:47Zurn: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 parplot2022-11-18T07:37:40ZJohannes Rankejranke@uni-bremen.de2022-11-18T07:37:40Zurn: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.
Update docs2022-11-16T14:18:10ZJohannes Rankejranke@uni-bremen.de2022-11-16T14:18:10Zurn:sha1:26a4b9e03fe0f3d8e777ad52f97685a98ff4462eAutomatic 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
Show 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.
Attempt at automatic setting of random effects2022-11-04T17:12:03ZJohannes Rankejranke@uni-bremen.de2022-11-04T17:12:03Zurn:sha1:9d013773edc0dc30a98c6218655726d3ad944e3f
Based on parameters in the separate fits that fail the t-test.
Make it easy to override maxsteps for lsoda2022-11-04T17:09:50ZJohannes Rankejranke@uni-bremen.de2022-11-04T17:09:50Zurn:sha1:85cb80385bb26f40d1c1a40bbda457dd29c4cc23
The hope was to be more successful in saemix fits, but I did not notice
an improvement (e.g. for a failing likelihood calculation with importance
sampling, where the error message suggested to increase maxsteps).
Never fail with errors in saem.mmkin2022-11-04T06:48:04ZJohannes Rankejranke@uni-bremen.de2022-11-04T06:48:04Zurn:sha1:0389d523f049945c85eba42d4a006523595043f0
I think it is always preferable to be able to investigate the
saemix object returned.