mkin/tests/testthat/FOCUS_2006_D.csf, branch v0.9.49.6Fitting kinetic models to chemical degradation data (also on github)https://erac.jrwb.de/mkin/atom?h=v0.9.49.62019-10-31T00:59:05ZAdd likelihood ratio test and other methods, fixes2019-10-31T00:59:05ZJohannes Rankejranke@uni-bremen.de2019-10-31T00:55:01Zurn:sha1:7091d3738e7e55acb20edb88772b228f6f5b6c98
The likelihood ratio test method is lrtest, in addition,
methods for update and residuals were added.
Fix the cutoff for likelihood based intervals2019-10-28T12:23:40ZJohannes Rankejranke@uni-bremen.de2019-10-28T12:23:40Zurn:sha1:bd761d879a95872f82e6d8f893634a61e122a938
The cutoff now matches what is given by Venzon and Moolgavkar (1988).
Also, confidence intervals closely match intervals obtained with
stats4::confint in the test case where an stats4::mle object
is created from the likelihood function in one test case.
Static documentation rebuilt by pkgdown
Fix checks and tests2019-10-26T20:52:53ZJohannes Rankejranke@uni-bremen.de2019-10-26T20:52:53Zurn:sha1:6e5630a0df7e857697ff2ce4730a5f7f45b67377
Static documentation rebuilt by pkgdown
Use roxygen for functions and methods2019-10-25T00:03:54ZJohannes Rankejranke@uni-bremen.de2019-10-24T22:37:42Zurn:sha1:0a3eb0893cb4bd1b12f07a79069d1c7f5e991495Improved visual testing2019-10-22T08:13:16ZJohannes Rankejranke@uni-bremen.de2019-10-22T08:13:16Zurn:sha1:f8d45402477a588f773f6fd300f3d4e914648773Refactor mkinfit, infrastructure work2019-10-21T10:11:34ZJohannes Rankejranke@uni-bremen.de2019-10-21T10:11:34Zurn:sha1:7624a2b8398b4ad665a3b0b622488e1893a5ee7c
mkinfit objects now include an ll() function to calculate the
log-likelihood. Part of the code was refactored, hopefully making it
easier to read and maintain. IRLS is currently the default algorithm for
the error model "obs", for no particular reason. This may be subject
to change when I get around to investigate.
Slow tests are now in a separate subdirectory and will probably
only be run by my own Makefile target.
Formatting of test logs is improved.
Roundtripping error model parameters works with a precision of 10% when
we use lots of replicates in the synthetic data (see slow tests). This
is not new in this commit, but as I think it is reasonable this
closes #7.
Support summarizing older fits2019-07-08T14:30:55ZJohannes Rankejranke@uni-bremen.de2019-07-08T14:30:55Zurn:sha1:67d032fb345f8e0afc7628d7525da5b7f0a98f79
generated with mkin < 0.9.49.5
Static documentation rebuilt by pkgdown2019-07-05T13:57:24ZJohannes Rankejranke@uni-bremen.de2019-07-05T13:57:24Zurn:sha1:4596667b19f032232ceb8f3f762aaad5d69c15beAdd check and test logs2019-07-03T15:04:11ZJohannes Rankejranke@uni-bremen.de2019-07-03T15:04:11Zurn:sha1:2fb8a479b9075681ab69063127f4e58a1f9b2052Adapt tests to new algorithms and output2019-06-05T13:45:31ZJohannes Rankejranke@uni-bremen.de2019-06-05T13:45:31Zurn:sha1:4b323789265213bd65165873e7efe5e45a579275
One of the tests exceeded the number of iterations when using the
d_3 error model algorithm, so only use "direct" in this case.