mkin/vignettes/FOCUS_D.html, branch C_analyticalFitting kinetic models to chemical degradation data (also on github)https://cgit.jrwb.de/mkin/atom?h=C_analytical2020-10-15T08:25:48ZReintroduce saemix helper functions2020-10-15T08:25:48ZJohannes Rankejranke@uni-bremen.de2020-10-15T08:25:48Zurn:sha1:954f7514144a281b73e9b47ac88a6b13e8799f31Fix issues for release2020-10-08T07:31:35ZJohannes Rankejranke@uni-bremen.de2020-10-08T07:31:35Zurn:sha1:bc3825ae2d12c18ea3d3caf17eb23c93fef180b8Use all cores per default, confint tolerance2020-05-26T16:52:01ZJohannes Rankejranke@uni-bremen.de2020-05-26T16:38:51Zurn:sha1:675a733fa2acc08daabb9b8b571c7d658f281f73
Also, use more intelligent starting values for the variance of the
random effects for saemix. While this does not appear to speed up
the convergence, it shows where this variance is greatly reduced
by using mixed-effects models as opposed to the separate independent
fits.
Avoid merge() and data.frame() in cost function2020-05-11T03:18:32ZJohannes Rankejranke@uni-bremen.de2020-05-11T03:15:19Zurn:sha1:234c9059a95e104917e488a6ddd2313234a96cdc
also for deSolve and eigenvalue based solutions. This noticeably increases
performance for these methods, see test.log and benchmark vignette.
Change implementation of analytical solutions2020-05-06T19:33:12ZJohannes Rankejranke@uni-bremen.de2020-05-06T19:33:12Zurn:sha1:1195dfc8bdbf7c131d6c6ec30fedbbe746af1bee
Preparing for symbolic solutions for more than one compound
Remove reference to archived kinfit package2019-05-02T16:54:22ZJohannes Rankejranke@uni-bremen.de2019-05-02T16:54:22Zurn:sha1:6ddb7575f37d9d534f014cbd105b2f07660d59c6
from vignettes/mkin.Rmd
Static documentation rebuilt by pkgdown
Direct error model fitting works2019-04-04T15:21:13ZJohannes Rankejranke@uni-bremen.de2019-04-04T13:42:23Zurn:sha1:7a1d3d031aa23fce723ac4f4c8e4bb5d64959447
- No IRLS required
- Removed optimization algorithms other than Port
- Removed the dependency on FME
- Fitting the error model 'obs' is much faster for the FOCUS_2006_D
dataset and the FOMC_SFO model (1 second versus 3.4 seconds)
- Vignettes build slower. Compiled models needs 3 minutes instead of 1.5
- For other vignettes, the trend is less clear. Some fits are faster,
even for error_model = "const". FOCUS_Z is faster (34.9 s versus
44.1 s)
- Standard errors and confidence intervals are slightly smaller
- Removed code for plotting during the fit, as I hardly ever used it
- Merged the two cost functions (using transformed and untransformed
parameters) into one log-likelihood function
Restore NAMESPACE2019-01-31T15:55:20ZJohannes Rankejranke@uni-bremen.de2019-01-31T15:55:20Zurn:sha1:3eefecf0adfbb30b8fb895c244dea6903bcb3e9c
which was accidentally overwritten by pkgdown -> roxygen
Correct references to the Rocke and Lorenzato model2018-07-18T13:58:46ZJohannes Rankejranke@uni-bremen.de2018-07-18T13:18:30Zurn:sha1:0b98c459c30a0629a728acf6b311de035c55fb64
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y.
Rebuild static documentation.
Load mkin quietly in vignettes2018-01-14T17:37:07ZJohannes Rankejranke@uni-bremen.de2018-01-14T17:37:07Zurn:sha1:373d98038c514c5152478127a8a2b9b390ee1b58
Static documentation articles rebuilt by pkgdown::build_articles()