mkin/build.log, branch v0.9.49.5Fitting kinetic models to chemical degradation data (also on github)https://erac.jrwb.de/mkin/atom?h=v0.9.49.52019-06-04T13:09:28ZAdditional algorithm "d_c", more tests, docs2019-06-04T13:09:28ZJohannes Rankejranke@uni-bremen.de2019-06-04T13:09:28Zurn:sha1:95178837d3f91e84837628446b5fd468179af2b9
The new algorithm tries direct optimization of the likelihood, as well
as a three step procedure. In this way, we consistently get the
model with the highest likelihood for SFO, DFOP and HS for all 12
new test datasets.
Fix a bug that could lead to wrong chi2 error levels2019-05-23T17:19:27ZJohannes Rankejranke@uni-bremen.de2019-05-23T17:19:27Zurn:sha1:db472848915a8065347b8f81477a86928b89fbcfImprove error model fitting2019-05-03T17:14:15ZJohannes Rankejranke@uni-bremen.de2019-05-03T17:14:15Zurn:sha1:1ef7008be2a72a0847064ad9c2ddcfa16b055482
Now we have a three stage fitting process for
nonconstant error models:
- Unweighted least squares
- Only optimize the error model
- Optimize both
Static documentation rebuilt by pkgdown
Build log2019-05-02T16:56:48ZJohannes Rankejranke@uni-bremen.de2019-05-02T16:56:48Zurn:sha1:de7b6acdd75a0f95f2a9522c22625810f4aa329aPrepare for CRAN release2019-05-02T15:51:07ZJohannes Rankejranke@uni-bremen.de2019-05-02T15:07:55Zurn:sha1:a4ca3451f1b5c37d10c6a41cb18a99b1631e8aa2
- Skip long running tests on CRAN as well to avoid timeout on winbuilder
- Don't install benchmark results in the package, they are only needed
in the git repository
- Don't run example in man/add_err.Rd as it takes > 10 s on winbuilder
- Rebuild docs
Better initials for error model parameters2019-05-02T11:17:05ZJohannes Rankejranke@uni-bremen.de2019-05-02T11:17:05Zurn:sha1:70591022c07f0e8fb4dd67789b7c8d78af8ebc18
- Also make it possible to specify initial values for error model
parameters.
- Run tests
- Rebuild docs
Adapt tests, vignettes and examples2019-04-10T08:17:35ZJohannes Rankejranke@uni-bremen.de2019-04-10T08:17:35Zurn:sha1:194659fcaccdd1ee37851725b8c72e99daa3a8cf
- Write the NEWS
- Static documentation rebuilt by pkgdown
- Adapt mkinerrmin
- Fix (hopefully all) remaining problems in mkinfit
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
NAFTA SOP Attachment vignette2019-02-26T19:33:32ZJohannes Rankejranke@uni-bremen.de2019-02-26T19:28:15Zurn:sha1:396e40d2c45d81a8e74c41a2f632665021e980a1
Also:
- Change rounding in print.nafta
- Add dots argument to nafta()
- Use cores=1 in examples
- Restrict N in IORE model to values > 0
Add another NAFTA dataset + test2019-02-26T08:12:50ZJohannes Rankejranke@uni-bremen.de2019-02-26T08:12:50Zurn:sha1:6693ee373c61d716e877386d6be16e3f9f0f40ab