mkin/R, branch nlmixrFitting kinetic models to chemical degradation data (also on github)https://cgit.jrwb.de/mkin/atom?h=nlmixr2021-11-17T11:59:49ZUpdate required saemix version, update tests2021-11-17T11:59:49ZJohannes Rankejranke@uni-bremen.de2021-11-17T11:59:49Zurn:sha1:d75378911cef79b3ed95daef71bf67db413d2ac8Round initial population values for nlmixr2021-10-08T12:48:20ZJohannes Rankejranke@uni-bremen.de2021-10-08T12:38:19Zurn:sha1:648637a60a9991cdc8d8d7cbe481cac7f36c953c
This avoids numerical instabilities that sometimes occur with the FOCEI
algorithm in nlmixr when the initial values are very close to the
optimum values
Fix nlmixr for logit transformed parameters2021-10-05T14:55:41ZJohannes Rankejranke@uni-bremen.de2021-10-05T14:55:41Zurn:sha1:121e38654eea03c91aa117da58fc342feff01756Reduce noise in nlmixr.mmkin output in examples2021-09-29T12:38:38ZJohannes Rankejranke@uni-bremen.de2021-09-29T12:38:38Zurn:sha1:cc50f8cad0f608cd2fb9d385f664fc4f53277b2bintervals() methods, more DFOP/tc variants2021-09-27T18:10:01ZJohannes Rankejranke@uni-bremen.de2021-09-27T18:10:01Zurn:sha1:5c15ef747568b3a9a9c094b6aa546dc80e3aa87aMerge branch 'master' into nlmixr2021-09-16T06:23:57ZJohannes Rankejranke@uni-bremen.de2021-09-16T06:23:57Zurn:sha1:212070667de33e4d4adc7f0ae7baf8e18ad51d3fFix Open EFSA URL, changelog for 1.0.52021-09-15T14:54:49ZJohannes Rankejranke@uni-bremen.de2021-09-15T14:54:49Zurn:sha1:2e77bf144a81852302571009b1fcd41f021eca4c
The EFSA URL failed on winbuilder because some cookie sets a different
domain, so I am now using \href{} with the full link as link text instead
of \url{}
Correction of the dimethenamid dataset2021-09-15T09:22:36ZJohannes Rankejranke@uni-bremen.de2021-09-15T09:22:36Zurn:sha1:35eaf4f7bac89b249ff488e4e3021d4226ed9e23
The data given in previous mkin versions for "Borstel 2" (Staudenmaier
2013) are in fact a subset of the "Borstel 1" data, with the "Borstel 2"
data simply being further analysed for isomer composition by
Staudenmaier (2013).
While correcting this, the URL of the RAR published by EFSA was
updated, as the EFSA Register of Questions was replaced by the
Open EFSA portal.
This also affects the recent publication in "Environments" [1], where
these two datasets were pooled. However, the influence on the final
results can be expected to be minimal. Out of the 16 observations for
the Borstel soil, five were erroneously duplicated which just changes
the weight of the different sampling points and modifies the variance.
The conclusions of the publication are qualitative and are not
considered to be affected.
[1] https://doi.org/10.3390/environments8080071
Some example evaluations of dimethenamid data2021-07-23T11:55:34ZJohannes Rankejranke@uni-bremen.de2021-07-23T11:55:34Zurn:sha1:40b78bed232798ecbeb72759cdf8d400ea35b31f
Evaluations with nlme, saemix and nlmixr are included
Test log parameters by default when deriving saemix starting parameters2021-06-23T15:02:20ZJohannes Rankejranke@uni-bremen.de2021-06-23T15:02:20Zurn:sha1:8f015900156981ecc2f1f6a1d5a078277ef3f454