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2021-10-08Round initial population values for nlmixrJohannes Ranke1-3/+3
This avoids numerical instabilities that sometimes occur with the FOCEI algorithm in nlmixr when the initial values are very close to the optimum values
2021-10-06Replace outdated JSS article URL by doiJohannes Ranke1-1/+1
Thanks to the hint of Achim Zeileis from the CRAN team
2021-10-05Update docsJohannes Ranke18-1572/+10195
2021-10-05Fix nlmixr for logit transformed parametersJohannes Ranke1-4/+11
2021-10-01Bump date to update online dev docsJohannes Ranke1-1/+1
2021-09-29Reduce noise in nlmixr.mmkin output in examplesJohannes Ranke6-4171/+99
2021-09-27intervals() methods, more DFOP/tc variantsJohannes Ranke43-250/+1255
2021-09-17Put the AIC comparison in a subsubsectionJohannes Ranke4-37/+54
2021-09-16Adapt and improve the dimethenamid vignetteJohannes Ranke65-642/+818
Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs
2021-09-16Remove GITHUB_PAT from .travis.ymlJohannes Ranke1-3/+0
I found that I can create a PAT with no extra privileges, thanks to https://itsalocke.com/blog/using-travis-make-sure-you-use-a-github-pat/ so I will add this to my travis account.
2021-09-16Try to diagnose the problem with remotesJohannes Ranke1-0/+2
2021-09-16Try to make remotes on travis work againJohannes Ranke1-0/+1
This tries to unset the environment variable GITHUB_PAT which seems to get in the way for installing using remotes::install_github on travis.
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke16-97/+65
2021-09-15Fix Open EFSA URL, changelog for 1.0.5v1.0.5Johannes Ranke4-6/+10
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{}
2021-09-15Update test result to corrected data, version bumpJohannes Ranke6-28/+21
2021-09-15Use my drat repo for saemix masterJohannes Ranke1-3/+1
2021-09-15Try to make remotes::install_github work againJohannes Ranke1-0/+1
2021-09-15Update link for travis badgeJohannes Ranke2-2/+2
2021-09-15Correction of the dimethenamid datasetJohannes Ranke3-18/+10
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
2021-08-04Improve AIC table in vignetteJohannes Ranke11-59/+73
2021-07-29Add citations to the DESCRIPTIONJohannes Ranke4-7/+17
2021-07-29Go back to 1.0.x version, update docsJohannes Ranke25-95/+103
2021-07-29Merge branch 'master' into nlmixrJohannes Ranke5-43/+36
2021-07-29Add publication to README, update docsJohannes Ranke5-43/+36
2021-07-27Fix dimethenamid vignette problems and update docsJohannes Ranke45-1072/+1131
2021-07-27Merge branch 'master' into nlmixrJohannes Ranke23-7/+7
2021-07-27Publication date for 1.0.4 in NEWS, update docsJohannes Ranke24-8/+8
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke55-9317/+8609
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-07-23Try explicit R version for travisJohannes Ranke1-1/+1
2021-07-23Update travis config, attempting to get R 4.1.0Johannes Ranke1-2/+0
2021-07-23Rerun tests, use current vdiffr on travisJohannes Ranke6-92/+58
2021-07-23Update vdiffr tests for version 1.0Johannes Ranke40-9110/+5248
2021-07-23Fix travis configJohannes Ranke1-0/+4
to use up to date versions of nlme, covr and devtools
2021-07-23Some example evaluations of dimethenamid dataJohannes Ranke24-20/+2349
Evaluations with nlme, saemix and nlmixr are included
2021-06-23Test log parameters by default when deriving saemix starting parametersJohannes Ranke1-1/+1
2021-06-23Fix documentation of default random effects for nlme.mmkinJohannes Ranke1-4/+3
2021-06-22Update development version of online docsJohannes Ranke8-9289/+1019
2021-06-17Let backtransform_odeparms handle nlmixr formation fractionsJohannes Ranke11-149/+243
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
2021-06-16Translate formation fractions to nlmixr languageJohannes Ranke4-12/+223
Works for the dimethenamid data, at least for FOCEI. Very little testing yet. The summary function does not yet handle the new transformations of formation fractions (that are in fact very old, as they were used in the very first version of mkin). The test file has no tests yet, just some code that may be used for testing.
2021-06-12Small cosmeticsJohannes Ranke4-13/+36
2021-06-11Fix package name for travis config...Johannes Ranke1-1/+1
2021-06-11Fix travis syntaxJohannes Ranke1-1/+4
2021-06-11Add packages necessary for shell commands on travisJohannes Ranke1-1/+1
2021-06-11Attempt to satisfy nlme version requirement on travisJohannes Ranke1-0/+1
2021-06-11Add system requirements for symengine on TravisJohannes Ranke1-0/+1
nlmixr depends on symengine
2021-06-11Finished 'summary.nlmixr.mmkin', checks, docsJohannes Ranke62-571/+15632
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke20-115/+1209
- All degradation models are specified as ODE models. This appears to be fast enough - Error models are being translated to nlmixr as close to the mkin error model as possible. When using the 'saem' backend, it appears not to be possible to use the same error model for more than one observed variable - No support yet for models with parallel formation of metabolites, where the ilr transformation is used in mkin per default - There is a bug in nlmixr which appears to be triggered if the data are not balanced, see nlmixrdevelopment/nlmixr#530 - There is a print and a plot method, the summary method is not finished
2021-04-21Merge branch 'master' into saemixJohannes Ranke134-374/+445
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke26-143/+158
2021-03-31Bug fix in plot.mkinfitJohannes Ranke128-248/+327
In residual plots, use xlab and xlim if appropriate

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