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2022-03-01Make it possible to specify a vector of fixed effectsJohannes Ranke1-1/+1
as obtained by mean_degparms(..., random = FALSE), instead of the list obtained by mean_degparms(, ... random = TRUE) that is passed by nlme.mmkin to nlme by default.
2022-02-28Add test for summary.nlmixr.mmkinJohannes Ranke3-0/+118
2022-02-28Relax a test for travisJohannes Ranke2-27/+27
2022-02-28Improve tests, skip some on TravisJohannes Ranke7-26/+73
Respect digits argument when printing correlations in summaries
2022-02-28Update travis config and _pkgdown.ymlJohannes Ranke3-7/+5
2022-02-28Update docsJohannes Ranke58-17943/+18865
2022-02-28Add nlmixr tests, reorganize, test intervals()Johannes Ranke6-176/+236
2022-02-28With saemix 3.0 on CRAN there's no need to check for it in testsJohannes Ranke5-126/+79
2022-02-28Improve dimethenamid vignetteJohannes Ranke3-241/+126
2022-02-28Improve algorithm summary for saemix fitsJohannes Ranke1-1/+3
2022-02-10GNUMakefile: Convince testthat to give dynamic outputJohannes Ranke2-161/+11
This means that we still get the \r in the test logs so so the postprocessing with sed works unmodified
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke19-1520/+1674
2022-02-08Merge branch 'nlmixr'Johannes Ranke316-3091/+27257
2022-01-11Update static docsnlmixrJohannes Ranke20-9255/+12062
2022-01-11Update the dimethenamid vignette with current saemixJohannes Ranke14-162/+153
Convergence is faster with this version (@ecomets mentioned that there was a bugfix lately that could lead to faster convergence). However, if I use too many iterations (i.e. 10 000 as in the last version of this vignette), I get an error in solving omega.teta during later iterations, apparently due to overparameterisation of the DFOP model in this case.
2021-12-08PD in Freiburg statt BremenJohannes Ranke1-1/+1
2021-11-18Update HTML version of READMEJohannes Ranke1-2/+2
2021-11-18Updates after changing the default branch to mainJohannes Ranke2-4/+4
2021-11-17Update required saemix version, update testsJohannes Ranke9-1526/+1525
2021-11-17Use the official master branch of saemixJohannes Ranke1-1/+1
As my changes were merged meanwhile
2021-11-17Update CAKE URLJohannes Ranke2-8/+5
2021-11-17Update CAKE URLJohannes Ranke2-8/+5
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
2021-10-06Replace 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
2021-10-01Update online docs to 1.0.5Johannes Ranke15-42/+46
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

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