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2022-02-28Improve algorithm summary for saemix fitsJohannes Ranke1-1/+3
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke3-3/+13
2021-11-17Update required saemix version, update testsJohannes Ranke1-3/+2
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
2021-10-05Fix nlmixr for logit transformed parametersJohannes Ranke1-4/+11
2021-09-29Reduce noise in nlmixr.mmkin output in examplesJohannes Ranke1-14/+25
2021-09-27intervals() methods, more DFOP/tc variantsJohannes Ranke2-2/+181
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke1-5/+2
2021-09-15Fix Open EFSA URL, changelog for 1.0.5v1.0.5Johannes Ranke1-1/+1
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{}
2021-09-15Correction of the dimethenamid datasetJohannes Ranke1-2/+2
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
2021-07-23Some example evaluations of dimethenamid dataJohannes Ranke2-14/+24
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
2021-06-17Let backtransform_odeparms handle nlmixr formation fractionsJohannes Ranke4-18/+29
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
2021-06-16Translate formation fractions to nlmixr languageJohannes Ranke3-12/+124
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 Ranke2-11/+34
2021-06-11Finished 'summary.nlmixr.mmkin', checks, docsJohannes Ranke4-35/+51
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke7-56/+802
- 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 Ranke2-3/+4
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-2/+3
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-1/+1
In residual plots, use xlab and xlim if appropriate
2021-03-20Fix mkin calculation of saemix residualsJohannes Ranke1-1/+1
2021-03-19test_log_parms for plot.mixed.mmkin, roxygen runJohannes Ranke2-2/+9
2021-03-16Convenience option to set nbiter.saemixJohannes Ranke1-1/+5
2021-03-09Some improvements for borderline casesJohannes Ranke3-9/+61
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-24Reset graphical parameters with on.exit()Johannes Ranke4-5/+5
plot.mixed.mmkin did not reset graphical parameters at all. The other plotting functions did not use on.exit, so this change should make the use of the plotting functions safer.
2021-02-24Reset graphical parameters with on.exit()Johannes Ranke4-5/+5
plot.mixed.mmkin did not reset graphical parameters at all. The other plotting functions did not use on.exit, so this change should make the use of the plotting functions safer.
2021-02-15Merge branch 'master' into saemixJohannes Ranke1-0/+5
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-0/+5
Also bump version to 1.0.3.
2021-02-13Merge branch 'master' into saemixJohannes Ranke1-2/+9
Run make testcheck to regenerate logs with merge conflicts
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-2/+9
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Reintroduce interface to saemixJohannes Ranke4-5/+806
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke7-33/+40
The errors in the example code were in the \dontrun sections, so they were not caught by CRAN checks. In addition, the static help files generated with pkgdown were cached, so I noticed the errors only after completely regenerating the documentation for version 1.0.0.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke4-806/+5
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
2021-01-25Some more plotting improvementsJohannes Ranke2-6/+6
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke2-3/+5
See NEWS.md. Closes #12
2021-01-22We do not need to suppress saemix plots any moreJohannes Ranke1-12/+1
This makes fitting with saem within parallel::mclapply much faster and, surprisingly, much less hungry for RAM.
2021-01-11Rebuild docsJohannes Ranke1-1/+1
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke1-0/+2
Address release critical check and test issues
2020-12-21plot.mixed: Possibility to overlay predictionsJohannes Ranke1-6/+31
2020-12-19Possibility to override automatic starting parameters for saemJohannes Ranke1-4/+10
2020-12-19Dimethenamid data, normalisation optionsJohannes Ranke3-8/+40
2020-12-16And add the second candidate modelJohannes Ranke1-0/+4
2020-12-16Print the model not the data for D24Johannes Ranke1-1/+1
2020-12-16Add printout of d24 model and update docsJohannes Ranke1-0/+1
2020-12-15Remove leftoversJohannes Ranke1-3/+2
2020-12-10nlme with varConstProp is releasedJohannes Ranke1-0/+3
Also fix incompatibility with saem fits from earlier mkin versions
2020-12-09Make saem using mkinpredict work againJohannes Ranke2-47/+54
I threw out mclapply as it did not play well with the linear algebra routines used in the saemix code. Most of the change is actually indentation in the code creating the model function. But there is an important fix in mkinpredict which I had broken.
2020-12-09Add more tests and fix HS in saemJohannes Ranke1-2/+2
2020-12-09More testsJohannes Ranke2-5/+5

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