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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
2020-12-09Test print method for mixed.mmkinJohannes Ranke1-2/+2
2020-12-09Some more testsJohannes Ranke1-2/+2
2020-12-08mixed.mmkin and test coverageJohannes Ranke5-57/+188
2020-12-07Possibility to use saemix transformations in some casesJohannes Ranke1-45/+127
Namely for SFO, DFOP, SFO-SFO and DFOP-SFO
2020-12-07Attempt to be more failsafe in saemix runsJohannes Ranke1-2/+8
2020-12-03Small doc improvementJohannes Ranke1-2/+2
2020-12-02Possibility to specify random effects structuresJohannes Ranke1-17/+13
The default is pdDiag again, as we often have a small number of datasets in degradation kinetics.
2020-11-30Complete rebuild of static docs of dev versionJohannes Ranke1-2/+4
2020-11-30Log-Cholesky parameterisation as default in nlme.mmkinJohannes Ranke3-20/+29
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke3-36/+37
Depends on inline >= 0.16.2 (including the bug fixes from eddelbuettel/inline#18), which provides 'moveDLL' to store the DLL for a compiled function in a safe place in case the argument 'dll_dir' is specified in the call to 'mkinmod'. Huge thanks to Dirk @eddelbuettel for his review and support for the work on the inline package.
2020-11-24Support storing mkinmod compiled code as CFunc objectsJohannes Ranke3-34/+53
With automatic reloading in mkinfit and mkinpredict in case the DLL is not loaded and the original DLL path has been cleaned up. Depends on jranke/inline@974bdea04fcedfafaab231e6f359c88270b56cb9 See inline#13
2020-11-20export create_deg_funcJohannes Ranke1-0/+1
2020-11-19Depend on parallel, doc improvementsJohannes Ranke3-25/+24
By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9.

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