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2023-02-17Finish adapting to upcoming deSolveJohannes Ranke1-12/+10
2022-11-16We get about 25% performance gainJohannes Ranke1-0/+14
with the custom lsoda call, avoiding repeated getNativeSymbolInfo calls. It's just that we should not be calling foreign functions from different packages, because the may change without notice. Using getNativeSymbolInfo for "call_lsoda" avoids the CRAN note, and a similar call could probably be used for "unlock_solver", avoiding the NOTE in checks for cran, but we should not do this in a CRAN package.
2022-03-14Reduce check time for CRAN, releasev1.1.0Johannes Ranke1-4/+3
2022-03-01Add some more testsJohannes Ranke1-1/+2
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.
2021-06-23Fix documentation of default random effects for nlme.mmkinJohannes Ranke1-4/+3
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke1-1/+1
- 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
2021-03-09Some improvements for borderline casesJohannes Ranke1-1/+1
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-18/+18
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.
2020-12-09More testsJohannes Ranke1-1/+1
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 Ranke1-19/+28
2020-11-10Digits for summary methods, print.saem.mmkinJohannes Ranke1-3/+4
2020-11-09I do not have a parms.nlme.mmkin methodJohannes Ranke1-2/+1
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke1-4/+5
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method.
2020-11-09Merge plot methods for nlme.mmkin and saem.mmkinJohannes Ranke1-0/+3
This avoids code duplication
2020-11-09object$mmkin_orig -> object$mmkinJohannes Ranke1-3/+3
2020-11-08Improve saem method, add summaryJohannes Ranke1-4/+11
Also make the endpoints function work for saem objects.
2020-11-05Fix link and update docsJohannes Ranke1-2/+2
2020-11-04Revert to use starting values for random effects in nlme.mmkinJohannes Ranke1-1/+1
2020-11-03Do not test residuals per default, improve nlme.mmkinJohannes Ranke1-1/+1
Do not give starting values for random effects in nlme.mmkin.
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke1-6/+40
Improve and update docs
2020-10-26Put the legend in its own area for plot.nlme.mmkinJohannes Ranke1-0/+2
2020-10-24Fix a bug for nlme with parent only, improve examplesJohannes Ranke1-29/+8
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke1-0/+2
Update docs
2020-10-22Really fix check for nlme::varConstPropJohannes Ranke1-1/+2
And add output for nlme fit translating the mkinfit error model "obs" into nlme::varIdent().
2020-10-22Improve interface to experimental version of nlmeJohannes Ranke1-7/+55
The experimental nlme version in my drat repository contains the variance function structure varConstProp which makes it possible to use the two-component error model in generalized nonlinear models using nlme::gnls() and in mixed effects models using nlme::nlme().
2020-07-20Require upcoming nlme version, remove anova.nlme.mmkinJohannes Ranke1-29/+0
The method is no longer necessary, now that Bug 17761 is fixed upstream https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
2020-05-12Update vignettes and docsJohannes Ranke1-1/+0
2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke1-1/+1
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke1-8/+27
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke1-0/+5
2020-04-15Include random effects in starting parametersJohannes Ranke1-4/+96
- mean_degparms() now optionally returns starting values for fixed and random effects, which makes it possible to obtain acceptable fits also in more difficult cases (with more parameters) - Fix the anova method, as it is currently not enough to inherit from lme: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761 - Show fit information, and per default also errmin information in plot.nlme.mmkin() - Examples for nlme.mmkin: Decrease tolerance and increase the number of iterations in the PNLS step in order to be able to fit FOMC-SFO and DFOP-SFO
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke1-4/+5
2020-04-14Add a nlme method for mmkin row objectsJohannes Ranke1-0/+85

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