| Age | Commit message (Collapse) | Author | Files | Lines | |
|---|---|---|---|---|---|
| 2022-03-01 | Make it possible to specify a vector of fixed effects | Johannes Ranke | 1 | -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. | |||||
| 2021-06-23 | Fix documentation of default random effects for nlme.mmkin | Johannes Ranke | 1 | -4/+3 | |
| 2021-06-09 | Rudimentary support for setting up nlmixr models | Johannes Ranke | 1 | -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 | |||||
| 2021-03-09 | Some improvements for borderline cases | Johannes Ranke | 1 | -1/+1 | |
| - fit_with_errors for saem() - test_log_parms for mean_degparms() and saem() | |||||
| 2021-02-04 | Documentation improvements, mainly fixing example code | Johannes Ranke | 1 | -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. | |||||
| 2020-12-09 | More tests | Johannes Ranke | 1 | -1/+1 | |
| 2020-12-02 | Possibility to specify random effects structures | Johannes Ranke | 1 | -17/+13 | |
| The default is pdDiag again, as we often have a small number of datasets in degradation kinetics. | |||||
| 2020-11-30 | Complete rebuild of static docs of dev version | Johannes Ranke | 1 | -2/+4 | |
| 2020-11-30 | Log-Cholesky parameterisation as default in nlme.mmkin | Johannes Ranke | 1 | -19/+28 | |
| 2020-11-10 | Digits for summary methods, print.saem.mmkin | Johannes Ranke | 1 | -3/+4 | |
| 2020-11-09 | I do not have a parms.nlme.mmkin method | Johannes Ranke | 1 | -2/+1 | |
| 2020-11-09 | saemix.mmkin and nlme.mmkin inherit from mixed.mmkin | Johannes Ranke | 1 | -4/+5 | |
| With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method. | |||||
| 2020-11-09 | Merge plot methods for nlme.mmkin and saem.mmkin | Johannes Ranke | 1 | -0/+3 | |
| This avoids code duplication | |||||
| 2020-11-09 | object$mmkin_orig -> object$mmkin | Johannes Ranke | 1 | -3/+3 | |
| 2020-11-08 | Improve saem method, add summary | Johannes Ranke | 1 | -4/+11 | |
| Also make the endpoints function work for saem objects. | |||||
| 2020-11-05 | Fix link and update docs | Johannes Ranke | 1 | -2/+2 | |
| 2020-11-04 | Revert to use starting values for random effects in nlme.mmkin | Johannes Ranke | 1 | -1/+1 | |
| 2020-11-03 | Do not test residuals per default, improve nlme.mmkin | Johannes Ranke | 1 | -1/+1 | |
| Do not give starting values for random effects in nlme.mmkin. | |||||
| 2020-10-27 | Add summary method for nlme.mmkin objects | Johannes Ranke | 1 | -6/+40 | |
| Improve and update docs | |||||
| 2020-10-26 | Put the legend in its own area for plot.nlme.mmkin | Johannes Ranke | 1 | -0/+2 | |
| 2020-10-24 | Fix a bug for nlme with parent only, improve examples | Johannes Ranke | 1 | -29/+8 | |
| 2020-10-24 | Plot method for nlme.mmkin objects | Johannes Ranke | 1 | -0/+2 | |
| Update docs | |||||
| 2020-10-22 | Really fix check for nlme::varConstProp | Johannes Ranke | 1 | -1/+2 | |
| And add output for nlme fit translating the mkinfit error model "obs" into nlme::varIdent(). | |||||
| 2020-10-22 | Improve interface to experimental version of nlme | Johannes Ranke | 1 | -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(). | |||||
| 2020-07-20 | Require upcoming nlme version, remove anova.nlme.mmkin | Johannes Ranke | 1 | -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 | |||||
| 2020-05-12 | Update vignettes and docs | Johannes Ranke | 1 | -1/+0 | |
| 2020-04-18 | Fix NOTE, prepare for releasev0.9.49.10 | Johannes Ranke | 1 | -1/+1 | |
| 2020-04-18 | Avoid assignment to .GlobalEnv for CRAN | Johannes Ranke | 1 | -8/+27 | |
| 2020-04-15 | Adapt endpoint() to also work for nlme.mmkin objects | Johannes Ranke | 1 | -0/+5 | |
| 2020-04-15 | Include random effects in starting parameters | Johannes Ranke | 1 | -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 | |||||
| 2020-04-15 | A plot method for nlme.mmkin fits | Johannes Ranke | 1 | -4/+5 | |
| 2020-04-14 | Add a nlme method for mmkin row objects | Johannes Ranke | 1 | -0/+85 | |
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index : mkin | |
| Fitting kinetic models to chemical degradation data (also on github) | Johannes Ranke |
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