Age | Commit message (Collapse) | Author | Files | Lines | |
---|---|---|---|---|---|
2022-11-01 | Add read_spreadsheet | Johannes Ranke | 1 | -0/+55 | |
2022-11-01 | Fix plotting saem fits with covariates | Johannes Ranke | 2 | -0/+11 | |
2022-11-01 | Fix illparms tests | Johannes Ranke | 1 | -1/+1 | |
2022-11-01 | Improved printing for illparms() | Johannes Ranke | 1 | -2/+5 | |
For the case of single fits and no ill-defined parameters found | |||||
2022-10-31 | Fix R CMD check | Johannes Ranke | 3 | -3/+14 | |
2022-10-29 | Update multistart docs | Johannes Ranke | 1 | -2/+2 | |
2022-10-28 | Rename parhist to parplot and make it generic | Johannes Ranke | 3 | -11/+14 | |
That parhist name was not the brightest idea, as it does not show histograms. | |||||
2022-10-28 | Export status method for mhmkin, move to status.R | Johannes Ranke | 1 | -0/+6 | |
2022-10-28 | Rename 'convergence' method to 'status' | Johannes Ranke | 3 | -40/+39 | |
The reason is that it is misleading in the case of saem.mmkin objects, because convergence is not really checked there. | |||||
2022-10-26 | Update multistart example code and vignette | Johannes Ranke | 1 | -9/+2 | |
2022-10-26 | Remove kernel density estimate from llhist | Johannes Ranke | 1 | -3/+2 | |
2022-10-25 | Complete documentation and fix a bug | Johannes Ranke | 3 | -4/+19 | |
The bug was introduced by the changes in summary.saem.mmkin.R and surfaced in the tests when using saemix transformations. | |||||
2022-10-21 | Add a simple anova method for model comparison | Johannes Ranke | 4 | -1/+57 | |
Update docs | |||||
2022-10-14 | Select best fit from multistart, use in parhist | Johannes Ranke | 2 | -4/+32 | |
- Add 'best' and 'which.best' generics with methods for multistart objects - Per default, scale the parameters in parhist plots using the fit with the highest log likelihood. | |||||
2022-10-05 | Simplify the removal of random effects | Johannes Ranke | 1 | -0/+12 | |
This is achieved by introducing the argument 'no_random_effect' to the saem function. | |||||
2022-09-29 | Add set_nd_nq previously in pfm | Johannes Ranke | 1 | -0/+103 | |
pfm depends on mkin anyways, so reexporting set_nd_nq and set_nd_nq_focus in pfm should provide reasonable continuity. | |||||
2022-09-28 | Fix handling of multistart fits with failures | Johannes Ranke | 2 | -4/+7 | |
2022-09-19 | Make the multistart method work on Windows | Johannes Ranke | 1 | -7/+19 | |
2022-09-19 | Improve parhist and llhist | Johannes Ranke | 1 | -7/+3 | |
In particular, adapt the display of parameter boxplots for saem fits using mkin transformations to the way used for saem fits using saemix transformations, i.e. always show parameters on the natural scale, and normalised them by dividing by the median from the multiple runs. | |||||
2022-09-16 | Improve multistart documentation, bugfix | Johannes Ranke | 3 | -14/+94 | |
- Split out llhist and parhist documentation - Add example code for multistart - Create a multistart vignette, because the example code fails when run by pkgdown - Fix multistart for the case of mkin transformations in the saem fit | |||||
2022-09-16 | Improve docs and update pkgdown | Johannes Ranke | 2 | -15/+16 | |
2022-09-16 | Diagnostic plots for multistart method | Johannes Ranke | 3 | -4/+25 | |
2022-09-13 | More work on multistart | Johannes Ranke | 3 | -2/+14 | |
2022-08-14 | Basic multistart method for saem.mmkin objects | Johannes Ranke | 3 | -9/+55 | |
2022-08-10 | Update docs | Johannes Ranke | 1 | -1/+6 | |
2022-08-10 | Batch processing for hierarchical fits | Johannes Ranke | 3 | -7/+112 | |
- 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel. - 'R/saem.R': 'logLik' and 'update' methods for 'saem.mmkin' objects. - 'R/illparms.R': Add methods for 'saem.mmkin' and 'mhmkin' objects. tests: Use 2 cores on travis, should work according to docs | |||||
2022-07-26 | Import parallel instead of depending on it | Johannes Ranke | 1 | -2/+2 | |
This cleans up the startup message. Loading parallel is not that important, users wanting to use it will know what to do. Also, add codemeta.json to .Rbuildignore | |||||
2022-07-21 | Summary method for mmkin objects | Johannes Ranke | 4 | -1/+122 | |
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters | |||||
2022-05-18 | Remove outdated comment in FOCUS L vignette, update docs | Johannes Ranke | 2 | -12/+12 | |
This also adds the first benchmark results obtained on my laptop system | |||||
2022-04-13 | More control of y axes in plot.mkinfit, updates | Johannes Ranke | 1 | -1/+2 | |
Documentation and test results were updated, the latter with regard to the previous work on plot.mixed.mmkin. | |||||
2022-04-09 | Improvements to mean_degparms() and plot.mixed.mmkin() | Johannes Ranke | 3 | -4/+22 | |
- New argument 'default_log_parms' for mean_degparms() - 'plot.mixed.mmkin': Pass the frame argument also to residual plots, take the 'default_log_parms' argument for 'mean_degparms' used for constructing approximate population curves, plot population curve last to avoid that it is covered by data | |||||
2022-03-19 | Improvements to CAKE_export() | Johannes Ranke | 1 | -2/+2 | |
2022-03-16 | Use saemix in help page, typo in vignette | Johannes Ranke | 1 | -35/+36 | |
2022-03-14 | Reduce check time for CRAN, releasev1.1.0 | Johannes Ranke | 3 | -5/+6 | |
2022-03-07 | Remove nlmixr interface for release of mkin 1.1.0 | Johannes Ranke | 6 | -426/+3 | |
I am postponing my attempts to get the nlmixr interface to CRAN, given some problems with nlmixr using R-devel under Windows, see https://github.com/nlmixrdevelopment/nlmixr/issues/596 and https://github.com/r-hub/rhub/issues/512, which is fixed by the removal of nlmixr from the testsuite. For the tests to be more platform independent, the biphasic mixed effects models test dataset was defined in a way that fitting should be more robust (less ill-defined). | |||||
2022-03-03 | Update link to 2,4-D data | Johannes Ranke | 1 | -1/+1 | |
2022-03-02 | Make tests more platform independent, update docs | Johannes Ranke | 1 | -2/+1 | |
2022-03-02 | Fix nlmixr fits with parallel metabolites | Johannes Ranke | 1 | -0/+24 | |
2022-03-02 | Add a test for tffm0() | Johannes Ranke | 1 | -8/+12 | |
2022-03-01 | Add some more tests | Johannes Ranke | 1 | -0/+1 | |
2022-02-09 | Adapt saemix interface to saemix 3.0 on CRAN | Johannes Ranke | 2 | -0/+4 | |
2021-10-05 | Update docs | Johannes Ranke | 1 | -3/+5 | |
2021-09-29 | Reduce noise in nlmixr.mmkin output in examples | Johannes Ranke | 1 | -14/+25 | |
2021-09-27 | intervals() methods, more DFOP/tc variants | Johannes Ranke | 4 | -4/+54 | |
2021-09-16 | Merge branch 'master' into nlmixr | Johannes Ranke | 1 | -5/+2 | |
2021-09-15 | Fix Open EFSA URL, changelog for 1.0.5v1.0.5 | Johannes Ranke | 1 | -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{} | |||||
2021-09-15 | Update test result to corrected data, version bump | Johannes Ranke | 1 | -2/+2 | |
2021-07-23 | Merge branch 'master' into nlmixr | Johannes Ranke | 4 | -17/+28 | |
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object | |||||
2021-06-17 | Let backtransform_odeparms handle nlmixr formation fractions | Johannes Ranke | 3 | -4/+89 | |
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr | |||||
2021-06-11 | Finished 'summary.nlmixr.mmkin', checks, docs | Johannes Ranke | 6 | -28/+48 | |