mkin/R/plot.mixed.mmkin.R, branch v1.2.0Fitting kinetic models to chemical degradation data (also on github)https://erac.jrwb.de/mkin/atom?h=v1.2.02022-11-01T11:39:28ZFix plotting saem fits with covariates2022-11-01T11:39:28ZJohannes Rankejranke@uni-bremen.de2022-11-01T11:39:28Zurn:sha1:a787e5266628f859fd70454c5419721efa494887Remove purrr dependency2022-09-14T20:39:12ZJohannes Rankejranke@uni-bremen.de2022-09-14T20:39:12Zurn:sha1:af24cde56a49b532d7f65dd199d176e0ce3cac09
We now directly import from rlang and vctrs, which were indirect
dependencies anyways. purrr::map_dfr is deprecated in the upcoming purrr
1.0, and depends on dplyr (since when?) which is only suggested by
purrr. This would lead new installations of mkin to fail if dplyr is not
installed as well.
Improvements to mean_degparms() and plot.mixed.mmkin()2022-04-09T04:21:23ZJohannes Rankejranke@uni-bremen.de2022-04-09T04:21:23Zurn:sha1:c29e27b9bf5f5361db44e28b06da7b8a1e636e85
- 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
Adapt saemix interface to saemix 3.0 on CRAN2022-02-09T11:19:14ZJohannes Rankejranke@uni-bremen.de2022-02-09T11:19:14Zurn:sha1:d8f31d1323998f33d07535f55c81be380d93ca45Rudimentary support for setting up nlmixr models2021-06-09T15:00:41ZJohannes Rankejranke@uni-bremen.de2021-06-09T14:53:31Zurn:sha1:c6eb6b2bb598002523c3d34d71b0e4a99671ccd6
- 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
test_log_parms for plot.mixed.mmkin, roxygen run2021-03-19T10:22:07ZJohannes Rankejranke@uni-bremen.de2021-03-19T10:22:07Zurn:sha1:6d6dc7d53bf99b088af3488588574afc832fb7feReset graphical parameters with on.exit()2021-02-24T13:50:54ZJohannes Rankejranke@uni-bremen.de2021-02-24T13:46:10Zurn:sha1:28c0dff7d7191f854be610b5384e965d9b191f98
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.
Reintroduce interface to saemix2021-02-06T17:30:32ZJohannes Rankejranke@uni-bremen.de2021-02-06T17:30:32Zurn:sha1:48c463680b51fa767b4cd7bd62865f192d0354ac
Also after the upgrade from buster to bullseye of my local system, some
test results for saemix have changed.
Prepare for v1.0.02021-02-03T17:18:19ZJohannes Rankejranke@uni-bremen.de2021-02-03T15:41:31Zurn:sha1:f0ef23a7598e5d19648ae4edc2b74e0fba27a41c
- 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
Some more plotting improvements2021-01-25T16:55:06ZJohannes Rankejranke@uni-bremen.de2021-01-25T16:55:06Zurn:sha1:0280b9c8dcc77cb1d22964485462b27a56b96eca