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2022-11-01Fix plotting saem fits with covariatesJohannes Ranke1-46/+70
2022-09-14Remove purrr dependencyJohannes Ranke1-2/+3
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.
2022-04-09Improvements to mean_degparms() and plot.mixed.mmkin()Johannes Ranke1-5/+13
- 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
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke1-2/+3
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke1-0/+17
- 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
2021-03-19test_log_parms for plot.mixed.mmkin, roxygen runJohannes Ranke1-1/+7
2021-02-24Reset graphical parameters with on.exit()Johannes Ranke1-0/+1
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.
2021-02-06Reintroduce interface to saemixJohannes Ranke1-1/+22
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-22/+1
- 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 Ranke1-5/+5
2020-12-21plot.mixed: Possibility to overlay predictionsJohannes Ranke1-6/+31
2020-12-08mixed.mmkin and test coverageJohannes Ranke1-20/+41
2020-11-13Fixed plotting of non-analytical solutions in saemJohannes Ranke1-5/+3
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke1-1/+1
- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU assessment as mkindsg object with metadata - f_time_norm_focus() to do time-step normalisation using the FOCUS method - focus_soil_moisture data with default moisture contents at pF1, pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance - Dataset generation scripts in inst/dataset_generation - Depend on R >= 2.15.1 in order to facilitate the use of utils::globalVariables()
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke1-0/+236
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method.

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