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2022-09-14Remove purrr dependencyJohannes Ranke1-2/+2
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.
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke1-55/+0
- 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 Ranke1-3/+34
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2020-11-30Log-Cholesky parameterisation as default in nlme.mmkinJohannes Ranke1-1/+0
2020-11-05Fix mean_degparms() if only one optimised parameterJohannes Ranke1-5/+7
2020-10-26Put the legend in its own area for plot.nlme.mmkinJohannes Ranke1-1/+5
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-1/+1
Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke1-1/+1
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-3/+3
Still in preparation for analytical solutions of coupled models
2020-04-16mean_degparms: Fix rownames in random effectsJohannes Ranke1-1/+1
2020-04-15Include random effects in starting parametersJohannes Ranke1-70/+18
- 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
2020-04-14Add a nlme method for mmkin row objectsJohannes Ranke1-10/+7
2020-04-14Keep order of datasets in nlme_data, add a plotJohannes Ranke1-2/+9
2020-04-10Improve nlme function docsJohannes Ranke1-34/+33
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke1-0/+213

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