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2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke1-14/+54
- 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
2021-04-21Merge branch 'master' into saemixJohannes Ranke1-1/+1
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-3/+5
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-4/+10
In residual plots, use xlab and xlim if appropriate
2021-03-09Some improvements for borderline casesJohannes Ranke1-3/+3
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-15Fully rebuild docs, rerun tests and checkJohannes Ranke1-2/+2
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-1/+1
Also bump version to 1.0.3.
2021-02-13Merge branch 'master' into saemixJohannes Ranke1-2/+2
Run make testcheck to regenerate logs with merge conflicts
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-1/+1
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Reintroduce interface to saemixJohannes Ranke1-3/+12
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-1/+1
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.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-14/+5
- 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
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke1-6/+10
Address release critical check and test issues
2020-12-08mixed.mmkin and test coverageJohannes Ranke1-2/+7
2020-10-22Improve interface to experimental version of nlmeJohannes Ranke1-2/+2
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().
2020-10-08Fix issues for releaseJohannes Ranke1-8/+2
2020-07-15Improve handling of (partially) failing fitsJohannes Ranke1-3/+9
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.
2020-05-12Rerun tests and checks, CRAN commentsJohannes Ranke1-1/+1
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-2/+3
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Don't run visual tests on r-devel for nowJohannes Ranke1-2/+1
https://github.com/r-lib/vdiffr/issues/86
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-1/+1
Still in preparation for analytical solutions of coupled models
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-1/+2
Preparing for symbolic solutions for more than one compound
2020-04-20Updated build and check logsv0.9.49.11Johannes Ranke1-1/+1
2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke1-23/+3
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke1-8/+20
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke1-94/+8
2020-04-14Add a nlme method for mmkin row objectsJohannes Ranke1-4/+98
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke1-67/+4
2020-04-03Merge branch 'master' into mxkinJohannes Ranke1-8/+115
Merge DESCRIPTION manually to combine dependencies and rerun check to update check.log
2020-03-31Static documentation rebuilt by pkgdownJohannes Ranke1-4/+11
2020-03-30Add new dependenciesJohannes Ranke1-58/+14
2020-01-08Todays date in DESCRIPTION, update check logv0.9.49.8Johannes Ranke1-1/+2
2019-11-04Scaled residual plotsJohannes Ranke1-1/+1
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-1/+1
2019-10-22Go back to d_3 for errmod = "obs"Johannes Ranke1-26/+2
in the hope that this makes plotting cross-platform also for this error model
2019-10-21Local checkJohannes Ranke1-6/+23
2019-10-21Improve some plotting routines, more testsJohannes Ranke1-5/+3
Static documentation rebuilt by pkgdown
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-23/+8
mkinfit objects now include an ll() function to calculate the log-likelihood. Part of the code was refactored, hopefully making it easier to read and maintain. IRLS is currently the default algorithm for the error model "obs", for no particular reason. This may be subject to change when I get around to investigate. Slow tests are now in a separate subdirectory and will probably only be run by my own Makefile target. Formatting of test logs is improved. Roundtripping error model parameters works with a precision of 10% when we use lots of replicates in the synthetic data (see slow tests). This is not new in this commit, but as I think it is reasonable this closes #7.
2019-07-09Address winbuilder R-devel warning about usageJohannes Ranke1-3/+27
2019-07-09Adaptations for gmkinJohannes Ranke1-1/+1
Address winbuilder check problems, update check log, update of static docs
2019-07-03Add check and test logsJohannes Ranke1-10/+2
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-3/+11
The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets.
2019-05-03Improve error model fittingJohannes Ranke1-0/+1
Now we have a three stage fitting process for nonconstant error models: - Unweighted least squares - Only optimize the error model - Optimize both Static documentation rebuilt by pkgdown
2019-05-02Improve testsJohannes Ranke1-3/+3
- Improve control of the number of cores - Reduce the precision of the correlation matrix in the test summary output, as the exact results are platform dependent
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-13/+3
Static documentation rebuilt by pkgdown
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke1-5/+15
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0
2018-09-21Improve fitting the two-component error modelJohannes Ranke1-1/+1
with respect to accuracy and robustness.
2018-09-14Update NEWSJohannes Ranke1-1/+1
Static documentation rebuilt by pkgdown
2018-09-14Remove two vignettes from the package but not from docsJohannes Ranke1-4/+2
- Rebuild static documentation - Adapt test to new approach to two component error model where the model is inadequate

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