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2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke1-7/+4
This also adds the first benchmark results obtained on my laptop system
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-5/+5
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).
2022-03-02Make tests more platform independent, update docsJohannes Ranke1-354/+282
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-3/+3
In residual plots, use xlab and xlim if appropriate
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-3/+3
Also bump version to 1.0.3.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-27/+20
- 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
2020-10-15Update online docs for release versionJohannes Ranke1-92/+111
2020-05-27Add docs generated using released version 0.9.52Johannes Ranke1-4/+4
2020-05-12Update vignettes and docsJohannes Ranke1-3/+3
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-7/+7
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-127/+126
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-13/+35
Still in preparation for analytical solutions of coupled models
2020-05-07Static documentation rebuilt by pkgdownJohannes Ranke1-121/+84
2020-03-30Static documentation rebuilt by pkgdownJohannes Ranke1-27/+51
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-2/+2
2019-10-25Static documentation rebuilt by pkgdownJohannes Ranke1-45/+62
2019-09-19Static documentation rebuilt by pkgdownJohannes Ranke1-3/+3
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Static documentation rebuilt by pkgdownJohannes Ranke1-3/+3
to check if the link to the pfm package is correctly generated by pkgdown after preparing the pfm package docs accordingly
2019-09-18Add url: tag to _pkgdown.ymlJohannes Ranke1-3/+3
Static documentation rebuilt by pkgdown
2019-09-18Further corrections of the twa vignetteJohannes Ranke1-2/+2
Static documentation rebuilt by pkgdown
2019-09-18Correct and rebuild docsJohannes Ranke1-32/+42
- Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown
2019-07-09Adaptations for gmkinJohannes Ranke1-2/+2
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-4/+4
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke1-2/+2
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke1-2/+2
Static documentation rebuilt by pkgdown
2019-06-05Add error model algorithm to outputJohannes Ranke1-3/+3
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-5/+5
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.
2019-05-08Add functionality to plot the error modelJohannes Ranke1-3/+3
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2019-05-07Fix hessian calculationsJohannes Ranke1-2/+2
Static documentation rebuilt by pkgdown
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke1-5/+3
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke1-8/+10
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
2019-05-02Remove reference to archived kinfit packageJohannes Ranke1-1/+1
from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown
2019-05-02Prepare for CRAN releaseJohannes Ranke1-1/+1
- Skip long running tests on CRAN as well to avoid timeout on winbuilder - Don't install benchmark results in the package, they are only needed in the git repository - Don't run example in man/add_err.Rd as it takes > 10 s on winbuilder - Rebuild docs
2019-05-02Better initials for error model parametersJohannes Ranke1-28/+28
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-39/+37
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-03-04Make some example output more reproducibleJohannes Ranke1-1/+1
In order to avoid some unnecessary documentation rebuilds
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-2/+5
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke1-2/+2
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2019-02-25Static documentation rebuilt by current pkgdownJohannes Ranke1-3/+3
2019-02-25Add plotting tests, add nafta to pkgdownJohannes Ranke1-2/+2
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke1-3/+3
2019-02-22Static documentation rebuilt by pkgdownJohannes Ranke1-3/+3
2019-02-21Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
to get the codecov badge into the docs
2019-02-21Static documentation rebuilt by pkgdownJohannes Ranke1-3/+3
2019-02-21Make example logistic fit quietJohannes Ranke1-2/+2
2019-02-21Add the logistic modelJohannes Ranke1-2/+2
2019-01-31Restore NAMESPACEJohannes Ranke1-16/+149
which was accidentally overwritten by pkgdown -> roxygen
2019-01-31Correct title for CAKE_exportJohannes Ranke1-1/+1
Add NEWS entry. Static documentation rebuilt by pkgdown

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