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2023-04-20Fix and rebuild documentation, see NEWSJohannes Ranke1-22/+39
I had to fix the two pathway vignettes, as they did not work with the released version any more. So they and the multistart vignette which got some small fixes as well were rebuilt. Complete rebuild of the online docs with the released version. The documentation of the 'hierarchial_kinetics' format had to be fixed as well.
2022-11-17Complete update of online docs for v1.2.0Johannes Ranke1-17/+22
2022-08-10Update static docsJohannes Ranke1-126/+178
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke1-37/+38
This also adds the first benchmark results obtained on my laptop system
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-10/+10
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 Ranke1-544/+450
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-14/+14
In residual plots, use xlab and xlim if appropriate
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-67/+61
Also bump version to 1.0.3.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-86/+96
- 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 Ranke1-547/+229
2020-05-27Add docs generated using released version 0.9.52Johannes Ranke1-109/+107
2020-05-25First working version of saemix helper functionsJohannes Ranke1-11/+11
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-15Use markdown links in mkinfit documentationJohannes Ranke1-46/+48
2020-05-12Another documentation updateJohannes Ranke1-22/+22
2020-05-12Update vignettes and docsJohannes Ranke1-13/+13
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-21/+21
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke1-64/+69
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-110/+218
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-07Static documentation rebuilt by pkgdownJohannes Ranke1-124/+47
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke1-25/+19
2020-03-30Static documentation rebuilt by pkgdownJohannes Ranke1-47/+62
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-14/+14
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke1-15/+17
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-25Static documentation rebuilt by pkgdownJohannes Ranke1-225/+216
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-89/+83
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.
2019-09-19Static documentation rebuilt by pkgdownJohannes Ranke1-14/+14
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Static documentation rebuilt by pkgdownJohannes Ranke1-14/+14
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 Ranke1-14/+14
Static documentation rebuilt by pkgdown
2019-09-18Further corrections of the twa vignetteJohannes Ranke1-14/+14
Static documentation rebuilt by pkgdown
2019-09-18Correct and rebuild docsJohannes Ranke1-46/+60
- 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 Ranke1-24/+22
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-22/+29
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke1-14/+14
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke1-15/+15
Static documentation rebuilt by pkgdown
2019-06-05Add error model algorithm to outputJohannes Ranke1-22/+28
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-84/+121
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 Ranke1-14/+14
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 Ranke1-72/+104
Static documentation rebuilt by pkgdown
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke1-190/+149
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke1-199/+203
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 Ranke1-13/+13
from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown
2019-05-02Prepare for CRAN releaseJohannes Ranke1-13/+13
- 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 Ranke1-109/+117
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-790/+357
- 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 Ranke1-22/+22
In order to avoid some unnecessary documentation rebuilds
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-23/+23
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-22/+25
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke1-22/+22
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 Ranke1-22/+22
2019-02-25Static documentation rebuilt by current pkgdownJohannes Ranke1-24/+24

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