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2024-07-29Move coverage to pkgdown docsJohannes Ranke1-76/+60
The coverage report is neither successful on Travis nor in the github workflow set up with the usethis package. Therefore the code coverage report is generated locally and linked into the pkgdown docs.
2023-11-16Update pkgdown docs to bootstrap 5 with searchJohannes Ranke1-118/+74
2023-08-09Update static docsv1.2.5Johannes Ranke1-2/+2
2023-05-19Prepare release of v1.2.4v1.2.4Johannes Ranke1-6/+6
- Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release
2023-04-20Fix and rebuild documentation, see NEWSJohannes Ranke1-65/+251
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 Ranke1-33/+39
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke1-2/+2
This also adds the first benchmark results obtained on my laptop system
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-4/+4
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 Ranke1-49/+58
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 Ranke1-25/+34
Also bump version to 1.0.3.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-9/+9
- 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 Ranke1-28/+32
2020-05-27Add docs generated using released version 0.9.52Johannes Ranke1-7/+4
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke1-3/+6
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-4/+4
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-62/+51
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-1/+1
2019-10-25Static documentation rebuilt by pkgdownJohannes Ranke1-1/+2
2019-09-19Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Correct and rebuild docsJohannes Ranke1-11/+16
- 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 Ranke1-1/+1
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-9/+17
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-06-05Add error model algorithm to outputJohannes Ranke1-1/+1
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-3/+3
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 Ranke1-1/+1
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke1-1/+1
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke1-1/+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
2019-05-02Remove reference to archived kinfit packageJohannes Ranke1-10/+3
from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown
2019-05-02Better initials for error model parametersJohannes Ranke1-1/+1
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-2/+2
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-33/+33
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-0/+3
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2019-02-25Static documentation rebuilt by current pkgdownJohannes Ranke1-1/+1
2019-02-25Add plotting tests, add nafta to pkgdownJohannes Ranke1-1/+1
2019-02-22Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2019-02-21Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2019-02-21Add the logistic modelJohannes Ranke1-1/+1
2019-01-31Static documentation rebuilt by pkgdownJohannes Ranke1-17/+17
2018-11-26Support logLik and AIC for manual weightsJohannes Ranke1-1/+1
Static documentation rebuilt by pkgdown
2018-11-23Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2018-09-18Support maximum twa for HS, test, docsJohannes Ranke1-2/+2
2018-09-14Remove two vignettes from the package but not from docsJohannes Ranke1-3/+3
- Rebuild static documentation - Adapt test to new approach to two component error model where the model is inadequate
2018-09-14Exclude more example code from CRAN checksJohannes Ranke1-1/+1
to avoid NOTES about long execution times. Static documentation rebuilt by pkgdown with run_dont_run = TRUE
2018-09-14Static documentation rebuilt by pkgdownJohannes Ranke1-2/+2
Also update test log
2018-09-06Static documentation rebuilt by pkgdownJohannes Ranke1-29/+29
2018-07-18Correct references to the Rocke and Lorenzato modelJohannes Ranke1-2/+2
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.

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