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2022-10-26Don't test parhist and llhist on travis, docsJohannes Ranke1-0/+2
2022-10-04Add set_nd_nq to pkgdown topicsJohannes Ranke1-0/+1
2022-09-16Improve multistart documentation, bugfixJohannes Ranke1-2/+4
- Split out llhist and parhist documentation - Add example code for multistart - Create a multistart vignette, because the example code fails when run by pkgdown - Fix multistart for the case of mkin transformations in the saem fit
2022-09-16Improve docs and update pkgdownJohannes Ranke1-2/+5
2022-08-10Change dev branch used for docs, update static docsJohannes Ranke1-2/+2
2022-08-10Update static docsJohannes Ranke1-5/+9
2022-07-22Update static docsJohannes Ranke1-0/+3
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-4/+0
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).
2022-02-28Update travis config and _pkgdown.ymlJohannes Ranke1-2/+4
2021-09-27intervals() methods, more DFOP/tc variantsJohannes Ranke1-0/+3
2021-06-22Update development version of online docsJohannes Ranke1-0/+1
2021-06-11Finished 'summary.nlmixr.mmkin', checks, docsJohannes Ranke1-0/+3
2021-02-18Merge branch 'master' into saemixJohannes Ranke1-0/+3
2021-02-15Don't let pkgdown add release datesJohannes Ranke1-0/+3
It didn't pick up the release of 1.0.3, and most of the other release dates were duplicated.
2021-02-06Reintroduce interface to saemixJohannes Ranke1-2/+5
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/+0
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 Ranke1-7/+2
- 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
2020-12-19Update docsJohannes Ranke1-0/+1
2020-12-11Update static docsJohannes Ranke1-0/+1
2020-11-19Depend on parallel, doc improvementsJohannes Ranke1-6/+9
By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9.
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke1-3/+2
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method.
2020-11-09Add plot method for saem.mmkin objectsJohannes Ranke1-0/+1
2020-11-08Improve saem method, add summaryJohannes Ranke1-0/+1
Also make the endpoints function work for saem objects.
2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke1-0/+1
The reasons for this decision were - Creating an saemix generic in the saemix package caused problems with roxygen, because functions like saemix.plot.xy were documented in their help files as S3 methods, although explicitly exported with @export - Creating an saemix generic in this package is possible, but would make it necessary to load samix with exclude = "saemix" in order to avoid overwriting the generic when loading saemix. - The return object of such an saemix generic in this package cannot be an S3 class with class attribute c("saemix.mmkin", "SaemixObject") similar to nlme.mmkin, as saemix returns an S4 class. - Extending the S4 class SaemixObject using simple inheritance to a class SaemixMmkinObject with additional slots did not work as expected. When the initialize method was left untouched, it prevented creation of an SaemixMmkinObject even if it was based on an initialised SaemixObject, as the initialize method seems to always be called by new(). This could potentially be circumvented by a coerce method. If an alternative initialize method was used, an SaemixMmkinObject could be created. However, the methods written for SaemixObjects only worked in some instances, either because they checked for the class, and not for class inheritance (like compare.saemix), or because the initialize method was called for some reason. Therefore, the idea of creating a derived S4 class was abandoned. - A side effect of this decision is that the introduction of the saem generic opens the possibility to use the same generic also for other backends like nlmixr with the SAEM algorithm.
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke1-0/+1
Improve and update docs
2020-10-26Small editorial changeJohannes Ranke1-1/+1
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke1-0/+2
Update docs
2020-10-15Get current nlme version from CRAN on TravisJohannes Ranke1-2/+2
Also commit the dontrun instruction for saemix I had wanted to commit and switch back to devel mode for pkgdown
2020-10-15Update online docs for release versionJohannes Ranke1-2/+2
2020-10-08Fix issues for releaseJohannes Ranke1-2/+0
2020-05-27Change dev version label to info colorJohannes Ranke1-0/+1
instead of the orange danger color.
2020-05-27Create up to date pkgdown docs in development modeJohannes Ranke1-0/+3
2020-05-25First working version of saemix helper functionsJohannes Ranke1-0/+2
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-12Add a link to the benchmark vignette to the docsJohannes Ranke1-0/+2
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-0/+1
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke1-0/+1
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke1-0/+5
2020-04-04Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+1
2019-11-09Add a lack-of-fit testJohannes Ranke1-0/+1
- Switch an example dataset in the test setup to a dataset with replicates, adapt tests - Skip the test for lrtest with an update specification as it does not only fail when pkgdown generates static help pages, but also in testthat
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-0/+1
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke1-8/+11
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-26Fix checks and testsJohannes Ranke1-5/+7
Static documentation rebuilt by pkgdown
2019-10-21Improve tests, remove geometric_meanJohannes Ranke1-1/+0
2019-09-18Add url: tag to _pkgdown.ymlJohannes Ranke1-0/+2
Static documentation rebuilt by pkgdown
2019-06-19change to `superseded`Will Beasley1-1/+1
https://en.wiktionary.org/wiki/superseed
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-0/+2
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.
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke1-0/+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 Ranke1-0/+6

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