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2023-08-10Merge branch 'main' into devJohannes Ranke1-0/+2
2023-08-10Add a link to the new vignette in online docsJohannes Ranke1-0/+2
2023-05-19Start next versionJohannes Ranke1-2/+2
2023-05-19Prepare release of v1.2.4v1.2.4Johannes Ranke1-2/+2
- 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
2023-04-20Switch docs back to devel modeJohannes Ranke1-2/+2
2023-04-17Post release changes to the docsJohannes Ranke1-2/+2
The cyantraniliprole and dmta pathway vignettes were not working any more with the latest changes in deSolve and mkin. All docs need a rebuild.
2023-01-28Build online HTML versions of prebuilt vignettesJohannes Ranke1-9/+23
Also, give some structure to the menu for selecting articles
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke1-1/+2
2022-11-22Start new development versionJohannes Ranke1-2/+2
2022-11-18Make mixed model test data permanent to ensure reproducibilityJohannes Ranke1-1/+2
To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package.
2022-11-17Complete update of online docs for v1.2.0Johannes Ranke1-2/+2
2022-11-14Add saem benchmarks to indexJohannes Ranke1-1/+3
2022-11-03Update docsJohannes Ranke1-0/+2
2022-10-29Update multistart docsJohannes Ranke1-2/+2
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

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