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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
2019-02-25Add plotting tests, add nafta to pkgdownJohannes Ranke1-0/+1
2019-02-21Add the logistic modelJohannes Ranke1-0/+1
2019-01-31Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2018-11-26Include AIC.mmkin to static docsJohannes Ranke1-0/+1
Static documentation rebuilt by pkgdown
2018-11-23Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2018-09-14Remove two vignettes from the package but not from docsJohannes Ranke1-2/+2
- Rebuild static documentation - Adapt test to new approach to two component error model where the model is inadequate
2018-07-18Correct references to the Rocke and Lorenzato modelJohannes Ranke1-1/+1
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
2018-01-30Reweighting with two-component error modelJohannes Ranke1-0/+1
Static documentation except articles rebuilt by pkgdown
2018-01-05Update _pkgdown.ymlJohannes Ranke1-0/+1
Static documentation except articles rebuilt by pkgdown
2017-09-14Convert FOCUS Z vignette to rmarkdown/htmlJohannes Ranke1-0/+2
- Static documentation rebuilt by pkgdown::build_articles() - DESCRIPTION: Version bump and current date
2017-07-21Rename twa to max_twa_parent, update docsJohannes Ranke1-3/+4
2017-05-05Static documentation except articles rebuilt by pkgdownJohannes Ranke1-0/+1
2017-05-05Static docs except articles rebuilt with current pkgdownJohannes Ranke1-1/+0
2017-03-28Change vignette format for twa vignette, update docsJohannes Ranke1-0/+2
2016-12-08Static documentation except articles rebuilt by pkgdownJohannes Ranke1-0/+2
2016-11-18Fix links in README, configure navbar, rebuild docsJohannes Ranke1-1/+1
2016-11-18Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)Johannes Ranke1-2/+19
Again with the jranke branch of jranke/pkgdown
2016-11-18Do not use ends_with to keep orderingJohannes Ranke1-1/+0
2016-11-18Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)Johannes Ranke1-2/+2
Using branch 'jranke' on jranke/pkgdown, fixing issues hadley/pgkdown#178 and hadley/pkgdown#213 Remove plot=TRUE from mkinfit calls also in dontrun sections of examples to avoid a flood png files documenting the progress of the fit.
2016-11-03Static documentation rebuilt by pkgdown::build_site()Johannes Ranke1-1/+6
Using pkgdown with PR hadley/pkgdown#212
2016-10-26Complete pkgdown conf, rerun with current master branchJohannes Ranke1-14/+42
2016-10-06Static documentation rebuilt by pkgdown::build_site()Johannes Ranke1-0/+32

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