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2021-02-24Rebuild docsJohannes Ranke7-3/+3
2021-02-15Correct grant numbers in README, update docsJohannes Ranke2-0/+0
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke111-304/+298
Also bump version to 1.0.3.
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke7-3/+3
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke14-116/+148
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 Ranke125-1124/+4265
- 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 Ranke86-1479/+1596
2020-05-27Add docs generated using released version 0.9.52Johannes Ranke39-855/+308
2020-05-26Use all cores per default, confint toleranceJohannes Ranke7-104/+77
Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.
2020-05-25First working version of saemix helper functionsJohannes Ranke11-23/+520
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
2020-05-14Update version number, better example formattingJohannes Ranke2-16/+8
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-3/+80
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke2-11/+14
2020-05-12Another documentation updateJohannes Ranke1-22/+22
2020-05-12Add a link to the benchmark vignette to the docsJohannes Ranke1-0/+3
2020-05-12Update vignettes and docsJohannes Ranke67-777/+882
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke8-103/+88
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke49-870/+906
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke2-4/+14
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke13-270/+398
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-07Another overhaul of analytical solutionsJohannes Ranke12-118/+347
Still in preparation for analytical solutions of coupled models
2020-05-07Merge parent solutions to one fileJohannes Ranke6-6/+46
- Combine R/*.solution.R into R/parent_solutions.R - Create a roxygen family of related functions - Reduce redundancy by using the inherit tag - Change the parent.0 argument to parent_0 to match the corresponding parameter name used in mkinfit
2020-05-07Static documentation rebuilt by pkgdownJohannes Ranke14-581/+582
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke3-27/+21
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke3-6/+188
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke2-10/+48
2020-04-15Include random effects in starting parametersJohannes Ranke17-84/+200
- mean_degparms() now optionally returns starting values for fixed and random effects, which makes it possible to obtain acceptable fits also in more difficult cases (with more parameters) - Fix the anova method, as it is currently not enough to inherit from lme: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761 - Show fit information, and per default also errmin information in plot.nlme.mmkin() - Examples for nlme.mmkin: Decrease tolerance and increase the number of iterations in the PNLS step in order to be able to fit FOMC-SFO and DFOP-SFO
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke5-16/+592
2020-04-14Keep order of datasets in nlme_data, add a plotJohannes Ranke2-2/+34
2020-04-10Improve nlme function docsJohannes Ranke7-26/+114
2020-04-04Static documentation rebuilt by pkgdownJohannes Ranke3-5/+211
2020-04-03Compiled models article, reduce distractionsJohannes Ranke2-4/+8
- Added a section with platform specific notes on getting compiled models to work to the compiled models article - Don't return empty SFORB parameter list from endpoints() if there is no SFORB model - Avoid warnings when using standardized = TRUE in plot.mmkin()
2020-03-31Use inline documentation for R6 class mkindsJohannes Ranke2-26/+44
2020-03-30Static documentation rebuilt by pkgdownJohannes Ranke22-214/+353
2020-01-09Remove unused FME package from DESCRIPTION textJohannes Ranke2-2/+2
2019-12-16Argument ymax for plot.mmkinJohannes Ranke1-2/+6
2019-12-09Consistently use "two-component error model"Johannes Ranke2-5/+5
instead of "two component error model"
2019-11-13Improve formatting using markdownJohannes Ranke1-6/+6
2019-11-13Calculate Akaike weightsJohannes Ranke2-0/+220
2019-11-13Likelihood ratio test for mmkin columns with two fitsJohannes Ranke2-3/+7
2019-11-09Add a lack-of-fit testJohannes Ranke7-0/+349
- 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
2019-11-05Fix standardized residual plots in 'plot_res'Johannes Ranke2-4/+5
2019-11-04Static documentation rebuilt by pkgdownJohannes Ranke8-16/+31
2019-11-04Include fixed parameters in model names in lrtestJohannes Ranke2-16/+34
2019-11-01Another documentation fixJohannes Ranke1-5/+4
2019-11-01Make the 'quadratic' the default for 'confint'Johannes Ranke8-397/+104
Also the documentation was improved here and there
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke31-627/+141
2019-10-31Comment out example code that fails in pkgdownJohannes Ranke1-1/+6
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke8-49/+1223
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.

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