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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.
2019-10-29Return single parameters correctly from confintJohannes Ranke1-11/+22
Static documentation rebuilt by pkgdown
2019-10-28Parallel computation for confidence intervalsJohannes Ranke1-10/+113
Only on Linux at the moment. Some more examples in the help page. Remove the distribution argument for the quadratic method
2019-10-28Improve formattingJohannes Ranke1-2/+2
2019-10-28Fix the cutoff for likelihood based intervalsJohannes Ranke1-9/+22
The cutoff now matches what is given by Venzon and Moolgavkar (1988). Also, confidence intervals closely match intervals obtained with stats4::confint in the test case where an stats4::mle object is created from the likelihood function in one test case. Static documentation rebuilt by pkgdown
2019-10-26Fix checks and testsJohannes Ranke3-6/+470
Static documentation rebuilt by pkgdown
2019-10-25Static documentation rebuilt by pkgdownJohannes Ranke44-1272/+1273
2019-10-21Quote percent signs in Rhelp filesJohannes Ranke2-16/+14
Static documentation rebuilt by pkgdown
2019-10-21Static documentation rebuilt by pkgdownJohannes Ranke3-28/+22
2019-10-21Improve some plotting routines, more testsJohannes Ranke8-21/+44
Static documentation rebuilt by pkgdown

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