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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
2019-10-21Static documentation rebuilt by pkgdownJohannes Ranke1-6/+0
2019-10-21Improve tests, remove geometric_meanJohannes Ranke1-194/+0
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-89/+83
mkinfit objects now include an ll() function to calculate the log-likelihood. Part of the code was refactored, hopefully making it easier to read and maintain. IRLS is currently the default algorithm for the error model "obs", for no particular reason. This may be subject to change when I get around to investigate. Slow tests are now in a separate subdirectory and will probably only be run by my own Makefile target. Formatting of test logs is improved. Roundtripping error model parameters works with a precision of 10% when we use lots of replicates in the synthetic data (see slow tests). This is not new in this commit, but as I think it is reasonable this closes #7.
2019-09-19Revert a change in the original add_err functionJohannes Ranke1-4/+4
that I made in the first attempt to work around the issue with the %in% operator in the example code Static documentation rebuilt by pkgdown
2019-09-19Static documentation rebuilt by pkgdownJohannes Ranke8-24/+486
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Static documentation rebuilt by pkgdownJohannes Ranke5-23/+23
to check if the link to the pfm package is correctly generated by pkgdown after preparing the pfm package docs accordingly
2019-09-18Add url: tag to _pkgdown.ymlJohannes Ranke5-23/+23
Static documentation rebuilt by pkgdown
2019-09-18Further corrections of the twa vignetteJohannes Ranke5-22/+22
Static documentation rebuilt by pkgdown
2019-09-18Correct and rebuild docsJohannes Ranke52-640/+1088
- Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown
2019-07-09Adaptations for gmkinJohannes Ranke7-38/+37
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke52-84/+91
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke5-21/+21
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke6-23/+23
Static documentation rebuilt by pkgdown
2019-06-05Add error model algorithm to outputJohannes Ranke7-39/+108
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke89-201/+474
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.
2019-05-08Add functionality to plot the error modelJohannes Ranke17-36/+308
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2019-05-07Fix hessian calculationsJohannes Ranke14-221/+300
Static documentation rebuilt by pkgdown

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