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2019-12-16Argument ymax for plot.mmkinJohannes Ranke1-1/+3
2019-12-09Consistently use "two-component error model"Johannes Ranke1-1/+1
instead of "two component error model"
2019-11-13Improve formatting using markdownJohannes Ranke1-6/+6
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+47
2019-11-13Likelihood ratio test for mmkin columns with two fitsJohannes Ranke1-1/+5
2019-11-09Add a lack-of-fit testJohannes Ranke1-0/+81
- 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 Ranke1-3/+4
2019-11-04Scaled residual plotsJohannes Ranke2-9/+22
2019-11-04Include fixed parameters in model names in lrtestJohannes Ranke2-6/+10
2019-11-01Another documentation fixJohannes Ranke1-3/+2
2019-11-01Make the 'quadratic' the default for 'confint'Johannes Ranke5-34/+55
Also the documentation was improved here and there
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke2-1/+23
2019-10-31Comment out example code that fails in pkgdownJohannes Ranke1-2/+5
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke7-6/+122
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-29Return single parameters correctly from confintJohannes Ranke1-9/+11
Static documentation rebuilt by pkgdown
2019-10-28Parallel computation for confidence intervalsJohannes Ranke1-7/+72
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 Ranke1-0/+1
2019-10-28Fix the cutoff for likelihood based intervalsJohannes Ranke1-4/+13
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 Ranke2-3/+7
Static documentation rebuilt by pkgdown
2019-10-26parms and confint methodsJohannes Ranke2-0/+83
The confint method can do profile likelihood based confidence intervals!
2019-10-25Use roxygen for functions and methodsJohannes Ranke38-1705/+1656
2019-10-22Go back to d_3 for errmod = "obs"Johannes Ranke1-3/+2
in the hope that this makes plotting cross-platform also for this error model
2019-10-22Improved visual testingJohannes Ranke1-3/+0
2019-10-21Quote percent signs in Rhelp filesJohannes Ranke2-3/+3
Static documentation rebuilt by pkgdown
2019-10-21Adress errors and notes on winbuilderJohannes Ranke1-1/+1
2019-10-21Improve some plotting routines, more testsJohannes Ranke3-17/+40
Static documentation rebuilt by pkgdown
2019-10-21Improve tests, remove geometric_meanJohannes Ranke1-22/+0
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-10/+8
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 Ranke1-1/+1
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 Ranke1-146/+146
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-19Comment out the code of the add_err() functionJohannes Ranke1-148/+146
as it leads to problems with current pkgdown versions r-lib/pkgdown#1149
2019-09-18Correct and rebuild docsJohannes Ranke1-2/+42
- Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown
2019-09-02Some changes to improve plots on beamer slidesJohannes Ranke3-3/+13
2019-07-09Address winbuilder R-devel warning about usageJohannes Ranke2-2/+12
2019-07-09Adaptations for gmkinJohannes Ranke2-3/+10
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-1/+2
2019-07-02TypoJohannes Ranke1-1/+1
2019-06-04Add sources for test data for better transparencyJohannes Ranke1-0/+55
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke3-0/+44
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.
2019-05-31Experimental data for finding error model algorithmJohannes Ranke1-0/+65
2019-05-21Clarify the relation of the two-component error modelJohannes Ranke1-2/+3
in relation to the original version by Rocke and Lorenzato
2019-05-08Add functionality to plot the error modelJohannes Ranke3-7/+106
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2019-05-02Prepare for CRAN releaseJohannes Ranke1-1/+2
- Skip long running tests on CRAN as well to avoid timeout on winbuilder - Don't install benchmark results in the package, they are only needed in the git repository - Don't run example in man/add_err.Rd as it takes > 10 s on winbuilder - Rebuild docs
2019-05-02Better initials for error model parametersJohannes Ranke1-0/+7
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke10-182/+89
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-04-04Direct error model fitting worksJohannes Ranke1-29/+17
- No IRLS required - Removed optimization algorithms other than Port - Removed the dependency on FME - Fitting the error model 'obs' is much faster for the FOCUS_2006_D dataset and the FOMC_SFO model (1 second versus 3.4 seconds) - Vignettes build slower. Compiled models needs 3 minutes instead of 1.5 - For other vignettes, the trend is less clear. Some fits are faster, even for error_model = "const". FOCUS_Z is faster (34.9 s versus 44.1 s) - Standard errors and confidence intervals are slightly smaller - Removed code for plotting during the fit, as I hardly ever used it - Merged the two cost functions (using transformed and untransformed parameters) into one log-likelihood function
2019-03-04Make some example output more reproducibleJohannes Ranke3-11/+18
In order to avoid some unnecessary documentation rebuilds
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke2-1/+6
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke6-6/+45
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0

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