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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
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke15-390/+300
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke22-277/+282
Now we have a three stage fitting process for nonconstant error models: - Unweighted least squares - Only optimize the error model - Optimize both Static documentation rebuilt by pkgdown
2019-05-02Remove reference to archived kinfit packageJohannes Ranke5-20/+20
from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown
2019-05-02Prepare for CRAN releaseJohannes Ranke6-23/+21
- 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 Ranke31-175/+183
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke69-1170/+721
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-03-04Make some example output more reproducibleJohannes Ranke10-870/+126
In order to avoid some unnecessary documentation rebuilds
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke14-104/+108
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke50-53/+209
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke16-75/+310
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 Ranke12-54/+309
2019-02-25Static documentation rebuilt by current pkgdownJohannes Ranke49-106/+116
2019-02-25Add plotting tests, add nafta to pkgdownJohannes Ranke9-55/+61
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke14-56/+876
2019-02-22Static documentation rebuilt by pkgdownJohannes Ranke9-57/+58
2019-02-21Static documentation rebuilt by pkgdownJohannes Ranke8-54/+54
to get the codecov badge into the docs
2019-02-21Static documentation rebuilt by pkgdownJohannes Ranke45-114/+113
2019-02-21Make example logistic fit quietJohannes Ranke9-100/+54

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