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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 Ranke5-6/+477
Static documentation rebuilt by pkgdown
2019-10-25Static documentation rebuilt by pkgdownJohannes Ranke48-1277/+1275
2019-10-21Quote percent signs in Rhelp filesJohannes Ranke2-16/+14
Static documentation rebuilt by pkgdown
2019-10-21Static documentation rebuilt by pkgdownJohannes Ranke7-32/+38
2019-10-21Improve some plotting routines, more testsJohannes Ranke8-21/+44
Static documentation rebuilt by pkgdown
2019-10-21Static documentation rebuilt by pkgdownJohannes Ranke2-9/+0
2019-10-21Improve tests, remove geometric_meanJohannes Ranke1-194/+0
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke2-90/+87
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 Ranke17-72/+534
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Static documentation rebuilt by pkgdownJohannes Ranke10-63/+63
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 Ranke12-66/+252
Static documentation rebuilt by pkgdown
2019-09-18Further corrections of the twa vignetteJohannes Ranke10-63/+63
Static documentation rebuilt by pkgdown
2019-09-18Correct and rebuild docsJohannes Ranke68-890/+1590
- 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 Ranke36-737/+954
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke83-1018/+827
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke14-71/+72
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke15-82/+82
Static documentation rebuilt by pkgdown
2019-06-05Add error model algorithm to outputJohannes Ranke15-102/+179
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke141-389/+671
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 Ranke26-87/+360
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 Ranke22-902/+940
Static documentation rebuilt by pkgdown
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke26-1047/+998
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke42-565/+575
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 Ranke10-70/+63
from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown
2019-05-02Prepare for CRAN releaseJohannes Ranke10-65/+63
- 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 Ranke70-397/+401
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke102-1798/+1863
- 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 Ranke14-903/+159
In order to avoid some unnecessary documentation rebuilds
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke23-608/+651
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke59-79/+262
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke40-99/+1275
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 Ranke18-88/+343
2019-02-25Static documentation rebuilt by current pkgdownJohannes Ranke60-146/+156
2019-02-25Add plotting tests, add nafta to pkgdownJohannes Ranke15-90/+96
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke18-89/+910
2019-02-22Static documentation rebuilt by pkgdownJohannes Ranke15-91/+92
2019-02-21Static documentation rebuilt by pkgdownJohannes Ranke12-81/+82
to get the codecov badge into the docs
2019-02-21Static documentation rebuilt by pkgdownJohannes Ranke55-161/+160
2019-02-21Make example logistic fit quietJohannes Ranke12-130/+84
2019-02-21Add the logistic modelJohannes Ranke19-101/+403
2019-01-31Restore NAMESPACEJohannes Ranke35-150/+2292
which was accidentally overwritten by pkgdown -> roxygen
2019-01-31Correct title for CAKE_exportJohannes Ranke7-34/+35
Add NEWS entry. Static documentation rebuilt by pkgdown
2019-01-31Static documentation rebuilt by pkgdownJohannes Ranke57-3119/+1236
2018-11-26Include AIC.mmkin to static docsJohannes Ranke11-80/+86
Static documentation rebuilt by pkgdown
2018-11-26Add AIC method for mmkin column objectsJohannes Ranke13-86/+305
Static documentation rebuilt by pkgdown

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