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2019-10-25Static documentation rebuilt by pkgdownJohannes Ranke1-225/+216
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.
2019-09-19Static documentation rebuilt by pkgdownJohannes Ranke1-14/+14
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Static documentation rebuilt by pkgdownJohannes Ranke1-14/+14
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 Ranke1-14/+14
Static documentation rebuilt by pkgdown
2019-09-18Further corrections of the twa vignetteJohannes Ranke1-14/+14
Static documentation rebuilt by pkgdown
2019-09-18Correct and rebuild docsJohannes Ranke1-46/+60
- 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 Ranke1-24/+22
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-22/+29
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke1-14/+14
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke1-15/+15
Static documentation rebuilt by pkgdown
2019-06-05Add error model algorithm to outputJohannes Ranke1-22/+28
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-84/+121
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 Ranke1-14/+14
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 Ranke1-72/+104
Static documentation rebuilt by pkgdown
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke1-190/+149
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke1-199/+203
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 Ranke1-13/+13
from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown
2019-05-02Prepare for CRAN releaseJohannes Ranke1-13/+13
- 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 Ranke1-109/+117
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-790/+357
- 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 Ranke1-22/+22
In order to avoid some unnecessary documentation rebuilds
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-23/+23
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-22/+25
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke1-22/+22
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 Ranke1-22/+22
2019-02-25Static documentation rebuilt by current pkgdownJohannes Ranke1-24/+24
2019-02-25Add plotting tests, add nafta to pkgdownJohannes Ranke1-23/+23
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke1-23/+23
2019-02-22Static documentation rebuilt by pkgdownJohannes Ranke1-23/+23
2019-02-21Static documentation rebuilt by pkgdownJohannes Ranke1-23/+23
to get the codecov badge into the docs
2019-02-21Static documentation rebuilt by pkgdownJohannes Ranke1-30/+30
2019-02-21Make example logistic fit quietJohannes Ranke1-21/+21
2019-02-21Add the logistic modelJohannes Ranke1-23/+23
2019-01-31Restore NAMESPACEJohannes Ranke1-16/+890
which was accidentally overwritten by pkgdown -> roxygen
2019-01-31Static documentation rebuilt by pkgdownJohannes Ranke1-916/+41
2018-11-26Include AIC.mmkin to static docsJohannes Ranke1-23/+23
Static documentation rebuilt by pkgdown
2018-11-26Add AIC method for mmkin column objectsJohannes Ranke1-23/+23
Static documentation rebuilt by pkgdown
2018-11-26Further improvement of the logLik.mkinfit helpJohannes Ranke1-22/+22
Static documentation rebuilt by pkgdown
2018-11-26Static documentation rebuilt by pkgdownJohannes Ranke1-22/+22
2018-11-26Support logLik and AIC for manual weightsJohannes Ranke1-22/+22
Static documentation rebuilt by pkgdown
2018-11-23Static documentation rebuilt by pkgdownJohannes Ranke1-21/+21
2018-11-23Static documentation rebuilt by pkgdownJohannes Ranke1-24/+26
2018-09-18Static documentation rebuilt by pkgdownJohannes Ranke1-23/+23
2018-09-18Support maximum twa for HS, test, docsJohannes Ranke1-31/+31
2018-09-14Skip more tests on CRANv0.9.47.5Johannes Ranke1-23/+23
Static documentation rebuilt by pkgdown
2018-09-14Skip some more tests on CRANJohannes Ranke1-23/+23
Static documentation rebuilt by pkgdown
2018-09-14Update NEWSJohannes Ranke1-23/+23
Static documentation rebuilt by pkgdown
2018-09-14Remove two vignettes from the package but not from docsJohannes Ranke1-33/+33
- Rebuild static documentation - Adapt test to new approach to two component error model where the model is inadequate
2018-09-14Exclude more example code from CRAN checksJohannes Ranke1-38/+798
to avoid NOTES about long execution times. Static documentation rebuilt by pkgdown with run_dont_run = TRUE

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