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2019-10-21Improve tests, remove geometric_meanJohannes Ranke1-10/+11
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-21/+21
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.
2019-07-08Support summarizing older fitsJohannes Ranke1-7/+8
generated with mkin < 0.9.49.5
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-6/+6
2019-07-03Add check and test logsJohannes Ranke1-6/+6
2019-06-05Adapt tests to new algorithms and outputJohannes Ranke1-377/+9
One of the tests exceeded the number of iterations when using the d_3 error model algorithm, so only use "direct" in this case.
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-9/+377
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 Ranke1-18/+13
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 Ranke1-9/+14
Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke1-8/+8
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
2019-05-02Improve testsJohannes Ranke1-19/+19
- Improve control of the number of cores - Reduce the precision of the correlation matrix in the test summary output, as the exact results are platform dependent
2019-05-02Better initials for error model parametersJohannes Ranke1-11/+11
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-24Improve output and update testsJohannes Ranke1-29/+12
Remove skipped tests as I do not intend to reactivate them
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-17/+22
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-4/+4
Static documentation rebuilt by pkgdown
2019-02-27Further increase test coverageJohannes Ranke1-6/+7
2019-02-27Increase test coverageJohannes Ranke1-14/+16
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke1-28/+15
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0
2019-02-26Add another NAFTA dataset + testJohannes Ranke1-17/+26
2019-02-25Test CAKE exportJohannes Ranke1-14/+23
2019-02-25Basic test for two-component reweightingJohannes Ranke1-9/+9
2019-02-25Shorten path to test plotJohannes Ranke1-9/+9
2019-02-25Fix tests and add plot and print for naftaJohannes Ranke1-6/+9
2019-02-25Add plotting tests, add nafta to pkgdownJohannes Ranke1-9/+11
2019-02-21Add the logistic modelJohannes Ranke1-93/+19
2018-09-21Improve fitting the two-component error modelJohannes Ranke1-13/+91
with respect to accuracy and robustness.
2018-09-20Fix testsJohannes Ranke1-8/+10
2018-09-18Support maximum twa for HS, test, docsJohannes Ranke1-9/+11
2018-09-14Skip more tests on CRANv0.9.47.5Johannes Ranke1-7/+6
Static documentation rebuilt by pkgdown
2018-09-14Skip some more tests on CRANJohannes Ranke1-10/+8
Static documentation rebuilt by pkgdown
2018-09-14Remove two vignettes from the package but not from docsJohannes Ranke1-8/+10
- Rebuild static documentation - Adapt test to new approach to two component error model where the model is inadequate
2018-09-14Static documentation rebuilt by pkgdownJohannes Ranke1-10/+17
Also update test log
2018-01-30Reweighting with two-component error modelJohannes Ranke1-5/+1
Static documentation except articles rebuilt by pkgdown
2017-09-07Static documentation except articles rebuilt by pkgdownJohannes Ranke1-208/+0
2017-07-21Improve devtools::test() call, update logsJohannes Ranke1-1/+1
2017-07-21Fix tests, try FOMC ill-defined againJohannes Ranke1-5/+209
2016-12-21TWA calculation for SFO, FOMC and DFOP (parent)Johannes Ranke1-0/+1
2016-11-17RebuildJohannes Ranke1-10/+13
2016-06-28Test the package using devtools to get a test.logJohannes Ranke1-7/+18
2016-04-21Avoid unnecessary stop in edge case, improve warningsJohannes Ranke1-1/+1
mkinfit: Do not error out in cases where the fit converges, but the Jacobian for the untransformed model cost can not be estimated. Give a warning instead and return NA for the t-test results. summary.mkinfit: Give a warning message when the covariance matrix can not be obtained. A test has been added to containing such an edge case to check that the warnings are correctly issued and the fit does not terminate.
2015-07-21Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-8/+2
r-forge
2015-07-20Avoid error message for SFORB in endpoints, updatesJohannes Ranke1-1/+0
2015-06-30Improve calculation of DT90 in endpoints(), check and testJohannes Ranke1-0/+1
2015-06-26Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-1/+1
r-forge
2015-06-23Version bump, keep logs of build, check and testJohannes Ranke1-0/+13

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