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2019-11-13Likelihood ratio test for mmkin columns with two fitsJohannes Ranke5-7/+15
2019-11-13Remove leftover lineJohannes Ranke1-2/+0
2019-11-12lrtest method for mmkin columns with two fitsJohannes Ranke1-0/+9
2019-11-09Add a lack-of-fit testJohannes Ranke20-27/+605
- 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 Ranke6-13/+17
2019-11-04Static documentation rebuilt by pkgdownJohannes Ranke9-16/+32
2019-11-04Scaled residual plotsJohannes Ranke10-45/+88
2019-11-04Include fixed parameters in model names in lrtestJohannes Ranke8-33/+68
2019-11-01Another documentation fixJohannes Ranke3-11/+8
2019-11-01Make the 'quadratic' the default for 'confint'Johannes Ranke25-471/+232
Also the documentation was improved here and there
2019-11-01Update link, increase tolerance of a test for Travisv0.9.49.7Johannes Ranke4-5/+5
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke94-2282/+362
2019-10-31Increase tolerance of a test for winbuilderv0.9.49.6Johannes Ranke2-2/+2
- Update DESCRIPTION for release
2019-10-31Reorganize tests to reduce time on winbuilderJohannes Ranke9-62/+52
2019-10-31Comment out example code that fails in pkgdownJohannes Ranke3-5/+16
2019-10-31More plots that are not reproducible on TravisJohannes Ranke1-1/+1
2019-10-31Increase numeric tolerance of three tests for TravisJohannes Ranke2-3/+3
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke33-129/+1672
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-29Return single parameters correctly from confintJohannes Ranke3-31/+48
Static documentation rebuilt by pkgdown
2019-10-28Parallel computation for confidence intervalsJohannes Ranke4-36/+268
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 Ranke3-2/+4
2019-10-28Fix the cutoff for likelihood based intervalsJohannes Ranke7-86/+105
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 Ranke15-33/+513
Static documentation rebuilt by pkgdown
2019-10-26Address some check and test failuresJohannes Ranke4-6/+7
2019-10-26parms and confint methodsJohannes Ranke9-75/+407
The confint method can do profile likelihood based confidence intervals!
2019-10-25Static documentation rebuilt by pkgdownJohannes Ranke48-1277/+1275
2019-10-25Use roxygen for functions and methodsJohannes Ranke75-3834/+5103
2019-10-22Somehow the figures weren't committed yetJohannes Ranke2-0/+195
2019-10-22Two more plotting testsJohannes Ranke2-4/+8
2019-10-22Update README.htmlJohannes Ranke1-15/+20
2019-10-22Skip the visual test that still fails on travisJohannes Ranke1-1/+2
2019-10-22Go back to d_3 for errmod = "obs"Johannes Ranke6-47/+20
in the hope that this makes plotting cross-platform also for this error model
2019-10-22Improved visual testingJohannes Ranke9-16/+487
2019-10-21Local checkJohannes Ranke1-6/+23
2019-10-21Quote percent signs in Rhelp filesJohannes Ranke4-19/+17
Static documentation rebuilt by pkgdown
2019-10-21Static documentation rebuilt by pkgdownJohannes Ranke7-32/+38
2019-10-21Adress errors and notes on winbuilderJohannes Ranke3-14/+4
2019-10-21Fix platform dependence of the correlation matrixJohannes Ranke4-29/+10
Especially on winbuilder (i386 and amd64)
2019-10-21Explicit solution_type for FOCUS D in testsJohannes Ranke5-11/+156
Because on winbuilder obviously gcc was not found, so the Eigenvalue based solution method was used, leading to a test failure when comparing the summary, as the solution method is listed
2019-10-21Skip an offensive test on TravisJohannes Ranke1-0/+1
2019-10-21Tests all pass locallyJohannes Ranke1-1/+1
2019-10-21Improve some plotting routines, more testsJohannes Ranke21-98/+792
Static documentation rebuilt by pkgdown
2019-10-21Static documentation rebuilt by pkgdownJohannes Ranke2-9/+0
2019-10-21Improve tests, remove geometric_meanJohannes Ranke16-304/+362
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke19-440/+535
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.
2019-10-21Improve test log formattingJohannes Ranke1-0/+1
2019-09-19Revert a change in the original add_err functionJohannes Ranke2-5/+5
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 Ranke20-219/+681
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
2019-09-18Static documentation rebuilt by pkgdownJohannes Ranke13-69/+67
to check if the link to the pfm package is correctly generated by pkgdown after preparing the pfm package docs accordingly

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