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2020-05-06Formatting, README update, color palette of R 4.xJohannes Ranke5-314/+314
2020-04-22Support SFORB with formation fractionsJohannes Ranke4-6/+21
2020-04-22Remove GPL header from test filesJohannes Ranke18-326/+0
2020-04-20Increase test tolerance for residualsJohannes Ranke2-3/+3
This was done to address the test failure on r-devel-linux-x86_64-debian-gcc on CRAN
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke4-16/+1
2020-04-17Fix summarizing old objectsJohannes Ranke1-1/+1
2020-04-17Add AIC, BIC and log likelihood to summary.mkinfitJohannes Ranke3-0/+15
2020-04-16Test the new endpoint function on nlme.mmkinJohannes Ranke1-0/+3
2020-04-16Increase test coverageJohannes Ranke2-2/+27
2020-04-09Add another visual test for coverageJohannes Ranke2-1/+135
2020-04-09Travis: Reduce another test toleranceJohannes Ranke1-1/+2
2020-04-09Tests on Travis: Residuals tolerance and skip another plotJohannes Ranke2-4/+4
2020-04-09Improve test coverage and fix nlme testJohannes Ranke6-5/+354
No idea why I had to do more assignments all of a sudden in test_nlme.R
2020-04-09Try mkinerrplot for obs and tc on Travis againJohannes Ranke2-1/+59
2020-04-08Use two assignments to avoid skipping another testJohannes Ranke1-1/+5
2020-04-08Make the nlme test file work with testthatJohannes Ranke2-3/+6
2020-04-07Add some tests for the nlme convenience functionsJohannes Ranke2-1/+64
2020-04-03Compiled models article, reduce distractionsJohannes Ranke1-1/+1
- Added a section with platform specific notes on getting compiled models to work to the compiled models article - Don't return empty SFORB parameter list from endpoints() if there is no SFORB model - Avoid warnings when using standardized = TRUE in plot.mmkin()
2020-03-31Static documentation rebuilt by pkgdownJohannes Ranke3-6/+6
2019-11-13Calculate Akaike weightsJohannes Ranke2-1/+13
2019-11-13Improve citationJohannes Ranke1-1/+2
2019-11-13Remove leftover lineJohannes Ranke1-2/+0
2019-11-09Add a lack-of-fit testJohannes Ranke4-11/+30
- 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 Ranke1-1/+1
2019-11-04Scaled residual plotsJohannes Ranke1-1/+1
2019-11-01Update link, increase tolerance of a test for Travisv0.9.49.7Johannes Ranke1-1/+1
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke3-2/+11
2019-10-31Increase tolerance of a test for winbuilderv0.9.49.6Johannes Ranke1-1/+1
- Update DESCRIPTION for release
2019-10-31Reorganize tests to reduce time on winbuilderJohannes Ranke8-52/+43
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 Ranke5-40/+82
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-28Fix the cutoff for likelihood based intervalsJohannes Ranke2-60/+45
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 Ranke2-7/+7
Static documentation rebuilt by pkgdown
2019-10-26Address some check and test failuresJohannes Ranke2-5/+5
2019-10-26parms and confint methodsJohannes Ranke2-53/+129
The confint method can do profile likelihood based confidence intervals!
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-1/+1
2019-10-22Somehow the figures weren't committed yetJohannes Ranke2-0/+195
2019-10-22Two more plotting testsJohannes Ranke1-0/+4
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 Ranke1-13/+13
in the hope that this makes plotting cross-platform also for this error model
2019-10-22Improved visual testingJohannes Ranke6-7/+479
2019-10-21Adress errors and notes on winbuilderJohannes Ranke2-13/+3
2019-10-21Fix platform dependence of the correlation matrixJohannes Ranke3-20/+5
Especially on winbuilder (i386 and amd64)
2019-10-21Explicit solution_type for FOCUS D in testsJohannes Ranke4-6/+147
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
2019-10-21Improve some plotting routines, more testsJohannes Ranke6-24/+664
Static documentation rebuilt by pkgdown
2019-10-21Improve tests, remove geometric_meanJohannes Ranke11-73/+351
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke7-137/+209
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 Ranke2-1/+30
generated with mkin < 0.9.49.5

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