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2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke1-1/+1
2020-04-17Fix summarizing old objectsJohannes Ranke1-1/+1
2020-04-16Increase test coverageJohannes Ranke1-1/+1
2020-04-09Improve test coverage and fix nlme testJohannes Ranke1-1/+1
No idea why I had to do more assignments all of a sudden in test_nlme.R
2020-04-08Make the nlme test file work with testthatJohannes Ranke1-1/+1
2020-04-07Add some tests for the nlme convenience functionsJohannes Ranke1-1/+1
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 Ranke1-1/+1
2019-11-13Calculate Akaike weightsJohannes Ranke1-1/+1
2019-11-09Add a lack-of-fit testJohannes Ranke1-1/+1
- 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
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-1/+1
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke1-1/+1
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 Ranke1-1/+1
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 Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-1/+1
2019-10-22Improved visual testingJohannes Ranke1-1/+1
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-1/+1
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 Ranke1-1/+1
generated with mkin < 0.9.49.5
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2019-07-03Add check and test logsJohannes Ranke1-1/+1
2019-06-05Adapt tests to new algorithms and outputJohannes Ranke1-1/+1
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 Ranke1-1/+1
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 Ranke1-1/+1
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 Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke1-1/+1
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
2019-05-02Better initials for error model parametersJohannes Ranke1-1/+1
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-24Improve output and update testsJohannes Ranke1-1/+1
Remove skipped tests as I do not intend to reactivate them
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-1/+1
- 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 Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-02-27Fix CAKE export test to actually workJohannes Ranke1-1/+6
Also test the model specification via the link argument
2019-02-26Add another NAFTA dataset + testJohannes Ranke1-1/+1
2019-02-25Test CAKE exportJohannes Ranke1-0/+52

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