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2020-07-15Improve handling of (partially) failing fitsJohannes Ranke1-1/+1
2020-06-15Fix a bug, update for current vdiffrJohannes Ranke1-1/+1
Vignette FOCUS_L failed as I had introduced a bug in the handling of warnings. Current vdiffr only runs visual tests if R < 4.1.0, skipping r-devel for now, see https://github.com/r-lib/vdiffr/commit/630a29d013361fd63fea242f531e2db6aef37919
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-1/+1
This revealed a bug in the data returned in mkinfit$data in the case of the d_3 algorithm, which also affected the residual plot - the data from the direct fitting was not returned even if this was the better method.
2020-05-28use_of_ff = "max" for shorthand models like "SFO"Johannes Ranke1-1/+1
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-1/+1
Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.
2020-05-12Rerun tests and checks, CRAN commentsJohannes Ranke1-1/+1
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-1/+1
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-10Default to analytical for coupled models if availableJohannes Ranke1-1/+1
This revealed that transforming rates is necessary for fitting the analytical solution of the SFO-SFO model to the FOCUS D dataset. Benchmarks show that fitting coupled models with deSolve got a bit slower through the latest changes
2020-05-09Avoid the call to merge for analytical solutionsJohannes Ranke1-1/+1
This increases performance up to a factor of five!
2020-05-08Roxygenize, adapt testsJohannes Ranke1-1/+1
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-1/+1
Still in preparation for analytical solutions of coupled models
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-1/+1
Preparing for symbolic solutions for more than one compound
2020-04-22Support SFORB with formation fractionsJohannes Ranke1-1/+1
2020-04-20Increase test tolerance for residualsJohannes Ranke1-1/+1
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 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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