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2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke2-5/+20
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Analytical solutions for all SFO variantsJohannes Ranke5-31/+64
2020-05-11Don't run visual tests on r-devel for nowJohannes Ranke2-0/+3
https://github.com/r-lib/vdiffr/issues/86
2020-05-11Reduce precision of traced parameters, formattingJohannes Ranke1-121/+121
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke3-14/+16
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 Ranke2-7/+16
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 Ranke3-2/+13
This increases performance up to a factor of five!
2020-05-08Roxygenize, adapt testsJohannes Ranke7-106/+111
2020-05-07Another overhaul of analytical solutionsJohannes Ranke7-73/+90
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
2020-05-06Formatting, 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

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