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2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke8-32/+51
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 Ranke5-24/+24
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
2020-05-12Address solaris platform dependence revealed on CRANJohannes Ranke1-1/+2
2020-05-11Release to CRANv0.9.50.1Johannes Ranke1-1/+2
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
2020-04-22Support 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 Ranke1-1/+3
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 Ranke4-5/+25
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 Ranke2-3/+3
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 Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-10-26Address some check and test failuresJohannes Ranke2-5/+5

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