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2020-11-06Fast analytical solutions for saemix, update.mmkinJohannes Ranke1-9/+16
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-11-04Revert to use starting values for random effects in nlme.mmkinJohannes Ranke1-5/+5
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke1-10/+10
Improve and update docs
2020-10-08Fix issues for releaseJohannes Ranke1-10/+10
2020-07-17mkinfit: Ignore unused components of state.iniJohannes Ranke1-4/+5
2020-07-15Improve handling of (partially) failing fitsJohannes Ranke1-5/+5
2020-06-15Test plots on r-devel onlyJohannes Ranke1-14/+25
following the arguments of Xavier Robin https://github.com/r-lib/vdiffr/issues/86#issuecomment-636447231
2020-06-15Fix a bug, update for current vdiffrJohannes Ranke1-11/+11
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
2020-05-29Improve handling of warnings, reorganize testsJohannes Ranke1-19/+12
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-11/+18
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 Ranke1-7/+7
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-10/+10
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 Ranke1-5/+5
2020-05-11Release to CRANv0.9.50.1Johannes Ranke1-3/+3
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-8/+8
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Analytical solutions for all SFO variantsJohannes Ranke1-27/+16
2020-05-11Don't run visual tests on r-devel for nowJohannes Ranke1-14/+25
https://github.com/r-lib/vdiffr/issues/86
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-10/+10
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 Ranke1-10/+10
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 Ranke1-16/+17
This increases performance up to a factor of five!
2020-05-08We do not need the n.outtimes argument for mkinfitJohannes Ranke1-9/+9
As we set the tolerance for ode() appropriately
2020-05-08Avoid duplicate merge in tc error model fitJohannes Ranke1-11/+11
This increases the performance in the complete test suite by about 20 secs from 120 to around 100 secs. I tried improving merge speed by using data.table on another branch, but this did not give a noticeable performance gain.
2020-05-08Slight performance gain by reducing default n.outtimesJohannes Ranke1-14/+14
2020-05-08Roxygenize, adapt testsJohannes Ranke1-7/+7
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-11/+11
Still in preparation for analytical solutions of coupled models
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-15/+15
Preparing for symbolic solutions for more than one compound
2020-04-22Support SFORB with formation fractionsJohannes Ranke1-9/+9
2020-04-20Increase test tolerance for residualsJohannes Ranke1-4/+4
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 Ranke1-9/+7
2020-04-17Fix summarizing old objectsJohannes Ranke1-7/+9
2020-04-16Increase test coverageJohannes Ranke1-10/+10
2020-04-09Add another visual test for coverageJohannes Ranke1-16/+16
2020-04-09Improve test coverage and fix nlme testJohannes Ranke1-16/+16
No idea why I had to do more assignments all of a sudden in test_nlme.R
2020-04-08Use two assignments to avoid skipping another testJohannes Ranke1-15/+11
2020-04-08Make the nlme test file work with testthatJohannes Ranke1-19/+10
2020-04-07Add some tests for the nlme convenience functionsJohannes Ranke1-9/+19
2020-04-03Compiled models article, reduce distractionsJohannes Ranke1-15/+15
- 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()
2020-03-31Use inline documentation for R6 class mkindsJohannes Ranke1-30/+15
2020-03-31Static documentation rebuilt by pkgdownJohannes Ranke1-18/+33
2019-11-13Calculate Akaike weightsJohannes Ranke1-10/+11
2019-11-09Add a lack-of-fit testJohannes Ranke1-11/+15
- 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 Ranke1-2/+2
2019-11-04Scaled residual plotsJohannes Ranke1-10/+10
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-12/+12
2019-10-31Reorganize tests to reduce time on winbuilderJohannes Ranke1-10/+9
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke1-7/+10
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 Ranke1-8/+8
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 Ranke1-9/+9
Static documentation rebuilt by pkgdown
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-4/+4
2019-10-22Two more plotting testsJohannes Ranke1-4/+4

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