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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
2019-10-22Go back to d_3 for errmod = "obs"Johannes Ranke1-2/+2
in the hope that this makes plotting cross-platform also for this error model
2019-10-22Improved visual testingJohannes Ranke1-5/+5
2019-10-21Fix platform dependence of the correlation matrixJohannes Ranke1-9/+5
Especially on winbuilder (i386 and amd64)
2019-10-21Explicit solution_type for FOCUS D in testsJohannes Ranke1-5/+9
Because on winbuilder obviously gcc was not found, so the Eigenvalue based solution method was used, leading to a test failure when comparing the summary, as the solution method is listed
2019-10-21Tests all pass locallyJohannes Ranke1-1/+1
2019-10-21Improve some plotting routines, more testsJohannes Ranke1-5/+5
Static documentation rebuilt by pkgdown
2019-10-21Improve tests, remove geometric_meanJohannes Ranke1-10/+11
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-21/+21
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 Ranke1-7/+8
generated with mkin < 0.9.49.5
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-6/+6
2019-07-03Add check and test logsJohannes Ranke1-6/+6
2019-06-05Adapt tests to new algorithms and outputJohannes Ranke1-377/+9
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 Ranke1-9/+377
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 Ranke1-18/+13
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 Ranke1-9/+14
Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke1-8/+8
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
2019-05-02Improve testsJohannes Ranke1-19/+19
- Improve control of the number of cores - Reduce the precision of the correlation matrix in the test summary output, as the exact results are platform dependent

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