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2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-1/+8
This is about twice as fast as deSolve compiled with FOCUS D
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-8/+5
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-09Avoid the call to merge for analytical solutionsJohannes Ranke4-22/+22
This increases performance up to a factor of five!
2020-05-08Slight performance gain by reducing default n.outtimesJohannes Ranke1-2/+2
2020-05-08Roxygenize, adapt testsJohannes Ranke1-1/+10
2020-05-07Another overhaul of analytical solutionsJohannes Ranke7-61/+86
Still in preparation for analytical solutions of coupled models
2020-05-07Merge parent solutions to one fileJohannes Ranke1-0/+6
- Combine R/*.solution.R into R/parent_solutions.R - Create a roxygen family of related functions - Reduce redundancy by using the inherit tag - Change the parent.0 argument to parent_0 to match the corresponding parameter name used in mkinfit
2020-05-07Static documentation rebuilt by pkgdownJohannes Ranke7-48/+143
2020-05-06Change implementation of analytical solutionsJohannes Ranke3-55/+63
Preparing for symbolic solutions for more than one compound
2020-04-22Support SFORB with formation fractionsJohannes Ranke1-2/+2
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke2-2/+17
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke2-2/+15
2020-04-15Include random effects in starting parametersJohannes Ranke4-73/+86
- mean_degparms() now optionally returns starting values for fixed and random effects, which makes it possible to obtain acceptable fits also in more difficult cases (with more parameters) - Fix the anova method, as it is currently not enough to inherit from lme: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761 - Show fit information, and per default also errmin information in plot.nlme.mmkin() - Examples for nlme.mmkin: Decrease tolerance and increase the number of iterations in the PNLS step in order to be able to fit FOMC-SFO and DFOP-SFO
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke3-4/+76
2020-04-14Add a nlme method for mmkin row objectsJohannes Ranke2-9/+78
2020-04-14Keep order of datasets in nlme_data, add a plotJohannes Ranke1-1/+7
2020-04-10Improve nlme function docsJohannes Ranke1-9/+9
2020-04-07Add some tests for the nlme convenience functionsJohannes Ranke1-2/+3
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke3-89/+140
2020-04-03Merge branch 'master' into mxkinJohannes Ranke4-20/+44
Merge DESCRIPTION manually to combine dependencies and rerun check to update check.log
2020-04-03Compiled models article, reduce distractionsJohannes Ranke2-1/+6
- 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 Ranke2-19/+38
2020-03-30Don't check for gcc on the path in mkinmodJohannes Ranke15-82/+246
Roxygen update -> formatting changes in Rd files
2020-03-30Fixed example codeJohannes Ranke1-8/+20
2020-03-30First nlme fits for models with a metaboliteJohannes Ranke16-82/+318
2019-12-16Argument ymax for plot.mmkinJohannes Ranke1-1/+3
2019-12-09Consistently use "two-component error model"Johannes Ranke1-1/+1
instead of "two component error model"
2019-11-13Improve formatting using markdownJohannes Ranke1-6/+6
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+47
2019-11-13Likelihood ratio test for mmkin columns with two fitsJohannes Ranke1-1/+5
2019-11-09Add a lack-of-fit testJohannes Ranke1-0/+81
- 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 Ranke1-3/+4
2019-11-04Scaled residual plotsJohannes Ranke2-9/+22
2019-11-04Include fixed parameters in model names in lrtestJohannes Ranke2-6/+10
2019-11-01Another documentation fixJohannes Ranke1-3/+2
2019-11-01Make the 'quadratic' the default for 'confint'Johannes Ranke5-34/+55
Also the documentation was improved here and there
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke2-1/+23
2019-10-31Comment out example code that fails in pkgdownJohannes Ranke1-2/+5
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke7-6/+122
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-29Return single parameters correctly from confintJohannes Ranke1-9/+11
Static documentation rebuilt by pkgdown
2019-10-28Parallel computation for confidence intervalsJohannes Ranke1-7/+72
Only on Linux at the moment. Some more examples in the help page. Remove the distribution argument for the quadratic method
2019-10-28Improve formattingJohannes Ranke1-0/+1
2019-10-28Fix the cutoff for likelihood based intervalsJohannes Ranke1-4/+13
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 Ranke2-3/+7
Static documentation rebuilt by pkgdown
2019-10-26parms and confint methodsJohannes Ranke2-0/+83
The confint method can do profile likelihood based confidence intervals!
2019-10-25Use roxygen for functions and methodsJohannes Ranke38-1705/+1656
2019-10-22Go back to d_3 for errmod = "obs"Johannes Ranke1-3/+2
in the hope that this makes plotting cross-platform also for this error model
2019-10-22Improved visual testingJohannes Ranke1-3/+0
2019-10-21Quote percent signs in Rhelp filesJohannes Ranke2-3/+3
Static documentation rebuilt by pkgdown
2019-10-21Adress errors and notes on winbuilderJohannes Ranke1-1/+1

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