aboutsummaryrefslogtreecommitdiff
path: root/man
AgeCommit message (Collapse)AuthorFilesLines
2020-10-22Improve interface to experimental version of nlmeJohannes Ranke3-8/+66
The experimental nlme version in my drat repository contains the variance function structure varConstProp which makes it possible to use the two-component error model in generalized nonlinear models using nlme::gnls() and in mixed effects models using nlme::nlme().
2020-10-15More gentle example for saemix with combined error modelJohannes Ranke1-1/+2
2020-10-15Get current nlme version from CRAN on TravisJohannes Ranke1-1/+2
Also commit the dontrun instruction for saemix I had wanted to commit and switch back to devel mode for pkgdown
2020-10-15Updating docs of current dev versionJohannes Ranke1-1/+25
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-0/+54
2020-10-08Fix issues for releaseJohannes Ranke1-54/+0
2020-09-10Regenerate docs with current roxygenJohannes Ranke2-3/+5
2020-07-15Improve testsJohannes Ranke1-2/+3
- Reduce significant digits for the objective function output in mkinfit(..., quiet = FALSE) as R and R-devel gave different output on my system - Add makefile target 'devtest' for testing with R-devel, in order to fix problems showing up with R-devel on Travis
2020-05-29Improve handling of warnings, reorganize testsJohannes Ranke1-0/+65
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-63/+0
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.
2020-05-27Improve mkinmod docsJohannes Ranke1-26/+39
2020-05-26Use all cores per default, confint toleranceJohannes Ranke5-10/+31
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.
2020-05-25Tell travis where to find the required saemix versionJohannes Ranke1-6/+4
2020-05-25First working version of saemix helper functionsJohannes Ranke1-0/+43
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-15Improve docsJohannes Ranke1-7/+1
2020-05-15Use markdown links in mkinfit documentationJohannes Ranke1-24/+24
2020-05-14Update version number, better example formattingJohannes Ranke1-1/+4
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-2/+17
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke1-1/+1
2020-05-12Another documentation updateJohannes Ranke1-11/+8
2020-05-12Update vignettes and docsJohannes Ranke1-1/+1
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke7-7/+7
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke30-225/+236
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-1/+8
This is about twice as fast as deSolve compiled in the case of 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"

Contact - Imprint