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2020-11-06Make saemix an S3 generic in this packageJohannes Ranke3-59/+113
This commit also defined saemix.mmkin for mmkin row objects. This works fine, but if we set the class of the returned object to c("saemix.mmkin", "saemix"), it is not an S4 class any more which make it impossible to use saemix functions on it.
2020-11-06Update benchmarks for dev versionJohannes Ranke5-69/+129
2020-11-06Fast analytical solutions for saemix, update.mmkinJohannes Ranke56-741/+1454
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-11-05Fix mean_degparms() if only one optimised parameterJohannes Ranke1-5/+7
2020-11-05Fix link and update docsJohannes Ranke10-97/+121
2020-11-04Revert to use starting values for random effects in nlme.mmkinJohannes Ranke7-20/+10
2020-11-04Update dynamic docsJohannes Ranke2-9/+13
2020-11-04Deprecate cores > 1 in saemix_modelJohannes Ranke1-3/+5
2020-11-03Do not test residuals per default, improve nlme.mmkinJohannes Ranke3-7/+14
Do not give starting values for random effects in nlme.mmkin.
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke22-93/+949
Improve and update docs
2020-10-26Small editorial changeJohannes Ranke1-1/+1
2020-10-26Put the legend in its own area for plot.nlme.mmkinJohannes Ranke21-115/+121
2020-10-26Fix another bug in plot.nlme.mmkinJohannes Ranke1-1/+2
2020-10-26Fix a bug in plot.nlme.mmkinJohannes Ranke1-1/+3
2020-10-24Fix a bug for nlme with parent only, improve examplesJohannes Ranke13-150/+32
2020-10-24Improve plot layoutJohannes Ranke6-61/+23
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke20-189/+624
Update docs
2020-10-24Printing method for mmkin objectsJohannes Ranke3-8/+53
2020-10-22Really fix check for nlme::varConstPropJohannes Ranke4-6/+53
And add output for nlme fit translating the mkinfit error model "obs" into nlme::varIdent().
2020-10-22Fix check for nlme::varConstPropJohannes Ranke2-1/+1
2020-10-22Try 2 to make travis use nlme from my drat repoJohannes Ranke1-1/+3
2020-10-22Update pkgdown docsJohannes Ranke22-113/+201
2020-10-22Improve interface to experimental version of nlmeJohannes Ranke9-24/+158
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 Ranke11-49/+47
2020-10-15Get current nlme version from CRAN on TravisJohannes Ranke3-3/+6
Also commit the dontrun instruction for saemix I had wanted to commit and switch back to devel mode for pkgdown
2020-10-15Don't run saemix examples on travis for nowJohannes Ranke1-1/+2
2020-10-15Update online docs for release versionJohannes Ranke142-2297/+2727
2020-10-15Updating docs of current dev versionJohannes Ranke36-156/+522
2020-10-15Use my saemix repo for travisJohannes Ranke1-1/+1
The official repo is not installable at the moment
2020-10-15Reintroduce saemix helper functionsJohannes Ranke10-47/+273
2020-10-08saemix dev version is not installable at the momentJohannes Ranke1-2/+0
2020-10-08Fix another URL, add devcheck targetv0.9.50.3Johannes Ranke11-11/+85
2020-10-08Fix issues for releaseJohannes Ranke92-1670/+1285
2020-10-08Avoid dep on dev version of saemix for releaseJohannes Ranke3-139/+3
2020-09-10Regenerate docs with current roxygenJohannes Ranke3-4/+6
2020-09-01Merge branch 'master' of kolab.jrwb.de:mkinJohannes Ranke3-31/+1
2020-09-01Back-calculated DT50 values for biphasic modelsJohannes Ranke2-1/+12
2020-07-20Require upcoming nlme version, remove anova.nlme.mmkinJohannes Ranke3-31/+1
The method is no longer necessary, now that Bug 17761 is fixed upstream https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
2020-07-17mkinfit: Ignore unused components of state.iniJohannes Ranke5-6/+20
2020-07-15Bump date to trigger Travis build after clearing cacheJohannes Ranke1-1/+1
2020-07-15Merge branch 'master' of kolab.jrwb.de:mkinJohannes Ranke0-0/+0
2020-07-15Improve testsJohannes Ranke5-49/+90
- 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
2020-07-15Improve testsJohannes Ranke5-49/+90
- Reduce significant digits for mkinfit(..., quiet = TRUE) as R and R-devel were different on my system - Add makefile target 'devtest' for testing with R-devel, in order to fix problems showing up with R-devel on Travis
2020-07-15Improve handling of (partially) failing fitsJohannes Ranke6-31/+48
2020-07-15Use try() within mmkinJohannes Ranke1-1/+1
This keeps mmkin from stopping if one of the fits fails. Instead, a try-error is assigned to the respective position in the mmkin object.
2020-06-15vdiffr dev version not really necessaryJohannes Ranke1-1/+0
2020-06-15Test plots on r-devel onlyJohannes Ranke21-237/+252
following the arguments of Xavier Robin https://github.com/r-lib/vdiffr/issues/86#issuecomment-636447231
2020-06-15Use current devel version of vdiffr on TravisJohannes Ranke1-1/+3
2020-06-15Fix a bug, update for current vdiffrJohannes Ranke7-118/+17
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 Ranke14-166/+354

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