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2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke1-1/+1
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke2-15/+32
2020-04-17Fix summarizing old objectsJohannes Ranke1-6/+12
2020-04-17Add AIC, BIC and log likelihood to summary.mkinfitJohannes Ranke1-0/+7
2020-04-16mean_degparms: Fix rownames in random effectsJohannes Ranke1-1/+1
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke2-8/+36
2020-04-15Include random effects in starting parametersJohannes Ranke3-79/+131
- 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
2020-04-15Show fit information even if show_errmin = FALSEJohannes Ranke1-4/+5
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke2-4/+108
2020-04-14Add a nlme method for mmkin row objectsJohannes Ranke2-10/+92
2020-04-14Keep order of datasets in nlme_data, add a plotJohannes Ranke1-2/+9
2020-04-10Improve nlme function docsJohannes Ranke1-34/+33
2020-04-07Improve documentation of mmkin objectsJohannes Ranke1-2/+3
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke3-175/+219
2020-04-03Merge branch 'master' into mxkinJohannes Ranke4-95/+105
Merge DESCRIPTION manually to combine dependencies and rerun check to update check.log
2020-04-03Compiled models article, reduce distractionsJohannes Ranke2-10/+16
- 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 Ranke1-24/+29
2020-03-31Static documentation rebuilt by pkgdownJohannes Ranke1-2/+4
2020-03-30Don't check for gcc on the path in mkinmodJohannes Ranke1-60/+57
Roxygen update -> formatting changes in Rd files
2020-03-30Fixed example codeJohannes Ranke1-3/+2
2020-03-30First nlme fits for models with a metaboliteJohannes Ranke1-40/+78
2020-03-29First automatic generation of an nlme modelJohannes Ranke2-58/+133
2020-03-27Merge branch 'master' into mxkinJohannes Ranke7-29/+214
2020-03-18Clarify comment in example codeJohannes Ranke1-1/+1
2020-02-14Delete trailing whitespaceJohannes Ranke1-11/+11
2019-12-16Argument ymax for plot.mmkinJohannes Ranke1-10/+16
2019-12-09Consistently use "two-component error model"Johannes Ranke1-1/+1
instead of "two component error model"
2019-11-13Improve formatting using markdownJohannes Ranke1-9/+7
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+60
2019-11-13Likelihood ratio test for mmkin columns with two fitsJohannes Ranke1-3/+2
2019-11-12lrtest method for mmkin columns with two fitsJohannes Ranke1-0/+9
2019-11-09Add a lack-of-fit testJohannes Ranke2-5/+118
- 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
2019-11-06Attempt of an overall model for an mmkin rowJohannes Ranke1-0/+58
2019-11-05Fix standardized residual plots in 'plot_res'Johannes Ranke1-3/+5
2019-11-04Scaled residual plotsJohannes Ranke2-23/+50
2019-11-04Include fixed parameters in model names in lrtestJohannes Ranke2-8/+18
2019-11-01Another documentation fixJohannes Ranke1-3/+2
2019-11-01Make the 'quadratic' the default for 'confint'Johannes Ranke5-34/+54
Also the documentation was improved here and there
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke3-7/+35
2019-10-31Comment out example code that fails in pkgdownJohannes Ranke1-2/+5
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke6-18/+191
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-29Return single parameters correctly from confintJohannes Ranke1-11/+15
Static documentation rebuilt by pkgdown
2019-10-28Parallel computation for confidence intervalsJohannes Ranke1-18/+82
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/+16
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 Ranke2-1/+4
Static documentation rebuilt by pkgdown
2019-10-26Address some check and test failuresJohannes Ranke2-1/+2
2019-10-26parms and confint methodsJohannes Ranke3-22/+190
The confint method can do profile likelihood based confidence intervals!
2019-10-25Use roxygen for functions and methodsJohannes Ranke33-2087/+3364
2019-10-22Go back to d_3 for errmod = "obs"Johannes Ranke1-1/+1
in the hope that this makes plotting cross-platform also for this error model

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