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2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke1-0/+3
Improve and update docs
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke1-0/+1
Update docs
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-0/+5
2020-10-08Fix issues for releaseJohannes Ranke1-5/+0
2020-07-20Require upcoming nlme version, remove anova.nlme.mmkinJohannes Ranke1-1/+0
The method is no longer necessary, now that Bug 17761 is fixed upstream https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-0/+1
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.
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-0/+1
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 Ranke1-0/+2
2020-05-25First working version of saemix helper functionsJohannes Ranke1-0/+2
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-0/+1
2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke1-0/+1
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke1-0/+2
2020-04-15Include random effects in starting parametersJohannes Ranke1-0/+3
- 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 Ranke1-0/+2
2020-04-14Add a nlme method for mmkin row objectsJohannes Ranke1-0/+2
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke1-1/+3
2020-04-03Merge branch 'master' into mxkinJohannes Ranke1-0/+1
Merge DESCRIPTION manually to combine dependencies and rerun check to update check.log
2020-03-31Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2020-03-30First nlme fits for models with a metaboliteJohannes Ranke1-0/+3
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+3
2019-11-13Likelihood ratio test for mmkin columns with two fitsJohannes Ranke1-0/+1
2019-11-09Add a lack-of-fit testJohannes Ranke1-0/+5
- 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
2019-11-04Scaled residual plotsJohannes Ranke1-0/+1
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-0/+5
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke1-0/+7
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-26Fix checks and testsJohannes Ranke1-0/+1
Static documentation rebuilt by pkgdown
2019-10-26parms and confint methodsJohannes Ranke1-0/+3
The confint method can do profile likelihood based confidence intervals!
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-34/+72
2019-04-04Direct error model fitting worksJohannes Ranke1-3/+1
- No IRLS required - Removed optimization algorithms other than Port - Removed the dependency on FME - Fitting the error model 'obs' is much faster for the FOCUS_2006_D dataset and the FOMC_SFO model (1 second versus 3.4 seconds) - Vignettes build slower. Compiled models needs 3 minutes instead of 1.5 - For other vignettes, the trend is less clear. Some fits are faster, even for error_model = "const". FOCUS_Z is faster (34.9 s versus 44.1 s) - Standard errors and confidence intervals are slightly smaller - Removed code for plotting during the fit, as I hardly ever used it - Merged the two cost functions (using transformed and untransformed parameters) into one log-likelihood function
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke1-4/+12
2019-01-31Restore NAMESPACEJohannes Ranke1-4/+28
which was accidentally overwritten by pkgdown -> roxygen
2019-01-31Static documentation rebuilt by pkgdownJohannes Ranke1-28/+4
2019-01-31Export to CAKE study fileJohannes Ranke1-0/+1
2018-11-26Add AIC method for mmkin column objectsJohannes Ranke1-0/+1
Static documentation rebuilt by pkgdown
2018-11-23Fix namespace declarationJohannes Ranke1-1/+1
2018-11-23Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2018-09-21Improve fitting the two-component error modelJohannes Ranke1-1/+2
with respect to accuracy and robustness.
2018-09-18Make mkinpredict generic and write a method for fitsJohannes Ranke1-0/+2
2016-12-07Use latex in plots when using tikzDeviceJohannes Ranke1-0/+1
2015-11-09Export print.mkinds and rebuild vignettesJohannes Ranke1-0/+1
2015-10-19Add the R6 class mkindsJohannes Ranke1-0/+1
2015-10-19Add a print method for mkinmod objectsJohannes Ranke1-0/+1
2015-07-20Avoid error message for SFORB in endpoints, updatesJohannes Ranke1-1/+2
2015-06-30Start to import or qualify functions from stats, utils et al.Johannes Ranke1-1/+2
2015-06-26Subsetting and plotting for mmkin objectsJohannes Ranke1-0/+2
Including documentation and documentation improvements for mmkin().
2015-06-25Small fixesJohannes Ranke1-1/+2
2015-06-20Low-level generation of compiled modelsJohannes Ranke1-1/+2
As it is unclear if and when ccSolve will be published on CRAN, the generation, compilation and use of the C version of the system of differential equations was developed for mkin, inspired and guided by the code from the ccSolve package. Many thanks again to Karline Soetaert for all of her work on this and other R packages. Now all model types, including the Hockey-Stick model for the parent compund and the IORE model for parent and/or metabolites can be compiled.
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke1-3/+2
2015-04-14Compile differential equation models with ccSolve packageJohannes Ranke1-1/+2
If the ccSolve package is available, and time is not in the right hand side of the equations (i.e. if only SFO and SFORB models are used), the differential equation model is compiled from auto-generated C code. Currently, one test (FOCUS 2006 D SFO_SFO) fails
2015-02-21Avoid NOTES in R CMD checkJohannes Ranke1-0/+3
- Export S3 methods - Avoid using undeclared variable names

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