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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
2014-04-25McCall 2,4,5-T dataset, lower bound for transform_rates=FALSEJohannes Ranke1-1/+2
2013-09-25- Fixed the NOTES listed by R CMD checkjranke1-4/+2
Candidate for publication on CRAN git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@97 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-11- Testing of the new fitting process with transformed parameters shows that ↵jranke1-1/+11
it is less stable than the way of fitting used in mkin 0.8. Presumably this is due to the frequent presence of products of two parameters (formation fractions and kinetic rate constants) in the differential equations. - mkinmod documentation was adapted to the new version - Introduce vim fold markers to the mkinmod source for convenience git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@24 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-10- Fitting and summaries now work with the new parameter transformations.jranke1-0/+1
- The SFORB models with metabolites is broken (see TODO) - Moved the vignette to the location recommended since R 2.14 - Added the missing documentation - Commented out the schaefer_complex_case test, as this version of mkin is not able to fit a model without sink and therefore mkin estimated parameters are quite different git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@22 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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