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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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