aboutsummaryrefslogtreecommitdiff
path: root/R/transform_odeparms.R
AgeCommit message (Collapse)AuthorFilesLines
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-5/+1
I am postponing my attempts to get the nlmixr interface to CRAN, given some problems with nlmixr using R-devel under Windows, see https://github.com/nlmixrdevelopment/nlmixr/issues/596 and https://github.com/r-hub/rhub/issues/512, which is fixed by the removal of nlmixr from the testsuite. For the tests to be more platform independent, the biphasic mixed effects models test dataset was defined in a way that fitting should be more robust (less ill-defined).
2021-06-17Let backtransform_odeparms handle nlmixr formation fractionsJohannes Ranke1-4/+9
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-7/+11
The errors in the example code were in the \dontrun sections, so they were not caught by CRAN checks. In addition, the static help files generated with pkgdown were cached, so I noticed the errors only after completely regenerating the documentation for version 1.0.0.
2020-11-06Fast analytical solutions for saemix, update.mmkinJohannes Ranke1-22/+39
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-05-15Improve docsJohannes Ranke1-16/+14
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-1/+1
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-180/+258
2019-02-21Add the logistic modelJohannes Ranke1-5/+6
2016-11-17Remove trailing whitespace, clean headersJohannes Ranke1-5/+5
Also ignore test.R in the top level directory, as it is not meant to be public
2015-06-20Low-level generation of compiled modelsJohannes Ranke1-6/+6
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.
2014-11-12IORE working for parent and metabolites, introduce mkinsubJohannes Ranke1-2/+3
2014-11-12Merge branch 'master' into ioreJohannes Ranke1-9/+28
2014-07-25Fix internal naming of g for transform_fractions=FALSEJohannes Ranke1-2/+13
2014-07-21Bugfix, model shorthand, state.ini[[1]] from observed dataJohannes Ranke1-7/+15
- The bug occurred when using transform_rates=FALSE for FOMC, DFOP or HS - Make it possible to use mkinfit("SFO", ...) - Take initial mean value at time zero for the variable with the highest value in the observed data - Update of vignette/FOCUS_L - Improve the Makefile to build single vignettes
2014-07-12First working fits with IORE modelJohannes Ranke1-1/+13
2014-07-02Move handling of implicitly fixed formation fractions to mkinfitJohannes Ranke1-6/+0
2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke1-38/+89
2014-06-25Remove old ID tag, improve commentJohannes Ranke1-1/+2
2014-05-20Step back regarding confidence intervals of formation fractionsJohannes Ranke1-2/+2
- Don't give confidence intervals for formation fractions that belong to a set, only for single formation fractions - Update the vignette with history and background - Correct 'isotropic' into 'isometric' in the ilr documentation, the README and the comments in transform_odeparms - Candidate for release to CRAN
2014-04-28Fix a bug recently introduced to the Hockey stick modelJohannes Ranke1-3/+3
2014-04-25McCall 2,4,5-T dataset, lower bound for transform_rates=FALSEJohannes Ranke1-2/+2
2014-04-22Possibility to fit without parameter transformationJohannes Ranke1-16/+25
2013-02-17- Added the examples vignette to the kinfit packagejranke1-0/+20
- Added calls to utils::globalVariables to make R CMD check pass cleanly without NOTES git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@62 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-10- Fitting and summaries now work with the new parameter transformations.jranke1-22/+48
- 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
2012-04-03- Separated model prediction out into a separate functionjranke1-0/+46
- Created separate functions for parameter transformations (not documented yet) - Fitting of analytical models works - SFO_SFO model works, complex models do not at the moment - summary.mkinfit not operational at the moment git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@21 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

Contact - Imprint