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2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke1-17/+5
The reasons for this decision were - Creating an saemix generic in the saemix package caused problems with roxygen, because functions like saemix.plot.xy were documented in their help files as S3 methods, although explicitly exported with @export - Creating an saemix generic in this package is possible, but would make it necessary to load samix with exclude = "saemix" in order to avoid overwriting the generic when loading saemix. - The return object of such an saemix generic in this package cannot be an S3 class with class attribute c("saemix.mmkin", "SaemixObject") similar to nlme.mmkin, as saemix returns an S4 class. - Extending the S4 class SaemixObject using simple inheritance to a class SaemixMmkinObject with additional slots did not work as expected. When the initialize method was left untouched, it prevented creation of an SaemixMmkinObject even if it was based on an initialised SaemixObject, as the initialize method seems to always be called by new(). This could potentially be circumvented by a coerce method. If an alternative initialize method was used, an SaemixMmkinObject could be created. However, the methods written for SaemixObjects only worked in some instances, either because they checked for the class, and not for class inheritance (like compare.saemix), or because the initialize method was called for some reason. Therefore, the idea of creating a derived S4 class was abandoned. - A side effect of this decision is that the introduction of the saem generic opens the possibility to use the same generic also for other backends like nlmixr with the SAEM algorithm.
2020-11-07Make deSolve predictions within saemix robustJohannes Ranke1-0/+3
Also, exclude the saemix function when loading saemix in the example code, to prevent overriding our generic
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-1/+1
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-8/+5
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-09Avoid the call to merge for analytical solutionsJohannes Ranke1-15/+20
This increases performance up to a factor of five!
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-11/+11
Still in preparation for analytical solutions of coupled models
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-51/+57
Preparing for symbolic solutions for more than one compound
2020-03-30First nlme fits for models with a metaboliteJohannes Ranke1-16/+41
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-64/+69
2018-09-18Make mkinpredict generic and write a method for fitsJohannes Ranke1-16/+26
2016-11-17Remove trailing whitespace, clean headersJohannes Ranke1-13/+13
Also ignore test.R in the top level directory, as it is not meant to be public
2016-06-24TypoJohannes Ranke1-1/+1
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke1-1/+1
2015-04-16Check compiled mkinmod versions in examples and testsJohannes Ranke1-1/+23
Tests all pass (Linux)
2014-07-14Nearly complete support for IORE, pending mkinerrminJohannes Ranke1-7/+12
2013-12-04Make it possible to use different ode solvers=1-6/+11
2013-10-11Some additions, fixes and formatting of the help files for mkinfit and ↵jranke1-21/+22
mkinpredict. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@110 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-25- Fixed the NOTES listed by R CMD checkjranke1-11/+22
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
2013-03-04Small updates of two mkin help filesjranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@73 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-07-03- Add rtol argument in order to increase the precision of deSolve basedjranke1-12/+17
predictions for complex models - Improve default values for atol and set rtol default to 1e-10 git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@49 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-05-07- Moved the call to mkinerrmin to summary.mkinfitjranke1-1/+1
- The argument to mkinerrmin is now an object of class mkinfit - Fixed the allocation of parameters to observed variables in mkinerrmin git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@37 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-23- Fixed the example in the mkinmod documentationjranke1-5/+11
- Fixed the vignette - Did not fix the unit tests for mkinmod yet git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@31 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-10- Fitting and summaries now work with the new parameter transformations.jranke1-0/+63
- 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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