Age | Commit message (Collapse) | Author | Files | Lines |
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Thanks to Tomas Kalibera for his analysis of the problem on the
r-package-devel mailing list and for the suggestion on how to
fix it. See the current benchmark vignette for the new data
on mkin 1.1.1 with R 4.2.1, with unprecedented performance.
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Depends on inline >= 0.16.2 (including the bug fixes from
eddelbuettel/inline#18), which provides 'moveDLL' to store the DLL for a
compiled function in a safe place in case the argument 'dll_dir' is
specified in the call to 'mkinmod'.
Huge thanks to Dirk @eddelbuettel for his review and support
for the work on the inline package.
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With automatic reloading in mkinfit and mkinpredict in case the
DLL is not loaded and the original DLL path has been cleaned up.
Depends on jranke/inline@974bdea04fcedfafaab231e6f359c88270b56cb9
See inline#13
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By depending on parallel instead of importing it, functions to set up
and stop a cluster are always available when mkin is loaded.
The use of multicore processing in mmkin on Windows is now documented in
the help file, which brings mkin closer to a version 1.0 #9.
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This increases performance up to a factor of five!
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Still in preparation for analytical solutions of coupled models
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- Combine R/*.solution.R into R/parent_solutions.R
- Create a roxygen family of related functions
- Reduce redundancy by using the inherit tag
- Change the parent.0 argument to parent_0 to match
the corresponding parameter name used in mkinfit
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Preparing for symbolic solutions for more than one compound
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Roxygen update -> formatting changes in Rd files
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Also ignore test.R in the top level directory, as it is not meant to
be public
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Closes #6.
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- Only declare the time variable in the C code when needed in the
derivatives.
- Add the option to show verbose output of cfunction() when compiling
the model to a shared library.
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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.
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- Many thanks @karlines for the hint in ccSolve#1 how to declare
the time variable and for writing the ccSolve package in the first
place
- Add tests for the compiled versions of the FOMC and DFOP models
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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
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- As a consequence, we do not need implicit formation fractions in
mkinfit
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checklist
- Added the spec list the the mkinmod objects
- It seems that the GUI model editor is fully functional
- Version bump due to the changes in the mkinmod function arguments, thought they are backward compatible
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@107 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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- Check that initial values specified using parms.ini are actually needed for the model, stop otherwise
- List all formation fractions in the same place in the summary, also if they were fitted in the model
- Include an FOMC model coupled to two metabolites in the unit tests
- Some updates needed because of the above
- Update of static documentation including the vignettes
- Update of the mkin vignettes in the vignettes directory
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@82 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@65 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@59 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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- Small fix in mkinplot
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@45 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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than one SFORB submodel is used
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@38 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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- Now the eigenvalue based solutions are nicely consistent with the deSolve solutions, if enough
output times are specified (100, sometimes more are needed, see test.R)
- Workaround for invilr not to produce NaN values so often
- Still a lot to do (see TODO)
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@30 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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model specifications -
a variant with minimal use of formation fractions, and a variant with formation fractions everywhere.
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@26 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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