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2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke1-1/+1
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke1-1/+1
2022-11-16We get about 25% performance gainJohannes Ranke1-1/+3
with the custom lsoda call, avoiding repeated getNativeSymbolInfo calls. It's just that we should not be calling foreign functions from different packages, because the may change without notice. Using getNativeSymbolInfo for "call_lsoda" avoids the CRAN note, and a similar call could probably be used for "unlock_solver", avoiding the NOTE in checks for cran, but we should not do this in a CRAN package.
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke1-3/+0
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2020-12-08mixed.mmkin and test coverageJohannes Ranke1-2/+2
2020-11-30Log-Cholesky parameterisation as default in nlme.mmkinJohannes Ranke1-1/+5
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke1-6/+21
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.
2020-11-24Support storing mkinmod compiled code as CFunc objectsJohannes Ranke1-16/+15
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
2020-11-19Depend on parallel, doc improvementsJohannes Ranke1-7/+50
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.
2020-05-27Improve mkinmod docsJohannes Ranke1-26/+39
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke1-27/+32
2020-05-09Avoid the call to merge for analytical solutionsJohannes Ranke1-1/+1
This increases performance up to a factor of five!
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-1/+1
Still in preparation for analytical solutions of coupled models
2020-04-22Support SFORB with formation fractionsJohannes Ranke1-2/+2
2020-03-30First nlme fits for models with a metaboliteJohannes Ranke1-2/+7
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-115/+123
2017-07-21Fix URLsJohannes Ranke1-1/+1
2017-05-05Static docs except articles rebuilt with current pkgdownJohannes Ranke1-1/+1
2015-11-09Exclude more mkinmod examples, as winbuilder NOTEs > 5 sJohannes Ranke1-1/+1
2015-07-22Remove periods in help file titlesJohannes Ranke1-1/+1
2015-06-23Hopefully fix compiling on Solaris, verbose optionJohannes Ranke1-2/+11
- 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.
2015-05-19Include output in README, use mkinsub() in example codeJohannes Ranke1-1/+19
2015-05-15Make mkinmod quiet in testsJohannes Ranke1-1/+4
2014-11-12Fix for IORE in mkinmodJohannes Ranke1-0/+5
2014-07-14Nearly complete support for IORE, pending mkinerrminJohannes Ranke1-5/+21
2014-07-12First working fits with IORE modelJohannes Ranke1-2/+3
2013-10-08- Added the possibility to specify the observed variable in mkinmod in a ↵jranke1-2/+5
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
2012-04-16Overhaul of mkinmod in order to make it possible to choose between different ↵jranke1-1/+11
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
2012-04-11- Testing of the new fitting process with transformed parameters shows that ↵jranke1-12/+9
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
2012-03-15Update kinfit and mkin to the latest version published on BerliOS.jranke1-7/+11
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@17 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2010-05-18Much more complete version that was just submitted to CRAN.jranke1-13/+18
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@9 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2010-05-11Initial upload of the upcoming multicompartment version of kinfit.jranke1-0/+44
Some functionality is still missing (chi2), some may never be implemented (FOMC model), but in general it is much more powerful than kinfit, owing to the powerful FME package. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@8 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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