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2023-04-06Fix a bug with moved DLLs and current deSolveJohannes Ranke1-4/+3
In mkinmod, dll_info was not included in the returned model object in the case that the DLL was moved to a user defined directory. This is now fixed.
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke1-1/+1
2023-01-04Update documentation of 'use_of_ff' argumentJohannes 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.
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke1-2/+2
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.
2020-12-03Small doc improvementJohannes Ranke1-2/+2
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke1-25/+35
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 Ranke1-28/+38
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 Ranke1-6/+12
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 Ranke1-1/+6
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 Ranke1-40/+3
Still in preparation for analytical solutions of coupled models
2020-05-07Merge parent solutions to one fileJohannes Ranke1-1/+1
- 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
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-0/+40
Preparing for symbolic solutions for more than one compound
2020-05-06Remove redundant commentsJohannes Ranke1-7/+0
2020-04-22Support SFORB with formation fractionsJohannes Ranke1-29/+17
2020-04-22Remove GPL header from test filesJohannes Ranke1-3/+3
2020-03-31Static documentation rebuilt by pkgdownJohannes Ranke1-2/+4
2020-03-30Don't check for gcc on the path in mkinmodJohannes Ranke1-60/+57
Roxygen update -> formatting changes in Rd files
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-383/+483
2019-02-27Comment out unused codeJohannes Ranke1-6/+6
2019-02-21Add the logistic modelJohannes Ranke1-7/+13
2016-11-18Show differential equations when printing mkinmodsJohannes Ranke1-0/+3
2016-11-17Remove trailing whitespace, clean headersJohannes Ranke1-10/+10
Also ignore test.R in the top level directory, as it is not meant to be public
2015-12-10Improve print method for mkinmodJohannes Ranke1-2/+3
2015-12-09Improve mkinmod error message for missing target compartment definitionJohannes Ranke1-0/+1
Closes #6.
2015-10-24Improve printing method for mkinmodJohannes Ranke1-1/+1
2015-10-19Add a print method for mkinmod objectsJohannes Ranke1-0/+16
2015-06-23Hopefully fix compiling on Solaris, verbose optionJohannes Ranke1-11/+23
- 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.
2015-06-20Suppress compiler warning for sometimes unused time variableJohannes Ranke1-1/+3
2015-06-20Low-level generation of compiled modelsJohannes Ranke1-31/+62
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.
2015-05-15Make mkinmod quiet in testsJohannes Ranke1-4/+4
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke1-3/+6
2015-04-17Make compiled FOMC and DFOP models workJohannes Ranke1-5/+4
- 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
2015-04-16Update copyright header, improve documentation of solution_typeJohannes Ranke1-1/+1
2015-04-14Compile differential equation models with ccSolve packageJohannes Ranke1-0/+34
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
2014-11-12Fix for IORE in mkinmodJohannes Ranke1-4/+4
2014-07-14Nearly complete support for IORE, pending mkinerrminJohannes Ranke1-10/+16
2014-07-12First working fits with IORE modelJohannes Ranke1-6/+22
2014-07-07Coefficient matrix for formation fractions, no sink and one pathwayJohannes Ranke1-22/+26
2014-07-02Do not introduce formation fractions for singular pathwaysJohannes Ranke1-4/+13
- As a consequence, we do not need implicit formation fractions in mkinfit
2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke1-3/+0
2014-07-01One more check, update source code commentJohannes Ranke1-2/+3
2013-12-04Remove mkinmod warning based on a misconceptionJohannes Ranke1-13/+2
2013-10-08- Added the possibility to specify the observed variable in mkinmod in a ↵jranke1-3/+4
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
2013-04-14- Update the TODO list, setting some requirements for version 1.0jranke1-0/+1
- 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
2013-02-18More work on the examples vignettejranke1-8/+16
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@65 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-12-13Small formatting improvementsjranke1-5/+8
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@59 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-06-28- Formatting improvement of mkinmodjranke1-14/+15
- 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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