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2015-06-26Subsetting and plotting for mmkin objectsJohannes Ranke3-3/+89
Including documentation and documentation improvements for mmkin().
2015-06-25Fix fitting with parLapply, doc fixJohannes Ranke1-0/+1
2015-06-25Add mmkin for testingJohannes Ranke1-0/+64
2015-06-23Fix the changed documentationJohannes Ranke1-3/+4
2015-06-23Small documenation changesJohannes Ranke3-10/+12
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.
2015-06-23Improve formatting of \dontrun sectionJohannes Ranke1-2/+4
2015-06-20Reorganize transform_odeparms example, reduce check timeJohannes Ranke1-1/+5
2015-06-20Low-level generation of compiled modelsJohannes Ranke2-3/+3
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.
2015-06-05Make the examples that are run more quietJohannes Ranke1-2/+2
2015-05-19Include output in README, use mkinsub() in example codeJohannes Ranke2-15/+33
2015-05-18Make checking faster, testing is done by testsJohannes Ranke3-13/+10
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke1-0/+1
2015-05-15Reduce time to run mkinfit exampleJohannes Ranke1-0/+2
2015-05-15Make mkinmod quiet in testsJohannes Ranke1-1/+4
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke1-0/+65
Conflicts (resolved manually, deleting code that I had integrated into the RUnit tests for testing the compiled version): .gitignore DESCRIPTION inst/unitTests/runit.mkinerrmin.R inst/unitTests/runit.mkinfit.R tests/testthat/test_mkinpredict_SFO_SFO.R vignettes/FOCUS_L.html
2015-05-15Add synthetic data generated for UBA expertise, testsJohannes Ranke1-0/+65
The new tests are based on the results documented in the expertise I wrote for the UBA (currently unpublished).
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke2-7/+11
2015-04-16Update copyright header, improve documentation of solution_typeJohannes Ranke1-2/+3
2015-04-16Check compiled mkinmod versions in examples and testsJohannes Ranke2-4/+41
Tests all pass (Linux)
2015-04-16Correctly close braces of examples sectionJohannes Ranke1-0/+1
2015-04-14Compile differential equation models with ccSolve packageJohannes Ranke1-2/+3
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
2014-11-23Use model as in the original publicationJohannes Ranke1-1/+1
2014-11-13Fix code/documentation mismatchJohannes Ranke1-2/+2
2014-11-13Expand the IORE example a bitJohannes Ranke1-3/+4
2014-11-12Add a hint about equivalence of FOMC and IORE modelsJohannes Ranke1-0/+2
2014-11-12Add an IORE example for parent decline kineticsJohannes Ranke1-0/+4
2014-11-12Fix for IORE in mkinmodJohannes Ranke1-0/+5
2014-11-12Merge branch 'master' of https://github.com/jranke/mkin into ioreJohannes Ranke1-1/+1
2014-11-12IORE working for parent and metabolites, introduce mkinsubJohannes Ranke2-0/+50
2014-11-12Fix the typo in the help page, tooJohannes Ranke1-1/+1
2014-11-12Merge branch 'master' into ioreJohannes Ranke4-23/+60
2014-10-29Correct name of the DFOP model according to FOCUS kineticsJohannes Ranke1-1/+1
2014-10-15Switch to using the Port algorithm per defaultJohannes Ranke1-12/+12
2014-10-14Add a comment about transforming fractionsJohannes Ranke1-4/+10
2014-08-25Bug fix and unit tests for mkinerrminJohannes Ranke1-0/+10
See NEWS.md for details
2014-07-24Improve formulationJohannes Ranke1-1/+1
2014-07-24Semantic correction in help fileJohannes Ranke1-1/+1
2014-07-24Bump version, better default for state.iniJohannes Ranke1-0/+1
2014-07-21Bugfix, model shorthand, state.ini[[1]] from observed dataJohannes Ranke2-7/+17
- 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
2014-07-17Handle non-convergence and maximum number of iterationsJohannes Ranke1-4/+14
For details see NEWS.md
2014-07-14Nearly complete support for IORE, pending mkinerrminJohannes Ranke2-12/+33
2014-07-14Merge bugfix release 0.9-31 from 'master' into ioreJohannes Ranke1-1/+1
2014-07-12First working fits with IORE modelJohannes Ranke3-3/+38
2014-07-11It is B. Mikolasch, not M. Mikolasch...Johannes Ranke1-1/+1
2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke3-16/+52
2014-06-26Fix naming of SFORB DT50_bx values, fix docsJohannes Ranke1-1/+1
2014-06-26Calculate additional DT50 values for non-SFO modelsJohannes Ranke1-5/+1
2014-06-26Add function for geometric meanJohannes Ranke1-0/+23
2014-06-26Start new version, add xlim to mkinresplotJohannes Ranke1-0/+4

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