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2015-06-20Correction and improvement of NEWSJohannes Ranke1-2/+2
2015-06-20Workaround for hadley/testthat#144Johannes Ranke1-0/+4
2015-06-20Suppress compiler warning for sometimes unused time variableJohannes Ranke1-1/+3
2015-06-20Low-level generation of compiled modelsJohannes Ranke17-89/+137
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.
2015-06-05FOCUS D vignette generated from MakefileJohannes Ranke1-83/+248
2015-06-05News entry for new vignette FOCUS_DJohannes Ranke1-0/+4
2015-06-05Add a simple vignette with an evaluation of FOCUS DJohannes Ranke3-1/+356
2015-06-05Make the examples that are run more quietJohannes Ranke1-2/+2
2015-05-19Typo in dummy fileJohannes Ranke1-1/+1
2015-05-19Forgot to commit the README source fileJohannes Ranke1-4/+4
2015-05-19Avoid distracting output in READMEJohannes Ranke1-144/+1
2015-05-19Include output in README, use mkinsub() in example codeJohannes Ranke14-32/+435
2015-05-19Code highlighting, use of mkinsub() in README.mdJohannes Ranke1-24/+30
2015-05-19Make compiled models more prominent in feature listJohannes Ranke1-3/+4
2015-05-19Link to compiled_models vignette, advertise NEWSJohannes Ranke1-1/+9
2015-05-18Fix format of NEWS.mdJohannes Ranke1-7/+3
2015-05-18Make checking faster, testing is done by testsJohannes Ranke5-15/+12
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke1-0/+1
2015-05-15Reduce time to run mkinfit exampleJohannes Ranke1-0/+2
2015-05-15Bump version as 0.9-35 is on CRAN nowJohannes Ranke1-1/+1
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke2-7/+6
2015-05-15Remove dead link to KinGUII pagev0.9-35Johannes Ranke1-6/+5
2015-05-15Remove missing files from svn before commiting to r-forgeJohannes Ranke1-1/+1
2015-05-15Clean up meta informationJohannes Ranke2-4/+4
2015-05-15Make mkinmod quiet in testsJohannes Ranke7-13/+16
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke19-431/+556
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
2015-05-15Update of vignettes during staticdoc documentationJohannes Ranke3-61/+61
2015-05-15Add synthetic data generated for UBA expertise, testsJohannes Ranke5-1/+135
The new tests are based on the results documented in the expertise I wrote for the UBA (currently unpublished).
2015-05-15Quote FME package name in DESCRIPTIONJohannes Ranke1-1/+1
2015-05-15Relax test tolerance for SFORB, FOCUS B and deSolveJohannes Ranke1-2/+2
While this was OK on my local windows machine, the test failed on winbuilder
2015-05-15Better description of the release procedureJohannes Ranke1-2/+2
2015-05-15Make FOMC test for FOCUS A robust towards non-convergenceJohannes Ranke1-5/+4
2015-05-15Also migrate test for mkinpredictJohannes Ranke1-28/+12
2015-05-15Correct the dateJohannes Ranke1-1/+1
2015-05-15Skip testing FOMC with FOCUS A WindowsJohannes Ranke1-9/+15
Testing the package on winbuilder shows that the Port algorithm does not converge on Windows with this combination, which is not a problem as the FOMC model is not appropriate for the dataset anyways.
2015-05-15Finished migration from RUnit to testthatJohannes Ranke9-316/+370
2015-05-14Start of migration from RUnit to testthatJohannes Ranke10-61/+58
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke10-15/+282
2015-04-17Add NEWS about compiled models, set the dateJohannes Ranke2-1/+14
2015-04-17Make compiled FOMC and DFOP models workJohannes Ranke3-6/+37
- 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
2015-04-16Add tests for default solution method, fix one testJohannes Ranke1-3/+12
2015-04-16Order of parameters needs to be right for compiled modelsJohannes Ranke1-1/+1
2015-04-16Test what I wanted to testJohannes Ranke1-1/+1
2015-04-16Update copyright header, improve documentation of solution_typeJohannes Ranke4-16/+22
2015-04-16Check compiled mkinmod versions in examples and testsJohannes Ranke5-7/+56
Tests all pass (Linux)
2015-04-16Merge branch 'compile_odes'Johannes Ranke5-14/+57
2015-04-16Correctly close braces of examples sectionJohannes Ranke1-0/+1
2015-04-16Pending commit of an updated vignetteJohannes Ranke1-77/+76
2015-04-14Compile differential equation models with ccSolve packageJohannes Ranke5-14/+56
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
2015-02-21Avoid NOTES in R CMD checkJohannes Ranke3-1/+6
- Export S3 methods - Avoid using undeclared variable names

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