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2015-06-23Small documenation changesJohannes Ranke5-15/+17
2015-06-23Hopefully fix compiling on Solaris, verbose optionJohannes Ranke3-14/+39
- 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
2015-06-22Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke8-57/+57
r-forge
2015-06-22Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke5-55/+52
r-forge
2015-06-22Another reorganisation of vignette building by GNUmakefileJohannes Ranke3-38/+31
2015-06-22Watch the vignettes built locally as well for buildingJohannes Ranke1-0/+2
2015-06-22Vignettes rebuilt by staticdocs::build_site() for r-forgeJohannes Ranke4-52/+48
2015-06-22Version bump, correct benchmark in vignette/compiled_modelsJohannes Ranke14-838/+447
Reorganisation of the vignette generation in the Makefile. Improved YAML header in the R markdown vignettes. Rebuilt vignettes with the package installed.
2015-06-21Rebuild vignettes with the released package installedJohannes Ranke6-59/+63
2015-06-21Vignettes as rebuilt for the static documentation for r-forgeJohannes Ranke4-33/+33
2015-06-21Do the t-test for untransformed parametersv0.9-36Johannes Ranke14-240/+340
2015-06-20Reorganize transform_odeparms example, reduce check timeJohannes Ranke1-1/+5
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

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