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2015-06-25Small fixesJohannes Ranke1-1/+1
2015-06-25Do not convert NEWS.md any more as it is now rendered on CRANJohannes Ranke1-4/+1
via wch/r-source@9ffe87264a1cd59a31a829f72d57af0f1bfa327a
2015-06-25Rename quick install target to quickinstallJohannes Ranke1-1/+1
2015-06-25Fix build targets in MakefileJohannes Ranke1-1/+0
2015-06-24Staticdocs site_path argument in build_site() now worksJohannes Ranke1-7/+6
This long-standing issue finally got fixed in 2f56137fc9ba60bfea54e575d233f4e696bb8a5a
2015-06-23Version bump, keep logs of build, check and testJohannes Ranke1-3/+3
2015-06-23Remove Rplots.pdf that is being built by staticdocsJohannes Ranke1-0/+2
2015-06-23Also copy figures generated by README.Rmd for staticdocs indexJohannes Ranke1-1/+1
2015-06-23Rename the check-no-vignettes target to quickcheckJohannes Ranke1-2/+2
and do not check using the --as-cran option to skip the check for CRAN incoming feasibility.
2015-06-22Another reorganisation of vignette building by GNUmakefileJohannes Ranke1-20/+29
2015-06-22Watch the vignettes built locally as well for buildingJohannes Ranke1-0/+2
2015-06-22Version bump, correct benchmark in vignette/compiled_modelsJohannes Ranke1-27/+10
Reorganisation of the vignette generation in the Makefile. Improved YAML header in the R markdown vignettes. Rebuilt vignettes with the package installed.
2015-06-20Low-level generation of compiled modelsJohannes Ranke1-1/+5
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.
2015-06-05Add a simple vignette with an evaluation of FOCUS DJohannes Ranke1-1/+4
2015-05-19Include output in README, use mkinsub() in example codeJohannes Ranke1-1/+4
2015-05-18Make checking faster, testing is done by testsJohannes Ranke1-1/+1
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke1-1/+1
2015-05-15Remove missing files from svn before commiting to r-forgeJohannes Ranke1-1/+1
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke1-4/+5
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
2015-05-15Better description of the release procedureJohannes Ranke1-2/+2
2015-05-15Finished migration from RUnit to testthatJohannes Ranke1-0/+1
2015-05-14Start of migration from RUnit to testthatJohannes Ranke1-2/+2
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke1-1/+4
2014-08-25Remove intermediate vignette files when cleaningJohannes Ranke1-0/+1
2014-07-21Bugfix, model shorthand, state.ini[[1]] from observed dataJohannes Ranke1-4/+11
- 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
2014-07-14Fix syncinc with r-forgeJohannes Ranke1-1/+1
2014-07-11Update of syncing to r-forge without git-svnJohannes Ranke1-15/+12
2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke1-5/+7
2014-06-30Format the NEWS file in markdown, add Makefile targetJohannes Ranke1-36/+5
2014-06-28Rename ChangeLog to NEWS, new entry style, Makefile updateJohannes Ranke1-1/+1
2014-06-27Add vignettes target, reorganizeJohannes Ranke1-17/+23
2014-06-27Show the upload date and time for winbuilderJohannes Ranke1-0/+1
2014-06-27Simplify and correct targets using $(TGZ) and $(TGZVNR)Johannes Ranke1-9/+6
2014-06-27Only update builds when neededJohannes Ranke1-6/+41
2014-05-08Improve the process of syncing the r-forge branchJohannes Ranke1-1/+1
2014-05-08Support building static documentation, build itJohannes Ranke1-0/+11
2014-05-08Always run tests without rebuilding vignettesJohannes Ranke1-9/+3
2014-02-27Format of gmkin workspace files, copyright, updatesJohannes Ranke1-1/+1
- Change the format of the workspace files of gmkin so they can be distributed in the mkin package - Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin - Restrict the unit test with the Schaefer data to parent and primary metabolites as formation fraction and DT50 for A2 are higly correlated and passing the test is platform dependent. For example, the test fails in 1 out of 14 platforms on CRAN as of today - Add Eurofins Regulatory AG copyright notices - Import FME and deSolve instead of depending on them to have cleaner startup
2013-12-04Make it possible to use different ode solvers=1-3/+19
2013-12-04Add Makefile targets without vignette buildingJohannes Ranke1-8/+9
2013-11-17Conflicts:jranke1-7/+13
README.md TODO git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@163 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-11Vignettes are not built from the makefilejranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@156 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-11Change quotes to single as backquotes execute automaticallyjranke1-3/+3
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@155 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-11Fix quotes in makefilejranke1-3/+3
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@154 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-11Test a git commit while svn not up to datejranke1-0/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@153 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-11Adapt the makefile to presumed git workflowjranke1-2/+4
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@151 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-11- Add a simple makefilejranke1-0/+62
- Add a .Rbuildignore file - Clean up unit tests a bit - Test the gwidgets notebook from the knitr demo git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@150 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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