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2016-11-18Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)Johannes Ranke1-2/+2
Using branch 'jranke' on jranke/pkgdown, fixing issues hadley/pgkdown#178 and hadley/pkgdown#213 Remove plot=TRUE from mkinfit calls also in dontrun sections of examples to avoid a flood png files documenting the progress of the fit.
2016-11-04Complete migration staticdocs -> pkgdownJohannes Ranke1-7/+2
2016-10-26Static documentation rebuilt by pkgdown::build_site()Johannes Ranke1-1/+1
2016-10-06Static documentation rebuilt by pkgdown::build_site()Johannes Ranke1-1/+1
2016-10-06Static documentation rebuilt by pkgdown::build_site()Johannes Ranke1-1/+6
2016-09-28Add drat target and rebuild for dratJohannes Ranke1-0/+3
2016-09-10Static documentation rebuilt by staticdocs::build_site()Johannes Ranke1-3/+1
2016-06-28Test the package using devtools to get a test.logJohannes Ranke1-2/+1
2016-06-28The location of my local svn directory has changedJohannes Ranke1-1/+1
2016-06-28Do not watch vignettes for builds without rebuilding themJohannes Ranke1-1/+1
This avoids the situation that a new function is needed in a vignette but the first thing that the build tries to do is building it.
2016-06-24Convert main vignette to Rmd/html, add_err(), fixesJohannes Ranke1-1/+1
2015-11-13Add plots to compiled_models vignette, rebuild staticdocsJohannes Ranke1-2/+2
2015-11-09Rebuild vignettes and static documentationJohannes Ranke1-8/+7
2015-11-09Do not include unnecessary mathjax in README.htmlJohannes Ranke1-1/+1
2015-10-02Some maintenanceJohannes Ranke1-2/+1
2015-08-22Generate README.html for my cgit setup on jrwb.deJohannes Ranke1-3/+6
2015-07-22index.r for grouping help topics in static documentationJohannes Ranke1-5/+3
2015-07-20Avoid error message for SFORB in endpoints, updatesJohannes Ranke1-0/+4
2015-07-01Corrections in the clean targetJohannes Ranke1-2/+2
2015-06-30Improve calculation of DT90 in endpoints(), check and testJohannes Ranke1-0/+4
2015-06-29Do not include plots and R output in READMEJohannes Ranke1-4/+0
This does not get rendered properly on CRAN, and is easily replaced by links to the static documentation on R-Forge.
2015-06-26Rebuilding vignettes with current version is up to the userJohannes Ranke1-2/+2
2015-06-26Copy README figures before starting interactive R for staticdocsJohannes Ranke1-2/+2
2015-06-26Pass R CMD check --as-cran, vignette rebuildJohannes Ranke1-2/+2
2015-06-26More plotting in help files, fix Make- and .*ignore filesJohannes Ranke1-4/+5
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

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