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2015-06-26Subsetting and plotting for mmkin objectsJohannes Ranke7-4/+201
Including documentation and documentation improvements for mmkin().
2015-06-25Small fixesJohannes Ranke2-2/+3
2015-06-25Add CRAN release dates to NEWS.mdJohannes Ranke3-46/+37
Remove leftovers from using a plain text NEWS file
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
2015-06-25Depend on parallel package, todays dateJohannes Ranke1-2/+2
2015-06-25Fix fitting with parLapply, doc fixJohannes Ranke2-1/+2
2015-06-25Fix build targets in MakefileJohannes Ranke1-1/+0
2015-06-25Add mmkin for testingJohannes Ranke3-1/+113
2015-06-24Update and format fixJohannes Ranke1-0/+20
Add newlines to NEWS.md to get correct formatting in NEWS
2015-06-24Staticdocs site_path argument in build_site() now worksJohannes Ranke2-9/+6
This long-standing issue finally got fixed in 2f56137fc9ba60bfea54e575d233f4e696bb8a5a
2015-06-23Version bump, keep logs of build, check and testJohannes Ranke7-4/+112
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-38Johannes Ranke5-60/+60
r-forge
2015-06-23Remove Rplots.pdf that is being built by staticdocsJohannes Ranke4-1/+4
2015-06-23Also copy figures generated by README.Rmd for staticdocs indexJohannes Ranke1-1/+1
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-37Johannes Ranke6-49/+49
r-forge
2015-06-23Set the correct date in DESCRIPTIONJohannes Ranke1-1/+1
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke6-47/+47
r-forge
2015-06-23Remove file that was accidentally addedJohannes Ranke1-0/+0
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.
2015-06-23Fix the changed documentationJohannes Ranke1-3/+4
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke6-58/+58
r-forge
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

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