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2016-06-28Bump version for new release, rebuild static docsJohannes Ranke4-51/+51
The test test_FOMC_ill-defined leads to errors on several architectures/distributions, as apparent from CRAN checks, so we need a new release. Static documentation rebuilt by staticdocs::build_site()
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke5-75/+59
2016-06-28Attempts to reduce vignette sizeJohannes Ranke8-66/+86
Reducing the size of some figures and switching of retina figures in the preamble only gives a small decrease in vignette size, but may be enough to get the size of the doc directory below 5 MB to avoid the NOTE in the corresponding check (which I did not get locally, nor on winbuilder using r-devel.
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke4-39/+39
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke4-40/+40
2016-06-28Avoid multicore fits in vignettes for passing CRAN checksJohannes Ranke7-97/+303
Also a small fix to the FOCUS Z vignette, and an update of the static documentation generated by staticdocs.
2016-06-28Convenience wrapper plot_sep, further vignette updatesJohannes Ranke3-122/+94
2016-06-27Complete mkin vignette, update FOCUS L vignetteJohannes Ranke5-466/+553
The mkin vignette now describes how confidence intervals and the t-test are calculated. The FOCUS L vignette is updated with the new floating toc provided by the current rmarkdown package, and also uses current, improved mkin functionality.
2016-06-24Convert main vignette to Rmd/html, add_err(), fixesJohannes Ranke4-93/+410
2016-03-25Remove outdated reference to the inline packageJohannes Ranke1-2/+1
2016-03-24Static documentation rebuilt by staticdocs::build_site()v0.9.42Johannes Ranke5-394/+210
2016-03-24Address feedback from CRAN submissionJohannes Ranke2-113/+304
- Put the CRAN URL that the badge points to into canonical form. I had missed the requirement to use the canonical form before, as the R CMD check message complained about a (possibily) invalid URL, so I overlooked the explanation later in the check log. Thanks to Uwe for his patience. Fix checked with winbuilder. - Slightly reduced the build time for the compiled_models vignette by skipping the warm-up. 3 repetitions are necessary for the autoplot method to work
2016-03-23Static documentation rebuilt by staticdocs::build_site()Johannes Ranke3-16/+16
2016-03-23Added 'from_max_mean' to 'mkinfit'.Johannes Ranke5-48/+48
- Now it is easier to do decline kinetics from the maximum occurrence - Static documentation rebuilt by staticdocs::build_site() - Fixed an URL in the README, thanks to the win-builder check with R-devel
2015-12-09Static documentation rebuilt by staticdocs::build_site()Johannes Ranke5-23/+23
2015-11-13Add plots to compiled_models vignette, rebuild staticdocsJohannes Ranke6-56/+74
2015-11-09Update staticdocsv0.9-41Johannes Ranke3-17/+17
2015-11-09Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke3-26/+21
r-forge
2015-11-09Rebuild vignettes and static documentationJohannes Ranke5-28/+33
2015-11-09Re-add the compiled models vignetteJohannes Ranke1-0/+101
This was accidentally deleted in 438a889c37ffdf8f0c6585092da6abdb63b4575e on June 30!
2015-11-09Export print.mkinds and rebuild vignettesJohannes Ranke4-4/+4
2015-07-21Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-40Johannes Ranke2-0/+0
r-forge
2015-07-21Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke4-4/+4
r-forge
2015-07-20Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke4-37/+37
r-forge
2015-07-20Avoid error message for SFORB in endpoints, updatesJohannes Ranke4-50/+50
2015-06-30Improve calculation of DT90 in endpoints(), check and testJohannes Ranke2-101/+0
2015-06-26Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-39Johannes Ranke5-49/+49
r-forge
2015-06-26Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke5-69/+54
r-forge
2015-06-26Pass R CMD check --as-cran, vignette rebuildJohannes Ranke5-74/+89
2015-06-26Do caching for the FOCUS_Z vignetteJohannes Ranke1-1/+1
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-38Johannes Ranke5-60/+60
r-forge
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-37Johannes Ranke5-49/+49
r-forge
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke5-47/+47
r-forge
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke5-58/+58
r-forge
2015-06-23Small documenation changesJohannes Ranke2-5/+5
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 Ranke1-18/+0
2015-06-22Vignettes rebuilt by staticdocs::build_site() for r-forgeJohannes Ranke4-52/+48
2015-06-22Version bump, correct benchmark in vignette/compiled_modelsJohannes Ranke9-788/+403
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 Ranke6-219/+232
2015-06-20Low-level generation of compiled modelsJohannes Ranke2-8/+6
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
2015-06-05Add a simple vignette with an evaluation of FOCUS DJohannes Ranke2-0/+352
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke2-0/+0
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
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke3-0/+256
2015-04-16Pending commit of an updated vignetteJohannes Ranke1-77/+76

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