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2017-10-10Add ORCID to DESCRIPTION, released versionv0.9.46.2Johannes Ranke1-0/+2
Static documentation except articles rebuilt by pkgdown
2017-09-14Convert FOCUS Z vignette to rmarkdown/htmlJohannes Ranke1-0/+4
- Static documentation rebuilt by pkgdown::build_articles() - DESCRIPTION: Version bump and current date
2017-09-14Update NEWS, static documentation except articles rebuilt by pkgdownv0.9.46.1Johannes Ranke1-0/+8
2017-07-29Bump version, update NEWS and rebuild pkdown docsv0.9.46Johannes Ranke1-0/+14
2016-12-21TWA calculation for SFO, FOMC and DFOP (parent)Johannes Ranke1-0/+6
2016-12-08Prepare for releaseJohannes Ranke1-1/+5
2016-10-06Static documentation rebuilt by pkgdown::build_site()Johannes Ranke1-54/+52
2016-09-10Plot using R model if compiled model is not availableJohannes Ranke1-0/+6
2016-09-10Forgot to include the latest NEWS entry in 0.9.44Johannes Ranke1-0/+6
2016-06-28Update NEWSJohannes Ranke1-2/+2
2016-06-28Convenience wrapper plot_sep, further vignette updatesJohannes Ranke1-0/+2
2016-06-27Complete mkin vignette, update FOCUS L vignetteJohannes Ranke1-1/+1
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.
2016-06-27Improve listing of weights in output, update NEWSJohannes Ranke1-1/+7
2016-06-25Now the old behaviour is restored for compatibility reasonsJohannes Ranke1-3/+1
When observed variables are not shown in separate plots, the residual plot is shown in the lower third of the total plotting area
2016-06-25Working state, but not backwards compatibleJohannes Ranke1-1/+7
In this commit, the separatation of plots for observed variables works. The formatting should be improved. However, in gmkin, plotting with show_residuals = TRUE is used, and the GUI expects that the residual plot is below the main plot. This behaviour should be restored.
2016-06-24Convert main vignette to Rmd/html, add_err(), fixesJohannes Ranke1-4/+10
2016-06-17Change the title of the package, small bugfixJohannes Ranke1-0/+4
2016-06-09Fix a bug in the listing of formation fractionsJohannes Ranke1-0/+4
The bug could only occur if a parent compound with a metabolite would end in the letter 'f' and was therefore not noticed earlier
2016-04-21Avoid unnecessary stop in edge case, improve warningsJohannes Ranke1-2/+10
mkinfit: Do not error out in cases where the fit converges, but the Jacobian for the untransformed model cost can not be estimated. Give a warning instead and return NA for the t-test results. summary.mkinfit: Give a warning message when the covariance matrix can not be obtained. A test has been added to containing such an edge case to check that the warnings are correctly issued and the fit does not terminate.
2016-03-25Remove outdated reference to the inline packageJohannes Ranke1-0/+6
2016-03-23Added 'from_max_mean' to 'mkinfit'.Johannes Ranke1-1/+5
- 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
2015-12-10Improve print method for mkinmodJohannes Ranke1-0/+2
2015-12-09Improve mkinmod error message for missing target compartment definitionJohannes Ranke1-0/+2
Closes #6.
2015-11-13Add plots to compiled_models vignette, rebuild staticdocsJohannes Ranke1-0/+2
2015-11-13Bump version, change to version number format as shown in summariesJohannes Ranke1-1/+5
2015-11-09Rebuild vignettes and static documentationJohannes Ranke1-1/+1
2015-10-21Avoid an error printing old mkinfit summariesJohannes Ranke1-0/+4
2015-10-19Add the R6 class mkindsJohannes Ranke1-2/+4
2015-10-19Add a print method for mkinmod objectsJohannes Ranke1-0/+2
2015-10-16Full compound names in models that are shown in the plotJohannes Ranke1-0/+2
2015-07-22index.r for grouping help topics in static documentationJohannes Ranke1-0/+2
2015-07-22Reformat NEWS.md, start new entryJohannes Ranke1-38/+42
It is not necessary to use capitals in the headings, as they are now typeset as HTML on CRAN and github.
2015-07-21Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-40Johannes Ranke1-1/+1
r-forge
2015-07-20Adapt NEWS entry to latest fix for importsJohannes Ranke1-1/+1
2015-06-30Improve calculation of DT90 in endpoints(), check and testJohannes Ranke1-1/+11
2015-06-26Advertise parallel processing in the NEWS fileJohannes Ranke1-1/+1
2015-06-26Fix x axis scaling in mkinparplotJohannes Ranke1-1/+5
2015-06-26Subsetting and plotting for mmkin objectsJohannes Ranke1-1/+3
Including documentation and documentation improvements for mmkin().
2015-06-25Add CRAN release dates to NEWS.mdJohannes Ranke1-44/+37
Remove leftovers from using a plain text NEWS file
2015-06-25Add mmkin for testingJohannes Ranke1-1/+3
2015-06-24Update and format fixJohannes Ranke1-0/+20
Add newlines to NEWS.md to get correct formatting in NEWS
2015-06-23Hopefully fix compiling on Solaris, verbose optionJohannes Ranke1-1/+5
- 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.
2015-06-22Version bump, correct benchmark in vignette/compiled_modelsJohannes Ranke1-0/+7
Reorganisation of the vignette generation in the Makefile. Improved YAML header in the R markdown vignettes. Rebuilt vignettes with the package installed.
2015-06-21Do the t-test for untransformed parametersv0.9-36Johannes Ranke1-0/+1
2015-06-20Correction and improvement of NEWSJohannes Ranke1-2/+2
2015-06-20Low-level generation of compiled modelsJohannes Ranke1-1/+1
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.
2015-06-05News entry for new vignette FOCUS_DJohannes Ranke1-0/+4
2015-05-18Fix format of NEWS.mdJohannes Ranke1-7/+3
2015-05-15Clean up meta informationJohannes Ranke1-1/+0
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke1-0/+7
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

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