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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2016-03-25Remove outdated reference to the inline packageJohannes Ranke1-0/+6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
2015-05-15Add synthetic data generated for UBA expertise, testsJohannes Ranke1-0/+2
The new tests are based on the results documented in the expertise I wrote for the UBA (currently unpublished).
2015-05-15Finished migration from RUnit to testthatJohannes Ranke1-0/+5
2015-04-17Add NEWS about compiled models, set the dateJohannes Ranke1-0/+13
2015-02-21Avoid NOTES in R CMD checkJohannes Ranke1-0/+2
- Export S3 methods - Avoid using undeclared variable names
2015-02-20Add termination message to mkinfit, prepare releaseJohannes Ranke1-0/+4
2015-02-20Fix printing the summary if iterations are not availableJohannes Ranke1-0/+1
This was broken for using method.modFit = "SANN"
2014-11-23Avoid spurious warning in mkinparplot, bump versionJohannes Ranke1-0/+6
2014-11-13Formatting and writing improvedJohannes Ranke1-1/+2
2014-11-12IORE working for parent and metabolites, introduce mkinsubJohannes Ranke1-0/+1
2014-11-12Merge branch 'master' into ioreJohannes Ranke1-6/+75
2014-10-22Always include 0 on y axis when plotting during the fitJohannes Ranke1-0/+2
2014-10-15Switch to using the Port algorithm per defaultJohannes Ranke1-0/+4
2014-10-14Further formatting improvement for differential equationsJohannes Ranke1-0/+4
2014-10-11Start new development versionJohannes Ranke1-0/+2
2014-10-11Updates intended for releasing mkin 0.9-33Johannes Ranke1-0/+2
2014-10-06Avoid a warning produced by initial fits in gmkinJohannes Ranke1-1/+2

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