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2016-04-21Avoid unnecessary stop in edge case, improve warningsJohannes Ranke1-1/+1
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2016-03-25Remove outdated reference to the inline packageJohannes Ranke1-2/+2
2016-03-24Address feedback from CRAN submissionJohannes Ranke1-1/+1
- 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
2016-03-23Added 'from_max_mean' to 'mkinfit'.Johannes Ranke1-2/+2
- 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
2015-11-13Add plots to compiled_models vignette, rebuild staticdocsJohannes Ranke1-2/+2
2015-11-13Bump version, change to version number format as shown in summariesJohannes Ranke1-1/+1
2015-11-09Export print.mkinds and rebuild vignettesJohannes Ranke1-2/+2
2015-10-19Add the R6 class mkindsJohannes Ranke1-1/+1
2015-10-19Add a print method for mkinmod objectsJohannes Ranke1-1/+1
2015-10-16Full compound names in models that are shown in the plotJohannes Ranke1-1/+1
2015-07-22Increment version number for developmentJohannes Ranke1-2/+2
2015-07-21Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-40Johannes Ranke1-1/+1
r-forge
2015-07-20Remove obvious CRAN URLJohannes Ranke1-3/+2
2015-07-20Avoid error message for SFORB in endpoints, updatesJohannes Ranke1-1/+1
2015-06-30Improve calculation of DT90 in endpoints(), check and testJohannes Ranke1-2/+2
2015-06-29Bump version, as 0.9-39 is now on CRANJohannes Ranke1-2/+2
2015-06-25Depend on parallel package, todays dateJohannes Ranke1-2/+2
2015-06-23Version bump, keep logs of build, check and testJohannes Ranke1-1/+1
2015-06-23Remove Rplots.pdf that is being built by staticdocsJohannes Ranke1-1/+1
2015-06-23Set the correct date in DESCRIPTIONJohannes Ranke1-1/+1
2015-06-22Version bump, correct benchmark in vignette/compiled_modelsJohannes Ranke1-2/+2
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 Ranke1-2/+2
2015-06-20Low-level generation of compiled modelsJohannes Ranke1-5/+4
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.
2015-05-18Make checking faster, testing is done by testsJohannes Ranke1-1/+1
2015-05-15Clean up meta informationJohannes Ranke1-3/+4
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke1-3/+3
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
2015-05-15Quote FME package name in DESCRIPTIONJohannes Ranke1-1/+1
2015-05-15Correct the dateJohannes Ranke1-1/+1
2015-05-15Finished migration from RUnit to testthatJohannes Ranke1-1/+1
2015-05-14Start of migration from RUnit to testthatJohannes Ranke1-2/+3
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke1-1/+1
2015-04-17Add NEWS about compiled models, set the dateJohannes Ranke1-1/+1
2015-04-14Compile differential equation models with ccSolve packageJohannes Ranke1-2/+4
If the ccSolve package is available, and time is not in the right hand side of the equations (i.e. if only SFO and SFORB models are used), the differential equation model is compiled from auto-generated C code. Currently, one test (FOCUS 2006 D SFO_SFO) fails
2015-02-20Add termination message to mkinfit, prepare releaseJohannes Ranke1-1/+1
2014-11-23Avoid spurious warning in mkinparplot, bump versionJohannes Ranke1-2/+2
2014-11-21Update date and static docs for release to CRANv0.9-34Johannes Ranke1-1/+1
2014-11-13Update the dateJohannes Ranke1-1/+1
2014-10-22Always include 0 on y axis when plotting during the fitJohannes Ranke1-1/+1
2014-10-15Switch to using the Port algorithm per defaultJohannes Ranke1-4/+4
2014-10-14Further formatting improvement for differential equationsJohannes Ranke1-1/+1
2014-10-12Use title case for the titleJohannes Ranke1-2/+2
Tried to adhere to the Chicago Manual of Style, but am not sure about "with".
2014-10-11Start new development versionJohannes Ranke1-1/+1
2014-10-11Updates intended for releasing mkin 0.9-33Johannes Ranke1-1/+1
2014-08-20Fix mkinfit for a special situationJohannes Ranke1-1/+1
See NEWS.md: When the parent was not the (only) variable with the highest value out of all variables in the observed data, it could happen that the initial value (state.ini) was not initialised.
2014-08-19Improve formatting of differential equations in outputJohannes Ranke1-2/+3
Rebuild of FOCUS_Z vignette with improved formatting
2014-07-25Fix internal naming of g for transform_fractions=FALSEJohannes Ranke1-1/+1
2014-07-24Bump version, better default for state.iniJohannes Ranke1-1/+1
2014-07-24Avoid artificial zero residual in mkinresplotJohannes Ranke1-1/+1
2014-07-23Parallel metabolite formation with formation fractions in mkinerrminJohannes Ranke1-1/+1
2014-07-21Bugfix, model shorthand, state.ini[[1]] from observed dataJohannes Ranke1-1/+1
- 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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