| Age | Commit message (Collapse) | Author | Files | Lines | |
|---|---|---|---|---|---|
| 2016-04-21 | Avoid unnecessary stop in edge case, improve warnings | Johannes Ranke | 1 | -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. | |||||
| 2016-03-25 | Remove outdated reference to the inline package | Johannes Ranke | 1 | -2/+2 | |
| 2016-03-24 | Address feedback from CRAN submission | Johannes Ranke | 1 | -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 | |||||
| 2016-03-23 | Added 'from_max_mean' to 'mkinfit'. | Johannes Ranke | 1 | -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 | |||||
| 2015-11-13 | Add plots to compiled_models vignette, rebuild staticdocs | Johannes Ranke | 1 | -2/+2 | |
| 2015-11-13 | Bump version, change to version number format as shown in summaries | Johannes Ranke | 1 | -1/+1 | |
| 2015-11-09 | Export print.mkinds and rebuild vignettes | Johannes Ranke | 1 | -2/+2 | |
| 2015-10-19 | Add the R6 class mkinds | Johannes Ranke | 1 | -1/+1 | |
| 2015-10-19 | Add a print method for mkinmod objects | Johannes Ranke | 1 | -1/+1 | |
| 2015-10-16 | Full compound names in models that are shown in the plot | Johannes Ranke | 1 | -1/+1 | |
| 2015-07-22 | Increment version number for development | Johannes Ranke | 1 | -2/+2 | |
| 2015-07-21 | Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-40 | Johannes Ranke | 1 | -1/+1 | |
| r-forge | |||||
| 2015-07-20 | Remove obvious CRAN URL | Johannes Ranke | 1 | -3/+2 | |
| 2015-07-20 | Avoid error message for SFORB in endpoints, updates | Johannes Ranke | 1 | -1/+1 | |
| 2015-06-30 | Improve calculation of DT90 in endpoints(), check and test | Johannes Ranke | 1 | -2/+2 | |
| 2015-06-29 | Bump version, as 0.9-39 is now on CRAN | Johannes Ranke | 1 | -2/+2 | |
| 2015-06-25 | Depend on parallel package, todays date | Johannes Ranke | 1 | -2/+2 | |
| 2015-06-23 | Version bump, keep logs of build, check and test | Johannes Ranke | 1 | -1/+1 | |
| 2015-06-23 | Remove Rplots.pdf that is being built by staticdocs | Johannes Ranke | 1 | -1/+1 | |
| 2015-06-23 | Set the correct date in DESCRIPTION | Johannes Ranke | 1 | -1/+1 | |
| 2015-06-22 | Version bump, correct benchmark in vignette/compiled_models | Johannes Ranke | 1 | -2/+2 | |
| Reorganisation of the vignette generation in the Makefile. Improved YAML header in the R markdown vignettes. Rebuilt vignettes with the package installed. | |||||
| 2015-06-21 | Do the t-test for untransformed parametersv0.9-36 | Johannes Ranke | 1 | -2/+2 | |
| 2015-06-20 | Low-level generation of compiled models | Johannes Ranke | 1 | -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. | |||||
| 2015-05-18 | Make checking faster, testing is done by tests | Johannes Ranke | 1 | -1/+1 | |
| 2015-05-15 | Clean up meta information | Johannes Ranke | 1 | -3/+4 | |
| 2015-05-15 | Merge branch 'master' into compile_odes | Johannes Ranke | 1 | -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 | |||||
| 2015-05-15 | Quote FME package name in DESCRIPTION | Johannes Ranke | 1 | -1/+1 | |
| 2015-05-15 | Correct the date | Johannes Ranke | 1 | -1/+1 | |
| 2015-05-15 | Finished migration from RUnit to testthat | Johannes Ranke | 1 | -1/+1 | |
| 2015-05-14 | Start of migration from RUnit to testthat | Johannes Ranke | 1 | -2/+3 | |
| 2015-04-18 | Add a vignette showing the performance of compiled models | Johannes Ranke | 1 | -1/+1 | |
| 2015-04-17 | Add NEWS about compiled models, set the date | Johannes Ranke | 1 | -1/+1 | |
| 2015-04-14 | Compile differential equation models with ccSolve package | Johannes Ranke | 1 | -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 | |||||
| 2015-02-20 | Add termination message to mkinfit, prepare release | Johannes Ranke | 1 | -1/+1 | |
| 2014-11-23 | Avoid spurious warning in mkinparplot, bump version | Johannes Ranke | 1 | -2/+2 | |
| 2014-11-21 | Update date and static docs for release to CRANv0.9-34 | Johannes Ranke | 1 | -1/+1 | |
| 2014-11-13 | Update the date | Johannes Ranke | 1 | -1/+1 | |
| 2014-10-22 | Always include 0 on y axis when plotting during the fit | Johannes Ranke | 1 | -1/+1 | |
| 2014-10-15 | Switch to using the Port algorithm per default | Johannes Ranke | 1 | -4/+4 | |
| 2014-10-14 | Further formatting improvement for differential equations | Johannes Ranke | 1 | -1/+1 | |
| 2014-10-12 | Use title case for the title | Johannes Ranke | 1 | -2/+2 | |
| Tried to adhere to the Chicago Manual of Style, but am not sure about "with". | |||||
| 2014-10-11 | Start new development version | Johannes Ranke | 1 | -1/+1 | |
| 2014-10-11 | Updates intended for releasing mkin 0.9-33 | Johannes Ranke | 1 | -1/+1 | |
| 2014-08-20 | Fix mkinfit for a special situation | Johannes Ranke | 1 | -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. | |||||
| 2014-08-19 | Improve formatting of differential equations in output | Johannes Ranke | 1 | -2/+3 | |
| Rebuild of FOCUS_Z vignette with improved formatting | |||||
| 2014-07-25 | Fix internal naming of g for transform_fractions=FALSE | Johannes Ranke | 1 | -1/+1 | |
| 2014-07-24 | Bump version, better default for state.ini | Johannes Ranke | 1 | -1/+1 | |
| 2014-07-24 | Avoid artificial zero residual in mkinresplot | Johannes Ranke | 1 | -1/+1 | |
| 2014-07-23 | Parallel metabolite formation with formation fractions in mkinerrmin | Johannes Ranke | 1 | -1/+1 | |
| 2014-07-21 | Bugfix, model shorthand, state.ini[[1]] from observed data | Johannes Ranke | 1 | -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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index : mkin | |
| Fitting kinetic models to chemical degradation data (also on github) | Johannes Ranke |
| aboutsummaryrefslogtreecommitdiff |
path: root/DESCRIPTION