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2018-01-07Don't run water sediment example to reduce time neededJohannes Ranke1-0/+2
Static documentation except articles rebuilt by pkgdown
2018-01-05Convert synthetic_data_for_UBA_2014 to mkindsJohannes Ranke2-5/+4
Static documentation except articles rebuilt by pkgdown
2018-01-05Experimental test data from UBA 2014 expertiseJohannes Ranke2-1/+53
- Typo in synthetic data for UBA - Static documentation except articles rebuilt by pkgdown
2017-11-16Add the code used for generating synthetic_data_for_UBAJohannes Ranke2-4/+83
Static documentation except articles rebuilt by pkgdown
2017-07-21Fix URLsJohannes Ranke13-13/+13
2017-07-21Rename twa to max_twa_parent, update docsJohannes Ranke1-4/+4
2017-05-05Static docs except articles rebuilt with current pkgdownJohannes Ranke14-14/+14
2016-12-21TWA calculation for SFO, FOMC and DFOP (parent)Johannes Ranke1-0/+40
2016-12-07Use latex in plots when using tikzDeviceJohannes Ranke2-0/+7
2016-11-18Improve examples for showing with pkgdownJohannes Ranke13-43/+72
- Use quiet= TRUE in dontrun sections - Use mkinsub in model definitions - Avoid \code{\link{}} in titles
2016-11-18Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)Johannes Ranke2-3/+3
Using branch 'jranke' on jranke/pkgdown, fixing issues hadley/pgkdown#178 and hadley/pkgdown#213 Remove plot=TRUE from mkinfit calls also in dontrun sections of examples to avoid a flood png files documenting the progress of the fit.
2016-11-17Remove trailing whitespace, clean headersJohannes Ranke13-85/+85
Also ignore test.R in the top level directory, as it is not meant to be public
2016-06-28Convenience wrapper plot_sep, further vignette updatesJohannes Ranke1-0/+5
2016-06-27Improve listing of weights in output, update NEWSJohannes Ranke2-9/+9
2016-06-27Show chi2 in plot.mkinfit, round with signifJohannes Ranke3-7/+18
2016-06-25Fix the plot margins for combined plotsJohannes Ranke3-9/+12
2016-06-25Now the old behaviour is restored for compatibility reasonsJohannes Ranke1-3/+8
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 Ranke3-20/+39
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 Ranke2-0/+103
2016-06-24TypoJohannes Ranke1-1/+1
2016-03-23Added 'from_max_mean' to 'mkinfit'.Johannes Ranke1-0/+8
- 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
2015-11-09Exclude more mkinmod examples, as winbuilder NOTEs > 5 sJohannes Ranke1-1/+1
2015-11-09Rebuild vignettes and static documentationJohannes Ranke1-2/+1
2015-10-19Add the R6 class mkindsJohannes Ranke2-0/+53
2015-10-19Add a print method for mkinmod objectsJohannes Ranke1-0/+19
2015-10-16Full compound names in models that are shown in the plotJohannes Ranke2-2/+14
2015-07-22Remove periods in help file titlesJohannes Ranke7-7/+7
2015-07-20Use UTF-8 in the Schaefer 07 help fileJohannes Ranke1-2/+2
2015-07-20Updates and fixes to documentationJohannes Ranke4-4/+3
2015-07-20Remove Rdversion tag that disappeared from "Writing R extensions"Johannes Ranke13-13/+0
2015-06-29Quiet fitting in examples and more links for static docs.Johannes Ranke9-11/+22
2015-06-26Pass R CMD check --as-cran, vignette rebuildJohannes Ranke2-3/+6
2015-06-26More plotting in help files, fix Make- and .*ignore filesJohannes Ranke6-20/+12
2015-06-26Subsetting and plotting for mmkin objectsJohannes Ranke3-3/+89
Including documentation and documentation improvements for mmkin().
2015-06-25Fix fitting with parLapply, doc fixJohannes Ranke1-0/+1
2015-06-25Add mmkin for testingJohannes Ranke1-0/+64
2015-06-23Fix the changed documentationJohannes Ranke1-3/+4
2015-06-23Small documenation changesJohannes Ranke3-10/+12
2015-06-23Hopefully fix compiling on Solaris, verbose optionJohannes Ranke1-2/+11
- 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.
2015-06-23Improve formatting of \dontrun sectionJohannes Ranke1-2/+4
2015-06-20Reorganize transform_odeparms example, reduce check timeJohannes Ranke1-1/+5
2015-06-20Low-level generation of compiled modelsJohannes Ranke2-3/+3
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.
2015-06-05Make the examples that are run more quietJohannes Ranke1-2/+2
2015-05-19Include output in README, use mkinsub() in example codeJohannes Ranke2-15/+33
2015-05-18Make checking faster, testing is done by testsJohannes Ranke3-13/+10
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke1-0/+1
2015-05-15Reduce time to run mkinfit exampleJohannes Ranke1-0/+2
2015-05-15Make mkinmod quiet in testsJohannes Ranke1-1/+4
2015-05-15Merge branch 'master' into compile_odesJohannes Ranke1-0/+65
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/+65
The new tests are based on the results documented in the expertise I wrote for the UBA (currently unpublished).

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