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2016-11-17Show diffs in correct mathematical form in summaryJohannes Ranke1-1/+2
2016-11-17Remove trailing whitespace, clean headersJohannes Ranke16-140/+136
Also ignore test.R in the top level directory, as it is not meant to be public
2016-09-10Plot using R model if compiled model is not availableJohannes Ranke1-2/+9
2016-06-28Convenience wrapper plot_sep, further vignette updatesJohannes Ranke1-0/+6
2016-06-27Improve listing of weights in output, update NEWSJohannes Ranke1-1/+7
2016-06-27Show chi2 in plot.mkinfit, round with signifJohannes Ranke2-6/+22
2016-06-25Fix the plot margins for combined plotsJohannes Ranke2-2/+37
2016-06-25Now the old behaviour is restored for compatibility reasonsJohannes Ranke1-10/+17
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 Ranke1-48/+88
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 Ranke2-7/+56
2016-06-17Change the title of the package, small bugfixJohannes Ranke1-1/+1
2016-06-17Remove misplaced commentJohannes Ranke1-4/+1
2016-06-09Fix a bug in the listing of formation fractionsJohannes Ranke1-4/+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 Ranke1-6/+14
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.
2016-03-23Added 'from_max_mean' to 'mkinfit'.Johannes Ranke1-1/+14
- 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 Ranke1-2/+3
2015-12-09Improve mkinmod error message for missing target compartment definitionJohannes Ranke1-0/+1
Closes #6.
2015-11-06Improve formatting of summaryJohannes Ranke1-4/+4
2015-10-24Improve printing method for mkinmodJohannes Ranke1-1/+1
2015-10-24Sort sampling times in mkindsJohannes Ranke1-1/+1
2015-10-21Avoid an error printing old mkinfit summariesJohannes Ranke1-5/+10
2015-10-19Add the R6 class mkindsJohannes Ranke1-1/+1
2015-10-19Make plot.mkinfit work with models where full_name components are NULLJohannes Ranke2-0/+67
2015-10-19Add a print method for mkinmod objectsJohannes Ranke1-0/+16
2015-10-16Full compound names in models that are shown in the plotJohannes Ranke2-5/+9
2015-07-20Avoid error message for SFORB in endpoints, updatesJohannes Ranke1-7/+14
2015-06-30Improve calculation of DT90 in endpoints(), check and testJohannes Ranke1-16/+22
2015-06-30Start to import or qualify functions from stats, utils et al.Johannes Ranke2-3/+3
2015-06-26Fix x axis scaling in mkinparplotJohannes Ranke1-1/+1
2015-06-26Subsetting and plotting for mmkin objectsJohannes Ranke2-0/+107
Including documentation and documentation improvements for mmkin().
2015-06-25Fix fitting with parLapply, doc fixJohannes Ranke1-1/+1
2015-06-25Add mmkin for testingJohannes Ranke1-0/+46
2015-06-23Hopefully fix compiling on Solaris, verbose optionJohannes Ranke1-11/+23
- 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.
2015-06-21Do the t-test for untransformed parametersv0.9-36Johannes Ranke1-18/+71
2015-06-20Suppress compiler warning for sometimes unused time variableJohannes Ranke1-1/+3
2015-06-20Low-level generation of compiled modelsJohannes Ranke7-62/+104
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.
2015-05-15Make mkinmod quiet in testsJohannes Ranke1-4/+4
2015-04-18Add a vignette showing the performance of compiled modelsJohannes Ranke1-3/+6
2015-04-17Make compiled FOMC and DFOP models workJohannes Ranke1-5/+4
- Many thanks @karlines for the hint in ccSolve#1 how to declare the time variable and for writing the ccSolve package in the first place - Add tests for the compiled versions of the FOMC and DFOP models
2015-04-16Order of parameters needs to be right for compiled modelsJohannes Ranke1-1/+1
2015-04-16Update copyright header, improve documentation of solution_typeJohannes Ranke3-14/+19
2015-04-16Check compiled mkinmod versions in examples and testsJohannes Ranke2-1/+5
Tests all pass (Linux)
2015-04-14Compile differential equation models with ccSolve packageJohannes Ranke2-9/+47
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
2015-02-21Avoid NOTES in R CMD checkJohannes Ranke1-1/+1
- Export S3 methods - Avoid using undeclared variable names
2015-02-20Add termination message to mkinfit, prepare releaseJohannes Ranke1-1/+9
2015-02-20Fix printing the summary if iterations are not availableJohannes Ranke1-1/+4
This was broken for using method.modFit = "SANN"
2014-11-23Simply get rid of the warnings when drawing arrowsJohannes Ranke1-8/+7
2014-11-23Avoid spurious warning in mkinparplot, bump versionJohannes Ranke1-4/+10
2014-11-12Fix for IORE in mkinmodJohannes Ranke1-4/+4
2014-11-12IORE working for parent and metabolites, introduce mkinsubJohannes Ranke3-4/+33

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