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2018-09-14Update NEWSJohannes Ranke1-2/+4
Static documentation rebuilt by pkgdown
2018-09-14Avoid nls crashes by checking for a correlation firstJohannes Ranke1-0/+7
2018-09-13Enable new error model in gmkinJohannes Ranke1-7/+20
Also improve the irls fitting of the error model and add a test for FOCUS_2006_C where the second component of the error model is zero
2018-07-18Correct references to the Rocke and Lorenzato modelJohannes Ranke3-6/+6
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
2018-07-04Improve IORE fitting, use 1.1 as N starting valueJohannes Ranke1-1/+4
2018-02-02mkinfit: Work around a bug in the current FME versionJohannes Ranke1-6/+15
that prevented the convergence message to be returned in the case of non-convergence.
2018-02-02Show R and mkin version used for fitting in the summaryJohannes Ranke1-2/+15
For fits generated with previous version, the version numbers used for fitting were not stored in the fit object. Therefore, the versions used for fitting can only be shown for fits generated with mkin containing this commit.
2018-01-30Reweighting with two-component error modelJohannes Ranke2-20/+92
Static documentation except articles rebuilt by pkgdown
2017-11-16Add the code used for generating synthetic_data_for_UBAJohannes Ranke1-3/+3
Static documentation except articles rebuilt by pkgdown
2017-09-06Use full fitted curve(s) for y axis scaling ...Johannes Ranke1-2/+1
... when using plot_sep() or plot.mkinfit(..., sep_obs = TRUE)
2017-09-06Fix comment that was copied without checkingJohannes Ranke1-1/+1
2017-09-06Fix scaling of residual plots ...Johannes Ranke1-2/+6
... in the case of separate plots for each observed variable as obtained with plot_sep() or plot.mkinfit(..., sep_obs = TRUE)
2017-07-21Rename twa to max_twa_parent, update docsJohannes Ranke1-2/+2
2016-12-21TWA calculation for SFO, FOMC and DFOP (parent)Johannes Ranke1-0/+65
2016-12-07Use latex in plots when using tikzDeviceJohannes Ranke2-4/+19
2016-11-18Show differential equations when printing mkinmodsJohannes Ranke1-0/+3
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

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