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2019-04-05Report negative log-likelihood during fitsJohannes Ranke1-4/+10
If not quiet = TRUE
2019-04-04Direct error model fitting worksJohannes Ranke1-366/+133
- No IRLS required - Removed optimization algorithms other than Port - Removed the dependency on FME - Fitting the error model 'obs' is much faster for the FOCUS_2006_D dataset and the FOMC_SFO model (1 second versus 3.4 seconds) - Vignettes build slower. Compiled models needs 3 minutes instead of 1.5 - For other vignettes, the trend is less clear. Some fits are faster, even for error_model = "const". FOCUS_Z is faster (34.9 s versus 44.1 s) - Standard errors and confidence intervals are slightly smaller - Removed code for plotting during the fit, as I hardly ever used it - Merged the two cost functions (using transformed and untransformed parameters) into one log-likelihood function
2019-03-04signif for DTx when printing nafta resultsJohannes Ranke1-1/+1
In order to be able to test cross-platform
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-3/+3
Static documentation rebuilt by pkgdown
2019-02-27Comment out unused codeJohannes Ranke2-27/+27
2019-02-27Increase test coverageJohannes Ranke1-8/+17
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke2-3/+7
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0
2019-02-26Add another NAFTA dataset + testJohannes Ranke1-1/+2
2019-02-25Static documentation rebuilt by current pkgdownJohannes Ranke1-3/+7
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke1-0/+105
2019-02-22Further adaptations for the logistic modelJohannes Ranke3-4/+9
- Make mmkin compatible - Return DT50 values corresponding to k0 and kmax - Turn incompatible parameter names in parms.ini from an error to a warning, in order to make it possible to use this argument in calls to mmkin
2019-02-21Add the logistic modelJohannes Ranke6-17/+43
2019-01-31Restore NAMESPACEJohannes Ranke1-16/+1
which was accidentally overwritten by pkgdown -> roxygen
2019-01-31Export to CAKE study fileJohannes Ranke1-0/+80
2018-11-26Add AIC method for mmkin column objectsJohannes Ranke1-0/+30
Static documentation rebuilt by pkgdown
2018-11-26Support logLik and AIC for manual weightsJohannes Ranke1-2/+11
Static documentation rebuilt by pkgdown
2018-11-23Add logLik method to enable AIC() on mkinfit modelsJohannes Ranke2-1/+36
Further relax two tests to pass build on Travis
2018-11-23Improve initialisation of mkindsJohannes Ranke1-10/+13
Check in work from the beginning of the week
2018-09-21Improve fitting the two-component error modelJohannes Ranke1-47/+83
with respect to accuracy and robustness.
2018-09-20Use the median absolute deviance for fittingJohannes Ranke1-5/+16
as the absolute value is a biased estimator for the standard deviation
2018-09-18Make mkinpredict generic and write a method for fitsJohannes Ranke1-25/+52
2018-09-18Support maximum twa for HS, test, docsJohannes Ranke1-2/+16
2018-09-15Remove correlation test as gmkin on windows still crashesJohannes Ranke1-18/+10
Clean up the code a bit
2018-09-15Respect reps argument in add_errJohannes Ranke1-2/+2
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

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