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2019-07-02TypoJohannes Ranke1-1/+1
2019-06-04Add sources for test data for better transparencyJohannes Ranke1-0/+55
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke3-0/+44
The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets.
2019-05-31Experimental data for finding error model algorithmJohannes Ranke1-0/+65
2019-05-21Clarify the relation of the two-component error modelJohannes Ranke1-2/+3
in relation to the original version by Rocke and Lorenzato
2019-05-08Add functionality to plot the error modelJohannes Ranke3-7/+106
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2019-05-02Prepare for CRAN releaseJohannes Ranke1-1/+2
- Skip long running tests on CRAN as well to avoid timeout on winbuilder - Don't install benchmark results in the package, they are only needed in the git repository - Don't run example in man/add_err.Rd as it takes > 10 s on winbuilder - Rebuild docs
2019-05-02Better initials for error model parametersJohannes Ranke1-0/+7
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke10-182/+89
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-04-04Direct error model fitting worksJohannes Ranke1-29/+17
- 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
2019-03-04Make some example output more reproducibleJohannes Ranke3-11/+18
In order to avoid some unnecessary documentation rebuilds
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke2-1/+6
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke6-6/+45
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 Ranke2-8/+9
2019-02-25Test printing the summary of an mkinfit objectJohannes Ranke1-2/+2
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke4-0/+136
2019-02-22Further adaptations for the logistic modelJohannes Ranke1-3/+4
- 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
2019-02-21Remove unused codeJohannes Ranke1-1/+0
2019-02-21Make example logistic fit quietJohannes Ranke1-1/+1
2019-02-21Add the logistic modelJohannes Ranke1-0/+68
2019-01-31Correct title for CAKE_exportJohannes Ranke1-1/+1
Add NEWS entry. Static documentation rebuilt by pkgdown
2019-01-31Export to CAKE study fileJohannes Ranke1-0/+73
2018-11-26Add AIC method for mmkin column objectsJohannes Ranke2-4/+52
Static documentation rebuilt by pkgdown
2018-11-26Further improvement of the logLik.mkinfit helpJohannes Ranke1-1/+3
Static documentation rebuilt by pkgdown
2018-11-26Static documentation rebuilt by pkgdownJohannes Ranke1-1/+19
2018-11-26Support logLik and AIC for manual weightsJohannes Ranke1-2/+4
Static documentation rebuilt by pkgdown
2018-11-23Add logLik method to enable AIC() on mkinfit modelsJohannes Ranke2-1/+44
Further relax two tests to pass build on Travis
2018-09-18Make mkinpredict generic and write a method for fitsJohannes Ranke1-16/+26
2018-09-18Support maximum twa for HS, test, docsJohannes Ranke1-1/+1
2018-09-14Exclude more example code from CRAN checksJohannes Ranke3-9/+12
to avoid NOTES about long execution times. Static documentation rebuilt by pkgdown with run_dont_run = TRUE
2018-09-13Enable new error model in gmkinJohannes Ranke1-2/+3
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
2018-09-06Small doc corrections and improvementsJohannes Ranke1-7/+8
2018-07-18Correct references to the Rocke and Lorenzato modelJohannes Ranke3-9/+23
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
2018-03-21Give a bit more advice on multicore use on WindowsJohannes Ranke1-1/+3
2018-03-11Adapt usage section in help for old dataset to lazy loadingJohannes Ranke5-5/+5
Rebuild pkgdown reference
2018-02-06Skip some tests on CRAN, more quiet examplesv0.9.47.1Johannes Ranke1-3/+3
2018-01-30Improve documentation of Rocke and Lorenzato modelJohannes Ranke1-2/+3
Static documentation except articles rebuilt by pkgdown
2018-01-30Reweighting with two-component error modelJohannes Ranke2-6/+47
Static documentation except articles rebuilt by pkgdown
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.

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