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2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-1/+1
In residual plots, use xlab and xlim if appropriate
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-1/+1
Also bump version to 1.0.3.
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-1/+1
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-1/+1
The errors in the example code were in the \dontrun sections, so they were not caught by CRAN checks. In addition, the static help files generated with pkgdown were cached, so I noticed the errors only after completely regenerating the documentation for version 1.0.0.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-2/+1
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
2021-01-11Rebuild docsJohannes Ranke1-1/+3
2020-12-19Dimethenamid data, normalisation optionsJohannes Ranke1-1/+0
2020-11-19Update tests, improve CAKE_export testJohannes Ranke1-0/+1
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-1/+1
2020-06-15Fix a bug, update for current vdiffrJohannes Ranke1-20/+4
Vignette FOCUS_L failed as I had introduced a bug in the handling of warnings. Current vdiffr only runs visual tests if R < 4.1.0, skipping r-devel for now, see https://github.com/r-lib/vdiffr/commit/630a29d013361fd63fea242f531e2db6aef37919
2020-05-29Improve handling of warnings, reorganize testsJohannes Ranke1-4/+20
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-1/+1
Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-1/+1
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-1/+1
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-1/+1
Still in preparation for analytical solutions of coupled models
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-1/+0
Preparing for symbolic solutions for more than one compound
2020-04-20Updated build and check logsv0.9.49.11Johannes Ranke1-1/+1
2020-04-07Add some tests for the nlme convenience functionsJohannes Ranke1-1/+1
2020-01-09Remove unused FME package from DESCRIPTION textJohannes Ranke1-1/+1
2019-11-04Scaled residual plotsJohannes Ranke1-1/+1
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-1/+1
2019-09-18Add url: tag to _pkgdown.ymlJohannes Ranke1-0/+9
Static documentation rebuilt by pkgdown
2019-09-18Correct and rebuild docsJohannes Ranke1-9/+0
- Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-0/+9
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.
2019-05-23Fix a bug that could lead to wrong chi2 error levelsJohannes Ranke1-9/+0
2019-05-03Improve error model fittingJohannes Ranke1-3/+1
Now we have a three stage fitting process for nonconstant error models: - Unweighted least squares - Only optimize the error model - Optimize both Static documentation rebuilt by pkgdown
2019-05-02Build logJohannes Ranke1-1/+3
2019-05-02Prepare for CRAN releaseJohannes Ranke1-3/+1
- 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 Ranke1-1/+3
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-0/+9
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-04-04Direct error model fitting worksJohannes Ranke1-9/+0
- 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
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke1-1/+0
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 Ranke1-0/+1
2019-02-25Shorten path to test plotJohannes Ranke1-3/+0
2019-02-25Fix tests and add plot and print for naftaJohannes Ranke1-0/+3
2019-02-21Remove unused codeJohannes Ranke1-1/+1
2018-09-18Support maximum twa for HS, test, docsJohannes Ranke1-1/+1
2018-09-14Update NEWSJohannes Ranke1-1/+1
Static documentation rebuilt by pkgdown
2018-09-14Exclude more example code from CRAN checksJohannes Ranke1-1/+1
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 Ranke1-1/+1
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 Ranke1-1/+1
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
2018-01-07Don't run water sediment example to reduce time neededJohannes Ranke1-1/+6
Static documentation except articles rebuilt by pkgdown
2018-01-05Update _pkgdown.ymlJohannes Ranke1-6/+1
Static documentation except articles rebuilt by pkgdown
2018-01-05Experimental test data from UBA 2014 expertiseJohannes Ranke1-1/+1
- Typo in synthetic data for UBA - Static documentation except articles rebuilt by pkgdown
2017-11-16Update URLS in mkin vignetteJohannes Ranke1-1/+6
Static documentation except articles rebuilt by pkgdown
2017-11-16Add the code used for generating synthetic_data_for_UBAJohannes Ranke1-6/+1
Static documentation except articles rebuilt by pkgdown
2017-10-10Add ORCID to DESCRIPTION, released versionv0.9.46.2Johannes Ranke1-1/+1
Static documentation except articles rebuilt by pkgdown
2017-09-18Change Depends to ImportsJohannes Ranke1-1/+1
as recommended, e.g. by Uwe Ligges in his useR! 2017 keynote
2017-09-07Update Date in DESCRIPTION, last build logJohannes Ranke1-1/+6

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