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2020-11-19Depend on parallel, doc improvementsJohannes Ranke3-96/+171
By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9.
2020-11-06Update benchmarks for dev versionJohannes Ranke1-0/+0
2020-10-15Update online docs for release versionJohannes Ranke1-0/+0
2020-10-15Reintroduce saemix helper functionsJohannes Ranke3-42/+69
2020-10-08Fix issues for releaseJohannes Ranke9-410/+420
2020-05-27Change dev version label to info colorJohannes Ranke1-0/+0
instead of the orange danger color.
2020-05-27Create up to date pkgdown docs in development modeJohannes Ranke1-0/+0
2020-05-26Use all cores per default, confint toleranceJohannes Ranke4-227/+259
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.
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke1-0/+0
2020-05-13Further formatting improvement of benchmark vignetteJohannes Ranke10-581/+564
Also, use .rmd extension instead of .Rmd for vignettes.
2020-05-12Update pkgdownJohannes Ranke1-0/+0
2020-05-12Improve formatting of benchmark vignetteJohannes Ranke3-39/+182
2020-05-12Update vignettes and docsJohannes Ranke6-186/+225
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke2-6/+6
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke4-120/+128
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-10Default to analytical for coupled models if availableJohannes Ranke3-137/+120
This revealed that transforming rates is necessary for fitting the analytical solution of the SFO-SFO model to the FOCUS D dataset. Benchmarks show that fitting coupled models with deSolve got a bit slower through the latest changes
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-58/+62
Preparing for symbolic solutions for more than one compound
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke2-176/+0
2020-04-03Compiled models article, reduce distractionsJohannes Ranke5-208/+542
- Added a section with platform specific notes on getting compiled models to work to the compiled models article - Don't return empty SFORB parameter list from endpoints() if there is no SFORB model - Avoid warnings when using standardized = TRUE in plot.mmkin()
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-0/+0
2019-09-19Static documentation rebuilt by pkgdownJohannes Ranke1-0/+0
Use lazy = TRUE in the pd target for generating pkgdown documentation
2019-09-18Static documentation rebuilt by pkgdownJohannes Ranke3-6/+4
to check if the link to the pfm package is correctly generated by pkgdown after preparing the pfm package docs accordingly
2019-09-18Add url: tag to _pkgdown.ymlJohannes Ranke1-0/+0
Static documentation rebuilt by pkgdown
2019-09-18Further corrections of the twa vignetteJohannes Ranke3-334/+159
Static documentation rebuilt by pkgdown
2019-09-18Correct and rebuild docsJohannes Ranke2-3/+4
- Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown
2019-09-18Add hockey stick formulas to maximum twa vignetteJohannes Ranke2-10/+391
2019-07-09Adaptations for gmkinJohannes Ranke1-0/+0
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke2-2/+2
2019-07-04Update README and introductory vignetteJohannes Ranke3-29/+84
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke1-0/+0
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke1-0/+0
Static documentation rebuilt by pkgdown
2019-06-05Merge branch 'algorithm'Johannes Ranke1-0/+0
2019-06-05Add error model algorithm to outputJohannes Ranke1-0/+0
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-0/+0
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.
2019-05-24TypoJohannes Ranke1-1/+1
2019-05-08Add functionality to plot the error modelJohannes Ranke1-0/+0
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2019-05-07Fix hessian calculationsJohannes Ranke1-0/+0
Static documentation rebuilt by pkgdown
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke1-0/+0
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke1-0/+0
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
2019-05-02Remove reference to archived kinfit packageJohannes Ranke6-290/+1676
from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown
2019-05-02Prepare for CRAN releaseJohannes Ranke4-29/+35
- 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
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke3-0/+4312
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-04-04Direct error model fitting worksJohannes Ranke4-220/+1650
- 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 Ranke1-0/+243
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0
2019-01-31Restore NAMESPACEJohannes Ranke2-60/+389
which was accidentally overwritten by pkgdown -> roxygen
2018-09-14Remove two vignettes from the package but not from docsJohannes Ranke7-642/+3454
- Rebuild static documentation - Adapt test to new approach to two component error model where the model is inadequate
2018-07-18Correct references to the Rocke and Lorenzato modelJohannes Ranke4-539/+440
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
2018-03-09Another rebuild of the static docsJohannes Ranke1-19/+19
Now with rbenchmark installed, to get results for the compiled_models vignette
2018-03-01Static documentation rebuilt using current pkgdown::build_site()Johannes Ranke2-347/+439
2018-01-16Updates in the FOCUS Z vignetteJohannes Ranke3-61/+50
To make the text consistent with the results produced by the current mkin version. Static documentation articles rebuilt by pkgdown::build_articles()

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