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2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke1-10/+14
Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel mailing list and for the suggestion on how to fix it. See the current benchmark vignette for the new data on mkin 1.1.1 with R 4.2.1, with unprecedented performance.
2022-03-02Make tests more platform independent, update docsJohannes Ranke1-3/+3
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke1-3/+3
2021-11-17Update required saemix version, update testsJohannes Ranke1-4/+4
2021-09-16Adapt and improve the dimethenamid vignetteJohannes Ranke1-5/+5
Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke1-26/+8
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke1-1/+16
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-07-23Rerun tests, use current vdiffr on travisJohannes Ranke1-7/+7
2021-04-21Merge branch 'master' into saemixJohannes Ranke1-45/+21
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-45/+21
In residual plots, use xlab and xlim if appropriate
2021-02-15Fully rebuild docs, rerun tests and checkJohannes Ranke1-2/+2
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-52/+26
Also bump version to 1.0.3.
2020-11-19Depend on parallel, doc improvementsJohannes Ranke1-44/+80
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.
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-6/+15
2020-10-08Fix issues for releaseJohannes Ranke1-6/+13
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-5/+5
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.
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-58/+56
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-58/+62
Preparing for symbolic solutions for more than one compound
2019-05-02Remove reference to archived kinfit packageJohannes Ranke1-65/+70
from vignettes/mkin.Rmd Static documentation rebuilt by pkgdown
2019-04-04Direct error model fitting worksJohannes Ranke1-46/+56
- 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
2019-01-31Restore NAMESPACEJohannes Ranke1-55/+383
which was accidentally overwritten by pkgdown -> roxygen
2018-07-18Correct references to the Rocke and Lorenzato modelJohannes Ranke1-54/+50
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
2018-01-14Load mkin quietly in vignettesJohannes Ranke1-8/+8
Static documentation articles rebuilt by pkgdown::build_articles()
2017-11-16Use html_vignette for FOCUS_D vignette, fix addressv0.9.46.3Johannes Ranke1-125/+54
Static documentation articles rebuilt by pkgdown::build_articles()
2017-07-21Fix another URL, vignette builder, rebuildJohannes Ranke1-9/+9
2017-05-05Static docs except articles rebuilt with current pkgdownJohannes Ranke1-10/+10
2016-11-18Fix links in README, configure navbar, rebuild docsJohannes Ranke1-10/+15
2016-11-17Use plot_sep in FOCUS D vignetteJohannes Ranke1-15/+18
2016-10-22Update way to specify encoding, improve FOCUS_L TOCJohannes Ranke1-16/+13
2016-09-28Add drat target and rebuild for dratJohannes Ranke1-0/+337
2016-09-10Static documentation rebuilt with current staticdocsJohannes Ranke1-332/+0
Using hadley/staticdocs commit #8c1069d from 8 days ago
2016-09-10Static documentation rebuilt by staticdocs::build_site()Johannes Ranke1-7/+7
2016-06-28Bump version for new release, rebuild static docsJohannes Ranke1-4/+4
The test test_FOMC_ill-defined leads to errors on several architectures/distributions, as apparent from CRAN checks, so we need a new release. Static documentation rebuilt by staticdocs::build_site()
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke1-11/+6
2016-06-28Attempts to reduce vignette sizeJohannes Ranke1-7/+12
Reducing the size of some figures and switching of retina figures in the preamble only gives a small decrease in vignette size, but may be enough to get the size of the doc directory below 5 MB to avoid the NOTE in the corresponding check (which I did not get locally, nor on winbuilder using r-devel.
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke1-3/+3
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke1-3/+3
2016-06-28Avoid multicore fits in vignettes for passing CRAN checksJohannes Ranke1-16/+73
Also a small fix to the FOCUS Z vignette, and an update of the static documentation generated by staticdocs.
2016-03-24Static documentation rebuilt by staticdocs::build_site()v0.9.42Johannes Ranke1-10/+10
2016-03-23Added 'from_max_mean' to 'mkinfit'.Johannes Ranke1-9/+9
- 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
2015-12-09Static documentation rebuilt by staticdocs::build_site()Johannes Ranke1-2/+2
2015-11-13Add plots to compiled_models vignette, rebuild staticdocsJohannes Ranke1-2/+2
2015-11-09Rebuild vignettes and static documentationJohannes Ranke1-2/+2
2015-11-09Export print.mkinds and rebuild vignettesJohannes Ranke1-2/+2
2015-07-21Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-2/+2
r-forge
2015-07-20Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-5/+5
r-forge
2015-07-20Avoid error message for SFORB in endpoints, updatesJohannes Ranke1-6/+6
2015-06-26Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-39Johannes Ranke1-3/+3
r-forge
2015-06-26Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-10/+5
r-forge
2015-06-26Pass R CMD check --as-cran, vignette rebuildJohannes Ranke1-9/+14

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