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2019-04-04Direct error model fitting worksJohannes Ranke1-160/+1514
- 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
2018-07-18Correct references to the Rocke and Lorenzato modelJohannes Ranke1-434/+337
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
2018-03-01Static documentation rebuilt using current pkgdown::build_site()Johannes Ranke1-345/+437
2018-01-14Load mkin quietly in vignettesJohannes Ranke1-40/+40
Static documentation articles rebuilt by pkgdown::build_articles()
2017-07-21Fix another URL, vignette builder, rebuildJohannes Ranke1-45/+45
2017-05-05Static docs except articles rebuilt with current pkgdownJohannes Ranke1-53/+53
2016-11-18Fix links in README, configure navbar, rebuild docsJohannes Ranke1-27/+27
2016-11-17RebuildJohannes Ranke1-32/+32
2016-11-17Improve yaml header, remove trailing whitespaceJohannes Ranke1-48/+58
Now the year is showing in the reference, and the TOC is not collapsed.
2016-10-22Update way to specify encoding, improve FOCUS_L TOCJohannes Ranke1-50/+56
2016-09-28Add drat target and rebuild for dratJohannes Ranke1-0/+830
2016-09-10Static documentation rebuilt with current staticdocsJohannes Ranke1-830/+0
Using hadley/staticdocs commit #8c1069d from 8 days ago
2016-09-10Static documentation rebuilt by staticdocs::build_site()Johannes Ranke1-31/+32
2016-06-28Bump version for new release, rebuild static docsJohannes Ranke1-28/+28
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 Ranke1-28/+28
2016-06-28Attempts to reduce vignette sizeJohannes Ranke1-30/+30
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 Ranke1-20/+20
2016-06-28Static documentation rebuilt by staticdocs::build_site()Johannes Ranke1-21/+21
2016-06-28Avoid multicore fits in vignettes for passing CRAN checksJohannes Ranke1-32/+34
Also a small fix to the FOCUS Z vignette, and an update of the static documentation generated by staticdocs.
2016-06-27Complete mkin vignette, update FOCUS L vignetteJohannes Ranke1-341/+301
The mkin vignette now describes how confidence intervals and the t-test are calculated. The FOCUS L vignette is updated with the new floating toc provided by the current rmarkdown package, and also uses current, improved mkin functionality.
2016-03-24Static documentation rebuilt by staticdocs::build_site()v0.9.42Johannes Ranke1-82/+82
2016-03-23Added 'from_max_mean' to 'mkinfit'.Johannes Ranke1-10/+10
- 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 Ranke1-32/+32
r-forge
2015-07-20Avoid error message for SFORB in endpoints, updatesJohannes Ranke1-44/+44
2015-06-26Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-39Johannes Ranke1-30/+30
r-forge
2015-06-26Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-37/+32
r-forge
2015-06-26Pass R CMD check --as-cran, vignette rebuildJohannes Ranke1-44/+49
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-38Johannes Ranke1-39/+39
r-forge
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵v0.9-37Johannes Ranke1-30/+30
r-forge
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-29/+29
r-forge
2015-06-23Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-30/+30
r-forge
2015-06-22Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-30/+30
r-forge
2015-06-22Vignettes rebuilt by staticdocs::build_site() for static documentation on ↵Johannes Ranke1-30/+30
r-forge
2015-06-22Vignettes rebuilt by staticdocs::build_site() for r-forgeJohannes Ranke1-36/+32
2015-06-22Version bump, correct benchmark in vignette/compiled_modelsJohannes Ranke1-479/+205
Reorganisation of the vignette generation in the Makefile. Improved YAML header in the R markdown vignettes. Rebuilt vignettes with the package installed.
2015-06-21Rebuild vignettes with the released package installedJohannes Ranke1-30/+30
2015-06-21Vignettes as rebuilt for the static documentation for r-forgeJohannes Ranke1-30/+30
2015-06-21Do the t-test for untransformed parametersv0.9-36Johannes Ranke1-169/+188
2015-04-16Pending commit of an updated vignetteJohannes Ranke1-77/+76
2014-12-18Updated vignettes during staticdoc generationJohannes Ranke1-30/+30
2014-11-21Update date and static docs for release to CRANv0.9-34Johannes Ranke1-277/+271
2014-10-15Switch to using the Port algorithm per defaultJohannes Ranke1-62/+73
2014-10-14Further formatting improvement for differential equationsJohannes Ranke1-45/+51
2014-10-11Updated vignettes by building static documentationJohannes Ranke1-97/+111
2014-08-25Bug fix and unit tests for mkinerrminJohannes Ranke1-51/+61
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