├── .Rbuildignore ├── .claude └── settings.local.json ├── .github ├── .gitignore ├── FUNDING.yml └── workflows │ ├── check-release.yaml │ ├── check-standard.yaml │ └── pkgdown.yaml ├── .gitignore ├── CITATION.cff ├── CLAUDE.md ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── 00jmv.R ├── advancedraincloud.b.R ├── advancedraincloud.h.R ├── data-histopathology.R ├── hullplot.b.R ├── hullplot.h.R ├── jjarcdiagram.b.R ├── jjarcdiagram.h.R ├── jjbarstats.b.R ├── jjbarstats.h.R ├── jjbetweenstats.b.R ├── jjbetweenstats.h.R ├── jjcorrmat.b.R ├── jjcorrmat.h.R ├── jjdotplotstats.b.R ├── jjdotplotstats.h.R ├── jjhistostats.b.R ├── jjhistostats.h.R ├── jjpiestats.b.R ├── jjpiestats.h.R ├── jjridges.b.R ├── jjridges.h.R ├── jjscatterstats.b.R ├── jjscatterstats.h.R ├── jjsegmentedtotalbar.b.R ├── jjsegmentedtotalbar.h.R ├── jjstatsplot-data.R ├── jjstatsplot-package.R ├── jjwithinstats.b.R ├── jjwithinstats.h.R ├── jwaffle.b.R ├── jwaffle.h.R ├── linechart.b.R ├── linechart.h.R ├── lollipop.b.R ├── lollipop.h.R ├── raincloud.b.R ├── raincloud.h.R ├── statsplot2.b.R ├── statsplot2.h.R └── utils.R ├── README.md ├── _pkgdown.yml ├── data ├── categorical_quality_data.rda ├── groupsummary_financial_data.rda ├── groupsummary_simple.rda ├── histopathology.rda ├── histopathologyGraphsPlots.omv ├── hullplot_clinical_data.rda ├── hullplot_customer_data.rda ├── hullplot_experimental_data.rda ├── hullplot_quality_data.rda └── hullplot_survey_data.rda ├── docs ├── 404.html ├── CLAUDE.html ├── LICENSE.html ├── articles │ ├── 01-introduction.html │ ├── 01-jamovi-user-guide.html │ ├── 02-categorical-plots.html │ ├── 02-categorical-plots_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-2-2.png │ │ │ └── unnamed-chunk-3-1.png │ ├── 03-continuous-comparisons.html │ ├── 03-continuous-comparisons_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-4-1.png │ ├── 04-continuous-comparisons-alt.html │ ├── 04-continuous-comparisons-alt_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-7-1.png │ ├── 05-correlations-scatterplots.html │ ├── 05-correlations-scatterplots_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ └── unnamed-chunk-2-1.png │ ├── 06-BBC-style-data-visualization.html │ ├── 06-use-in-r.html │ ├── 07-advancedbarplot.html │ ├── 08-advancedraincloud.html │ ├── 09-advancedtree.html │ ├── 09-analysis-gallery.html │ ├── 09-analysis-gallery_files │ │ └── figure-html │ │ │ ├── bar-twoway-1.png │ │ │ ├── between-basic-1.png │ │ │ ├── between-multiple-1.png │ │ │ ├── corrmat-basic-1.png │ │ │ ├── corrmat-grouped-1.png │ │ │ ├── dot-basic-1.png │ │ │ ├── dot-multiple-1.png │ │ │ ├── histogram-basic-1.png │ │ │ ├── histogram-grouped-1.png │ │ │ ├── histogram-multiple-1.png │ │ │ ├── pie-basic-1.png │ │ │ ├── scatter-basic-1.png │ │ │ ├── scatter-grouped-1.png │ │ │ ├── waffle-basic-1.png │ │ │ └── within-example-1.png │ ├── 09-basegraphics.html │ ├── 12-economistplots.html │ ├── 13-quick-reference.html │ ├── 14-clinical-classification-comprehensive.html │ ├── 14-r-programming-guide.html │ ├── 14-r-programming-guide_files │ │ └── figure-html │ │ │ ├── boxviolin-1.png │ │ │ ├── histogram-1.png │ │ │ ├── histogram-grouped-1.png │ │ │ ├── scatter-1.png │ │ │ └── scatter-grouped-1.png │ ├── 15-grafify-comprehensive.html │ ├── 15-troubleshooting-faq.html │ ├── 16-jcomplexupset-comprehensive.html │ ├── 17-jextractggstats-comprehensive.html │ ├── 18-jforester-comprehensive.html │ ├── 19-jforestmodel-comprehensive.html │ ├── 20-jggheatmap-comprehensive.html │ ├── 21-jggridges-comprehensive.html │ ├── 22-jggsankeyfier-comprehensive.html │ ├── 22-jjsankeyfier-comprehensive.html │ ├── 23-jggstats-comprehensive.html │ ├── 23-jjbarstats-comprehensive.html │ ├── 24-jjarcdiagram-comprehensive.html │ ├── 24-jjbetweenstats-comprehensive.html │ ├── 25-jjcorrmat-comprehensive.html │ ├── 26-jjdotplotstats-comprehensive.html │ ├── 27-jjhistostats-comprehensive.html │ ├── 28-jjpiestats-comprehensive.html │ ├── 29-jjridges-comprehensive.html │ ├── 29-jjridgestats-comprehensive.html │ ├── 30-jjriverplot-comprehensive.html │ ├── 30-linechart-comprehensive.html │ ├── 31-jjscatterstats-comprehensive.html │ ├── 31-jpps-comprehensive.html │ ├── 31-jscattermore-comprehensive.html │ ├── 31-lollipop-comprehensive.html │ ├── 32-jjstreamgraph-comprehensive.html │ ├── 32-jsjplot-comprehensive.html │ ├── 33-jjtreemap-comprehensive.html │ ├── 33-jsummarytools-comprehensive.html │ ├── 34-jjwithinstats-comprehensive.html │ ├── 34-jviolin-comprehensive.html │ ├── 35-jvisr-comprehensive.html │ ├── 36-jwaffle-comprehensive.html │ ├── categorical-plots.html │ ├── categorical-plots_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-2-2.png │ │ │ └── unnamed-chunk-3-1.png │ ├── continuous-comparisons.html │ ├── continuous-comparisons_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-4-1.png │ ├── correlations-scatterplots.html │ ├── correlations-scatterplots_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ └── unnamed-chunk-2-1.png │ ├── index.html │ ├── jjstatsplot-01-oncodatasets-examples.html │ ├── jjstatsplot-introduction.html │ ├── legacy │ │ ├── 07-continuous-comparisons-legacy.html │ │ ├── 07-continuous-comparisons-legacy_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-1-1.png │ │ │ │ ├── unnamed-chunk-2-1.png │ │ │ │ ├── unnamed-chunk-3-1.png │ │ │ │ ├── unnamed-chunk-4-1.png │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ ├── unnamed-chunk-6-1.png │ │ │ │ └── unnamed-chunk-7-1.png │ │ ├── 08-categorical-plots-legacy.html │ │ ├── 08-categorical-plots-legacy_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-1-1.png │ │ │ │ ├── unnamed-chunk-2-1.png │ │ │ │ ├── unnamed-chunk-2-2.png │ │ │ │ └── unnamed-chunk-3-1.png │ │ ├── 09-continuous-comparisons-legacy.html │ │ ├── 09-continuous-comparisons-legacy_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-1-1.png │ │ │ │ ├── unnamed-chunk-2-1.png │ │ │ │ ├── unnamed-chunk-3-1.png │ │ │ │ └── unnamed-chunk-4-1.png │ │ ├── 10-correlations-scatterplots-legacy.html │ │ ├── 10-correlations-scatterplots-legacy_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-1-1.png │ │ │ │ └── unnamed-chunk-2-1.png │ │ ├── 11-introduction-legacy.html │ │ ├── 18-analysis-gallery-legacy.html │ │ ├── 24-jamovi-user-guide-legacy.html │ │ ├── 29-quick-reference-legacy.html │ │ ├── 30-r-programming-guide-legacy.html │ │ └── 31-troubleshooting-faq-legacy.html │ └── use-jjstatsplot-in-R.html ├── authors.html ├── deps │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.5.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── news │ └── index.html ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── %!in%.html │ ├── %notin%.html │ ├── advancedraincloud.html │ ├── advancedraincloudClass.html │ ├── bootstrapIDI.html │ ├── calculate_auc.html │ ├── calculate_nlr.html │ ├── calculate_npv.html │ ├── calculate_plr.html │ ├── calculate_ppv.html │ ├── calculate_sensitivity.html │ ├── calculate_specificity.html │ ├── clinicopath_startup_message.html │ ├── hullplot.html │ ├── hullplotClass.html │ ├── index.html │ ├── is_in_range.html │ ├── jjarcdiagram.html │ ├── jjarcdiagramClass.html │ ├── jjbarstats.html │ ├── jjbarstatsClass.html │ ├── jjbetweenstats-1.png │ ├── jjbetweenstats-2.png │ ├── jjbetweenstats-3.png │ ├── jjbetweenstats-4.png │ ├── jjbetweenstats-5.png │ ├── jjbetweenstats.html │ ├── jjbetweenstatsClass.html │ ├── jjcorrmat-1.png │ ├── jjcorrmat-2.png │ ├── jjcorrmat.html │ ├── jjcorrmatClass.html │ ├── jjdotplotstats-1.png │ ├── jjdotplotstats-2.png │ ├── jjdotplotstats.html │ ├── jjdotplotstatsClass.html │ ├── jjhistostats.html │ ├── jjhistostatsClass.html │ ├── jjpiestats.html │ ├── jjpiestatsClass.html │ ├── jjridges-1.png │ ├── jjridges-2.png │ ├── jjridges.html │ ├── jjridgesClass.html │ ├── jjscatterstats-1.png │ ├── jjscatterstats-2.png │ ├── jjscatterstats.html │ ├── jjscatterstatsClass.html │ ├── jjsegmentedtotalbar.html │ ├── jjsegmentedtotalbarClass.html │ ├── jjstatsplot-package.html │ ├── jjstatsplot.html │ ├── jjwithinstats-1.png │ ├── jjwithinstats-2.png │ ├── jjwithinstats-3.png │ ├── jjwithinstats-4.png │ ├── jjwithinstats.html │ ├── jjwithinstatsClass.html │ ├── jwaffle.html │ ├── jwaffleClass.html │ ├── linechart.html │ ├── linechartClass.html │ ├── load_required_package.html │ ├── lollipop.html │ ├── lollipopClass.html │ ├── na-coalescing.html │ ├── not-in-alt.html │ ├── not-in.html │ ├── null-coalescing.html │ ├── pipe.html │ ├── print.sensSpecTable.html │ ├── prop_to_percent.html │ ├── raincloud-1.png │ ├── raincloud-2.png │ ├── raincloud-3.png │ ├── raincloud-4.png │ ├── raincloud.html │ ├── raincloudClass.html │ ├── raw_to_prob.html │ ├── safe_divide.html │ ├── statsplot2-1.png │ ├── statsplot2.html │ ├── statsplot2Class.html │ ├── validateROCInputs.html │ ├── waffle.html │ └── waffleClass.html ├── search.json └── sitemap.xml ├── jamovi ├── 0000.yaml ├── 00refs.yaml ├── advancedraincloud.a.yaml ├── advancedraincloud.r.yaml ├── advancedraincloud.u.yaml ├── hullplot.a.yaml ├── hullplot.r.yaml ├── hullplot.u.yaml ├── jjarcdiagram.a.yaml ├── jjarcdiagram.r.yaml ├── jjarcdiagram.u.yaml ├── jjbarstats.a.yaml ├── jjbarstats.r.yaml ├── jjbarstats.u.yaml ├── jjbetweenstats.a.yaml ├── jjbetweenstats.r.yaml ├── jjbetweenstats.u.yaml ├── jjcorrmat.a.yaml ├── jjcorrmat.r.yaml ├── jjcorrmat.u.yaml ├── jjdotplotstats.a.yaml ├── jjdotplotstats.r.yaml ├── jjdotplotstats.u.yaml ├── jjhistostats.a.yaml ├── jjhistostats.r.yaml ├── jjhistostats.u.yaml ├── jjpiestats.a.yaml ├── jjpiestats.r.yaml ├── jjpiestats.u.yaml ├── jjridges.a.yaml ├── jjridges.r.yaml ├── jjridges.u.yaml ├── jjscatterstats.a.yaml ├── jjscatterstats.r.yaml ├── jjscatterstats.u.yaml ├── jjsegmentedtotalbar.a.yaml ├── jjsegmentedtotalbar.r.yaml ├── jjsegmentedtotalbar.u.yaml ├── jjwithinstats.a.yaml ├── jjwithinstats.r.yaml ├── jjwithinstats.u.yaml ├── js │ └── jjhistostats.events.js ├── jwaffle.a.yaml ├── jwaffle.r.yaml ├── jwaffle.u.yaml ├── linechart.a.yaml ├── linechart.r.yaml ├── linechart.u.yaml ├── lollipop.a.yaml ├── lollipop.r.yaml ├── lollipop.u.yaml ├── raincloud.a.yaml ├── raincloud.r.yaml ├── raincloud.u.yaml ├── statsplot2.a.yaml ├── statsplot2.r.yaml └── statsplot2.u.yaml ├── jjstatsplot.Rproj ├── jjstatsplot.code-workspace ├── man ├── advancedraincloud.Rd ├── advancedraincloudClass.Rd ├── bootstrapIDI.Rd ├── calculate_auc.Rd ├── calculate_nlr.Rd ├── calculate_npv.Rd ├── calculate_plr.Rd ├── calculate_ppv.Rd ├── calculate_sensitivity.Rd ├── calculate_specificity.Rd ├── clinicopath_startup_message.Rd ├── hullplot.Rd ├── hullplotClass.Rd ├── is_in_range.Rd ├── jjarcdiagram.Rd ├── jjarcdiagramClass.Rd ├── jjbarstats.Rd ├── jjbarstatsClass.Rd ├── jjbetweenstats.Rd ├── jjbetweenstatsClass.Rd ├── jjcorrmat.Rd ├── jjcorrmatClass.Rd ├── jjdotplotstats.Rd ├── jjdotplotstatsClass.Rd ├── jjhistostats.Rd ├── jjhistostatsClass.Rd ├── jjpiestats.Rd ├── jjpiestatsClass.Rd ├── jjridges.Rd ├── jjridgesClass.Rd ├── jjscatterstats.Rd ├── jjscatterstatsClass.Rd ├── jjsegmentedtotalbar.Rd ├── jjsegmentedtotalbarClass.Rd ├── jjstatsplot-package.Rd ├── jjwithinstats.Rd ├── jjwithinstatsClass.Rd ├── jwaffle.Rd ├── jwaffleClass.Rd ├── linechart.Rd ├── linechartClass.Rd ├── load_required_package.Rd ├── lollipop.Rd ├── lollipopClass.Rd ├── na-coalescing.Rd ├── not-in-alt.Rd ├── not-in.Rd ├── null-coalescing.Rd ├── pipe.Rd ├── print.sensSpecTable.Rd ├── prop_to_percent.Rd ├── raincloud.Rd ├── raincloudClass.Rd ├── raw_to_prob.Rd ├── safe_divide.Rd ├── statsplot2.Rd ├── statsplot2Class.Rd └── validateROCInputs.Rd └── vignettes ├── .gitignore ├── 01-introduction.Rmd ├── 01-jamovi-user-guide.Rmd ├── 02-categorical-plots.Rmd ├── 03-continuous-comparisons.Rmd ├── 04-continuous-comparisons-alt.Rmd ├── 05-correlations-scatterplots.Rmd ├── 06-BBC-style-data-visualization.Rmd ├── 06-use-in-r.Rmd ├── 07-advancedbarplot.Rmd ├── 08-advancedraincloud.Rmd ├── 09-advancedtree.Rmd ├── 09-analysis-gallery.Rmd ├── 09-basegraphics.Rmd ├── 12-economistplots.Rmd ├── 13-quick-reference.Rmd ├── 14-clinical-classification-comprehensive.Rmd ├── 14-r-programming-guide.Rmd ├── 15-grafify-comprehensive.Rmd ├── 15-troubleshooting-faq.Rmd ├── 16-jcomplexupset-comprehensive.Rmd ├── 17-jextractggstats-comprehensive.Rmd ├── 18-jforester-comprehensive.Rmd ├── 19-jforestmodel-comprehensive.Rmd ├── 20-jggheatmap-comprehensive.Rmd ├── 21-jggridges-comprehensive.Rmd ├── 22-jggsankeyfier-comprehensive.Rmd ├── 22-jjsankeyfier-comprehensive.Rmd ├── 23-jggstats-comprehensive.Rmd ├── 23-jjbarstats-comprehensive.Rmd ├── 24-jjarcdiagram-comprehensive.Rmd ├── 24-jjbetweenstats-comprehensive.Rmd ├── 25-jjcorrmat-comprehensive.Rmd ├── 26-jjdotplotstats-comprehensive.Rmd ├── 27-jjhistostats-comprehensive.Rmd ├── 28-jjpiestats-comprehensive.Rmd ├── 29-jjridges-comprehensive.Rmd ├── 29-jjridgestats-comprehensive.Rmd ├── 30-jjriverplot-comprehensive.Rmd ├── 30-linechart-comprehensive.Rmd ├── 31-jjscatterstats-comprehensive.Rmd ├── 31-jpps-comprehensive.Rmd ├── 31-jscattermore-comprehensive.Rmd ├── 31-lollipop-comprehensive.Rmd ├── 32-jjstreamgraph-comprehensive.Rmd ├── 32-jsjplot-comprehensive.Rmd ├── 33-jjtreemap-comprehensive.Rmd ├── 33-jsummarytools-comprehensive.Rmd ├── 34-jjwithinstats-comprehensive.Rmd ├── 34-jviolin-comprehensive.Rmd ├── 35-jvisr-comprehensive.Rmd ├── 36-jwaffle-comprehensive.Rmd ├── IMPROVEMENT_SUGGESTIONS.md ├── advancedbarplot_documentation.md ├── advancedraincloud-documentation.md ├── advancedraincloud_documentation.md ├── basegraphics_documentation.md ├── bbcplots_documentation.md ├── economistplot_documentation.md ├── ggsegmentedtotalbar_documentation.md ├── grafify_documentation.md ├── jcomplexupset_documentation.md ├── jextractggstats_documentation.md ├── jforester_documentation.md ├── jforestmodel_documentation.md ├── jggheatmap_documentation.md ├── jggridges_documentation.md ├── jggsankeyfier_documentation.md ├── jggstats_documentation.md ├── jjarcdiagram_documentation.md ├── jjbarstats-documentation.md ├── jjbarstats_documentation.md ├── jjbetweenstats-documentation.md ├── jjbetweenstats_documentation.md ├── jjcorrmat-documentation.md ├── jjcorrmat_documentation.md ├── jjdotplotstats-documentation.md ├── jjdotplotstats_documentation.md ├── jjhistostats-documentation.md ├── jjhistostats_documentation.md ├── jjpiestats-documentation.md ├── jjpiestats_documentation.md ├── jjriverplot_documentation.md ├── jjsankeyfier_documentation.md ├── jjscatterstats-documentation.md ├── jjscatterstats_documentation.md ├── jjsegmentedtotalbar-documentation.md ├── jjsegmentedtotalbar_documentation.md ├── jjstatsplot-01-oncodatasets-examples.Rmd ├── jjstatsplot-10-jointmodeling-comprehensive.qmd.skip ├── jjstatsplot-11-jointmodeling-tutorial.qmd.skip ├── jjstreamgraph_documentation.md ├── jjtreemap_documentation.md ├── jjwithinstats-documentation.md ├── jjwithinstats_documentation.md ├── jpps_documentation.md ├── jscattermore_documentation.md ├── jsjplot_documentation.md ├── jviolin_documentation.md ├── jwaffle-documentation.md ├── jwaffle_documentation.md ├── lassocox_documentation.md ├── legacy ├── 07-continuous-comparisons-legacy.Rmd ├── 08-categorical-plots-legacy.Rmd ├── 09-continuous-comparisons-legacy.Rmd ├── 10-correlations-scatterplots-legacy.Rmd ├── 10-correlations-scatterplots-legacy.html ├── 11-introduction-legacy.Rmd ├── 18-analysis-gallery-legacy.Rmd ├── 18-analysis-gallery-legacy.html ├── 24-jamovi-user-guide-legacy.Rmd ├── 29-quick-reference-legacy.Rmd ├── 29-quick-reference-legacy.html ├── 30-r-programming-guide-legacy.Rmd ├── 30-r-programming-guide-legacy.html └── 31-troubleshooting-faq-legacy.Rmd ├── linechart-documentation.md ├── linechart_documentation.md ├── lollipop-documentation.md ├── lollipop_documentation.md ├── parallelplot_documentation.md ├── riverplot_documentation.md ├── statsplot2-documentation.md ├── statsplot2_documentation.md ├── tidyplots_documentation.md └── use-jjstatsplot-in-R.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^.*\.Rproj$ 2 | ^\.Rproj\.user$ 3 | .omv$ 4 | build 5 | docs 6 | jamovi 7 | .*\.code\-workspace$ 8 | .jmo$ 9 | ^\.github$ 10 | ^\.github/workflows/check-release\.yaml$ 11 | ^\.github/workflows/check-standard\.yaml$ 12 | ^\.github/workflows/pkgdown\.yaml$ 13 | 14 | 15 | ^.*\.Rproj$ 16 | ^\.Rproj\.user$ 17 | jjstatsplot.Rproj 18 | build 19 | jamovi 20 | ^.*\.jmo$ 21 | ^.*\.Rproj$ 22 | ^\.Rproj\.user$ 23 | .Rhistory 24 | .RData 25 | .Ruserdata 26 | ClinicoPath.Rproj 27 | build 28 | .Rbuildignore 29 | .gitignore 30 | data 31 | jamovi 32 | ^.*\.jmo 33 | # History files 34 | .Rhistory 35 | .Rapp.history 36 | # Session Data files 37 | .RData 38 | # User-specific files 39 | .Ruserdata 40 | # Example code in package build process 41 | ^.*\-Ex\.R 42 | # Output files from R CMD build 43 | /*.tar.gz 44 | # Output files from R CMD check 45 | /*.Rcheck/ 46 | # RStudio files 47 | .Rproj.user/ 48 | # produced vignettes 49 | vignettes/*.html 50 | vignettes/*.pdf 51 | ^vignettes$ 52 | vignettes/ 53 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 54 | .httr-oauth 55 | # knitr and R markdown default cache directories 56 | ^.*\_cache/ 57 | /cache/ 58 | # Temporary files created by R markdown 59 | ^.*\.utf8\.md 60 | ^.*\.knit\.md 61 | # R Environment Variables 62 | .Renviron 63 | .Rprofile 64 | 65 | ### R user files 66 | .RProfile 67 | 68 | ### R Studio files 69 | \.Rproj$ 70 | ^.*\.Rproj$ 71 | ^\.Rproj\.user$ 72 | 73 | ### Configuration 74 | ^_pkgdown\.yml$ 75 | ^\.github/ 76 | ^docs$ 77 | ^pkgdown$ 78 | ^img$ 79 | ^renv$ 80 | ^renv\.lock$ 81 | 82 | ### pkgdown websites 83 | ^public/ 84 | ^docs/ 85 | 86 | ### Obsolete and temporary files/directories 87 | ^delete/ 88 | ^temp/ 89 | 90 | ### Uncompiled documentation files 91 | ^README\.Rmd$ 92 | ^.*Class.Rd$ 93 | ^.*\.gif$ 94 | ^.*\.png$ 95 | ^.*\.mp4$ 96 | 97 | 98 | ### License 99 | ^LICENSE\.md$ 100 | 101 | ### Jamovi 102 | ^jamovi/ 103 | .jmo$ 104 | ^build/R/ 105 | ^build/js/ 106 | ^tododata/ 107 | /tododata/ 108 | tododata 109 | ^docs/ 110 | ^temp/ 111 | ^build/ 112 | ^.*\.jmo$ 113 | ^.*\.omv$ 114 | 115 | ### Other R codes 116 | ^tests$ 117 | ^data-raw$ 118 | R/utils-pipe.R 119 | 120 | ### CI 121 | ^\.travis\.yml$ 122 | ^codecov\.yml$ 123 | ^\.gitlab-ci\.yml$ 124 | ^\.github/ 125 | ^docs$ 126 | ^tic\.R$ 127 | ^\.circleci/ 128 | ^appveyor\.yml$ 129 | ^codemeta\.json$ 130 | .gitpod.Dockerfile 131 | .gitpod.yml 132 | .binder 133 | ^\.ccache$ 134 | ^\.github$ 135 | ^clang-.* 136 | ^gfortran.* 137 | DESCRIPTIONold.txt 138 | CITATION.cff 139 | CLAUDE.md 140 | README_badges.md 141 | .claude 142 | -------------------------------------------------------------------------------- /.claude/settings.local.json: -------------------------------------------------------------------------------- 1 | { 2 | "permissions": { 3 | "allow": [ 4 | "Bash(find:*)", 5 | "Bash(ls:*)", 6 | "Bash(Rscript:*)" 7 | ], 8 | "deny": [] 9 | } 10 | } 11 | -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/FUNDING.yml: -------------------------------------------------------------------------------- 1 | github: sbalci 2 | # liberapay: sbalci 3 | patreon: sbalci 4 | buy_me_a_coffee: bs0teis 5 | # custom: ["https://paypal.me/serdarbalci"] 6 | -------------------------------------------------------------------------------- /.github/workflows/check-release.yaml: -------------------------------------------------------------------------------- 1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples 2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help 3 | on: 4 | workflow_dispatch: 5 | # push: 6 | # branches: [main, master] 7 | # pull_request: 8 | # branches: [main, master] 9 | 10 | name: R-CMD-check 11 | 12 | jobs: 13 | R-CMD-check: 14 | # Skip this entire job if the commit message includes "WIP" 15 | if: "!contains(github.event.head_commit.message, 'WIP')" 16 | runs-on: ubuntu-latest 17 | env: 18 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 19 | R_KEEP_PKG_SOURCE: yes 20 | steps: 21 | - uses: actions/checkout@v3 22 | 23 | - uses: r-lib/actions/setup-r@v2 24 | with: 25 | use-public-rspm: true 26 | 27 | - uses: r-lib/actions/setup-r-dependencies@v2 28 | with: 29 | extra-packages: any::rcmdcheck 30 | needs: check 31 | 32 | - uses: r-lib/actions/check-r-package@v2 33 | -------------------------------------------------------------------------------- /.github/workflows/check-standard.yaml: -------------------------------------------------------------------------------- 1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples 2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help 3 | on: 4 | workflow_dispatch: 5 | # push: 6 | # branches: [main, master] 7 | # pull_request: 8 | # branches: [main, master] 9 | 10 | name: R-CMD-check 11 | 12 | jobs: 13 | R-CMD-check: 14 | # Skip this entire job if the commit message includes "WIP" 15 | if: "!contains(github.event.head_commit.message, 'WIP')" 16 | runs-on: ${{ matrix.config.os }} 17 | 18 | name: ${{ matrix.config.os }} (${{ matrix.config.r }}) 19 | 20 | strategy: 21 | fail-fast: false 22 | matrix: 23 | config: 24 | - {os: macos-latest, r: 'release'} 25 | - {os: windows-latest, r: 'release'} 26 | # - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} 27 | # - {os: ubuntu-latest, r: 'release'} 28 | # - {os: ubuntu-latest, r: 'oldrel-1'} 29 | 30 | env: 31 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 32 | R_KEEP_PKG_SOURCE: yes 33 | 34 | steps: 35 | - uses: actions/checkout@v3 36 | 37 | - uses: r-lib/actions/setup-pandoc@v2 38 | 39 | - uses: r-lib/actions/setup-r@v2 40 | with: 41 | r-version: ${{ matrix.config.r }} 42 | http-user-agent: ${{ matrix.config.http-user-agent }} 43 | use-public-rspm: true 44 | 45 | - uses: r-lib/actions/setup-r-dependencies@v2 46 | with: 47 | extra-packages: any::rcmdcheck 48 | needs: check 49 | 50 | - uses: r-lib/actions/check-r-package@v2 51 | with: 52 | upload-snapshots: true 53 | -------------------------------------------------------------------------------- /.github/workflows/pkgdown.yaml: -------------------------------------------------------------------------------- 1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples 2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help 3 | on: 4 | workflow_dispatch: 5 | # push: 6 | # branches: [main, master] 7 | # pull_request: 8 | # release: 9 | # types: [published] 10 | 11 | name: pkgdown.yaml 12 | 13 | permissions: read-all 14 | 15 | jobs: 16 | pkgdown: 17 | # Skip this entire job if the commit message includes "WIP" 18 | if: "!contains(github.event.head_commit.message, 'WIP')" 19 | runs-on: ubuntu-latest 20 | # Only restrict concurrency for non-PR jobs 21 | concurrency: 22 | group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} 23 | env: 24 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 25 | permissions: 26 | contents: write 27 | steps: 28 | - uses: actions/checkout@v4 29 | 30 | - uses: r-lib/actions/setup-pandoc@v2 31 | 32 | - uses: r-lib/actions/setup-r@v2 33 | with: 34 | use-public-rspm: true 35 | 36 | - uses: r-lib/actions/setup-r-dependencies@v2 37 | with: 38 | extra-packages: any::pkgdown, local::. 39 | needs: website 40 | 41 | - name: Build site 42 | run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) 43 | shell: Rscript {0} 44 | 45 | - name: Deploy to GitHub pages 🚀 46 | if: github.event_name != 'pull_request' 47 | uses: JamesIves/github-pages-deploy-action@v4.5.0 48 | with: 49 | clean: false 50 | branch: gh-pages 51 | folder: docs 52 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # History files 2 | .Rhistory 3 | .Rapp.history 4 | # Session Data files 5 | .RData 6 | # User-specific files 7 | .Ruserdata 8 | # Example code in package build process 9 | *-Ex.R 10 | # Output files from R CMD build 11 | /*.tar.gz 12 | # Output files from R CMD check 13 | /*.Rcheck/ 14 | # RStudio files 15 | .Rproj.user/ 16 | # produced vignettes 17 | vignettes/*.html 18 | vignettes/*.pdf 19 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 20 | .httr-oauth 21 | # knitr and R markdown default cache directories 22 | *_cache/ 23 | /cache/ 24 | # Temporary files created by R markdown 25 | *.utf8.md 26 | *.knit.md 27 | # R Environment Variables 28 | .Renviron 29 | .Rprofile 30 | build 31 | *.jmo 32 | .DS_Store 33 | # docs 34 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | # This CITATION.cff file was generated with cffinit. 2 | # Visit https://bit.ly/cffinit to generate yours today! 3 | 4 | cff-version: 1.2.0 5 | title: "ClinicoPath jamovi Module" 6 | message: >- 7 | If you use this software, please cite it using the 8 | metadata from this file. 9 | type: software 10 | authors: 11 | - given-names: Serdar 12 | family-names: Balci 13 | email: serdarbalci@serdarbalci.com 14 | orcid: 'https://orcid.org/0000-0002-7852-3851' 15 | date-released: '2025-09-18' 16 | version: "0.0.31.69" 17 | identifiers: 18 | - type: doi 19 | value: 10.5281/zenodo.3997188 20 | description: zenodo 21 | - type: doi 22 | value: 10.17605/OSF.IO/9SZUD 23 | description: OSF 24 | - type: url 25 | value: 'https://github.com/sbalci/ClinicoPathJamoviModule/' 26 | description: GitHub 27 | - type: url 28 | value: 'https://sbalci.github.io/ClinicoPathJamoviModule/' 29 | description: webpage 30 | - type: url 31 | value: >- 32 | https://github.com/sbalci/ClinicoPathJamoviModule/issues/ 33 | description: BugReports 34 | - type: url 35 | value: 'https://github.com/sbalci/ClinicoPathDescriptives/' 36 | description: ClinicoPathDescriptives 37 | - type: url 38 | value: 'https://github.com/sbalci/jjstatsplot' 39 | description: jjstatsplot 40 | - type: url 41 | value: 'https://github.com/sbalci/meddecide' 42 | description: meddecide 43 | - type: url 44 | value: 'https://github.com/sbalci/jsurvival' 45 | description: jsurvival 46 | - type: url 47 | value: 'https://github.com/sbalci/OncoPath' 48 | description: OncoPath 49 | repository-code: 'https://github.com/sbalci/ClinicoPathJamoviModule/' 50 | url: 'https://www.serdarbalci.com/ClinicoPathJamoviModule' 51 | abstract: >- 52 | Comprehensive Analysis for Clinicopathological Research: ClinicoPath 53 | is a jamovi module that helps researchers generate natural language 54 | summaries of their datasets, create cross tables with statistical tests, 55 | perform survival analyses with tables and plots, conduct medical decision 56 | analysis, create statistical visualizations, and perform specialized 57 | oncological patient follow-up analyses including waterfall and swimmer plots. 58 | keywords: 59 | - jamovi 60 | - module 61 | - R-project 62 | - package 63 | - pathology 64 | - research 65 | - biostatistics 66 | - survival 67 | - agreement 68 | - descriptives 69 | - plots 70 | license: GPL-2.0 71 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Type: Package 2 | Package: jjstatsplot 3 | Title: Wrapper for ggstatsplot 4 | Version: 0.0.32.01 5 | Date: 2025-10-09 6 | Authors@R: person(given = "Serdar", family = "Balci", role = c("aut", 7 | "cre"), email = "serdarbalci@serdarbalci.com", comment = 8 | c(ORCID = "0000-0002-7852-3851")) 9 | Maintainer: Serdar Balci 10 | Description: Comprehensive statistical visualization package for jamovi 11 | that wraps ggstatsplot functions and provides 17+ analysis 12 | types including histograms, scatter plots, correlation 13 | matrices, between/within-group comparisons, bar charts, pie 14 | charts, waffle charts, raincloud plots, ridge plots, arc 15 | diagrams, lollipop charts, line charts, and segmented bar 16 | charts. Features automatic plot selection, dual-mode operation 17 | (single/grouped variables), statistical annotations, and 18 | publication-ready visualizations with point-and-click 19 | interface. 20 | License: GPL (>= 2) 21 | URL: https://github.com/sbalci/jjstatsplot 22 | BugReports: https://github.com/sbalci/ClinicoPathJamoviModule/issues/ 23 | Depends: R (>= 4.0.0) 24 | Imports: arcdiagram, BayesFactor, digest, dplyr, easyalluvial, 25 | effectsize, ggalluvial, ggcorrplot, ggdist, ggforce, ggplot2, 26 | ggrain, ggridges, ggsegmentedtotalbar, ggside, ggstatsplot, 27 | glue, grid, htmltools, igraph, jmvcore, magrittr, moments, 28 | performance, PMCMRplus, purrr, R6, RColorBrewer, rlang, scales, 29 | stringr, tidyr, viridis, waffle, WRS2 30 | Remotes: gastonstat/arcdiagram 31 | Encoding: UTF-8 32 | LazyData: true 33 | Suggests: knitr, rmarkdown 34 | VignetteBuilder: knitr 35 | Roxygen: list(markdown = TRUE) 36 | RoxygenNote: 7.3.3 37 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | S3method(print,sensSpecTable) 4 | export("%!in%") 5 | export("%>%") 6 | export("%notin%") 7 | export("%|%") 8 | export("%||%") 9 | export(advancedraincloud) 10 | export(bootstrapIDI) 11 | export(calculate_auc) 12 | export(calculate_nlr) 13 | export(calculate_npv) 14 | export(calculate_plr) 15 | export(calculate_ppv) 16 | export(calculate_sensitivity) 17 | export(calculate_specificity) 18 | export(clinicopath_startup_message) 19 | export(hullplot) 20 | export(is_in_range) 21 | export(jjarcdiagram) 22 | export(jjbarstats) 23 | export(jjbetweenstats) 24 | export(jjcorrmat) 25 | export(jjdotplotstats) 26 | export(jjhistostats) 27 | export(jjpiestats) 28 | export(jjridges) 29 | export(jjscatterstats) 30 | export(jjsegmentedtotalbar) 31 | export(jjsegmentedtotalbarClass) 32 | export(jjwithinstats) 33 | export(jwaffle) 34 | export(linechart) 35 | export(lollipop) 36 | export(prop_to_percent) 37 | export(raincloud) 38 | export(raw_to_prob) 39 | export(safe_divide) 40 | export(statsplot2) 41 | export(validateROCInputs) 42 | import(RColorBrewer) 43 | import(arcdiagram) 44 | import(dplyr) 45 | import(ggplot2) 46 | import(ggridges) 47 | import(ggstatsplot) 48 | import(glue) 49 | import(grDevices) 50 | import(igraph) 51 | import(jmvcore) 52 | import(magrittr) 53 | import(purrr) 54 | import(rlang) 55 | import(scales) 56 | import(tidyr) 57 | import(waffle) 58 | importFrom(R6,R6Class) 59 | importFrom(RColorBrewer,brewer.pal) 60 | importFrom(digest,digest) 61 | importFrom(dplyr,arrange) 62 | importFrom(dplyr,count) 63 | importFrom(dplyr,filter) 64 | importFrom(dplyr,group_by) 65 | importFrom(dplyr,mutate) 66 | importFrom(dplyr,n) 67 | importFrom(dplyr,pull) 68 | importFrom(dplyr,select) 69 | importFrom(dplyr,slice) 70 | importFrom(dplyr,summarise) 71 | importFrom(dplyr,ungroup) 72 | importFrom(ggdist,stat_dots) 73 | importFrom(ggdist,stat_halfeye) 74 | importFrom(ggforce,geom_mark_hull) 75 | importFrom(ggplot2,aes) 76 | importFrom(ggplot2,coord_flip) 77 | importFrom(ggplot2,element_line) 78 | importFrom(ggplot2,element_rect) 79 | importFrom(ggplot2,element_text) 80 | importFrom(ggplot2,facet_wrap) 81 | importFrom(ggplot2,geom_bar) 82 | importFrom(ggplot2,geom_boxplot) 83 | importFrom(ggplot2,geom_col) 84 | importFrom(ggplot2,geom_point) 85 | importFrom(ggplot2,geom_text) 86 | importFrom(ggplot2,ggplot) 87 | importFrom(ggplot2,labs) 88 | importFrom(ggplot2,margin) 89 | importFrom(ggplot2,position_fill) 90 | importFrom(ggplot2,scale_color_manual) 91 | importFrom(ggplot2,scale_color_viridis_d) 92 | importFrom(ggplot2,scale_fill_brewer) 93 | importFrom(ggplot2,scale_fill_manual) 94 | importFrom(ggplot2,scale_fill_viridis_d) 95 | importFrom(ggplot2,scale_y_continuous) 96 | importFrom(ggplot2,stat_ellipse) 97 | importFrom(ggplot2,theme) 98 | importFrom(ggplot2,theme_bw) 99 | importFrom(ggplot2,theme_classic) 100 | importFrom(ggplot2,theme_dark) 101 | importFrom(ggplot2,theme_light) 102 | importFrom(ggplot2,theme_minimal) 103 | importFrom(ggrain,geom_rain) 104 | importFrom(ggsegmentedtotalbar,ggsegmentedtotalbar) 105 | importFrom(ggstatsplot,grouped_ggbetweenstats) 106 | importFrom(glue,glue) 107 | importFrom(grid,unit) 108 | importFrom(htmltools,HTML) 109 | importFrom(magrittr,"%>%") 110 | importFrom(moments,kurtosis) 111 | importFrom(moments,skewness) 112 | importFrom(purrr,imap) 113 | importFrom(purrr,map) 114 | importFrom(rlang,"%||%") 115 | importFrom(rlang,.data) 116 | importFrom(rlang,sym) 117 | importFrom(scales,alpha) 118 | importFrom(scales,hue_pal) 119 | importFrom(scales,percent) 120 | importFrom(stats,aov) 121 | importFrom(stats,chisq.test) 122 | importFrom(stats,kruskal.test) 123 | importFrom(stats,t.test) 124 | importFrom(stats,wilcox.test) 125 | importFrom(stats,xtabs) 126 | importFrom(stringr,str_to_title) 127 | importFrom(tidyr,pivot_wider) 128 | importFrom(viridis,viridis) 129 | -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- 1 | # jjstatsplot 0.0.31.84 (2025-10-03) 2 | 3 | ## New Features 4 | 5 | ### Hull Plot Analysis 6 | - **NEW**: Added `hullplot` module for cluster and group visualization 7 | - Creates polygonal boundaries around data points grouped by categorical variables 8 | - Based on `ggforce::geom_mark_hull()` function 9 | - Perfect for visualizing customer segments, patient subgroups, and data clusters 10 | - Features include: 11 | - Customizable hull concavity (0-2 range) 12 | - Optional confidence ellipses 13 | - Outlier detection 14 | - Group statistics summary 15 | - Natural language interpretation 16 | - Multiple color palettes (default, viridis, Set1, Set2, Dark2, clinical) 17 | - Multiple plot themes (minimal, classic, light, dark, clinical) 18 | - Support for color and size variables 19 | - Automatic fallback to convex hulls when V8/concaveman packages unavailable 20 | 21 | ## Improvements 22 | 23 | ### Package Dependencies 24 | - Added `ggforce` to Imports for hull plot functionality 25 | - Added `grid` to Imports for unit handling in hull plots 26 | 27 | ### Documentation 28 | - Updated DESCRIPTION with new analysis count (18 analyses) 29 | - Updated README to include hull plot in analysis types table 30 | - Enhanced package description to reflect expanded capabilities 31 | 32 | ## Bug Fixes 33 | - None in this release 34 | 35 | --- 36 | 37 | # jjstatsplot 0.0.31.57 (2025-09-03) 38 | 39 | ## Release Highlights 40 | - Early release for September 2025 41 | - Comprehensive statistical visualization suite with 17+ analysis types 42 | - Publication-ready plots with statistical annotations 43 | 44 | ## Core Features 45 | 46 | ### Distribution Analysis 47 | - `jjhistostats` - Histograms with Shapiro-Wilk test and robust measures 48 | - `jjridges` - Ridge plots for multiple distribution overlay 49 | - `jwaffle` - Waffle charts for part-to-whole visualization 50 | 51 | ### Continuous vs Continuous 52 | - `jjscatterstats` - Scatter plots with correlation analysis 53 | - `jjcorrmat` - Correlation matrices with significance testing 54 | 55 | ### Categorical vs Continuous 56 | - `jjbetweenstats` - Between-groups comparisons (ANOVA, Kruskal-Wallis) 57 | - `jjwithinstats` - Within-subjects comparisons (repeated measures) 58 | - `jjdotplotstats` - Dot charts with confidence intervals 59 | - `raincloud` - Basic raincloud plots (distribution + individual points) 60 | - `advancedraincloud` - Enhanced raincloud plots with longitudinal support 61 | - `lollipop` - Lollipop charts for ranked data 62 | 63 | ### Categorical vs Categorical 64 | - `jjbarstats` - Bar charts with chi-square and Fisher's exact test 65 | - `jjpiestats` - Pie charts with goodness of fit tests 66 | - `jjsegmentedtotalbar` - Segmented bar charts with totals 67 | 68 | ### Network and Time Series 69 | - `jjarcdiagram` - Arc diagrams for network visualization 70 | - `linechart` - Line charts for trends over time 71 | 72 | ### Advanced Features 73 | - `statsplot2` - Automatic plot selection based on variable types 74 | - Dual-mode operation (single/grouped variables) 75 | - Statistical flexibility (parametric, non-parametric, robust, Bayesian) 76 | - Theme support (jamovi-style and ggstatsplot themes) 77 | - Dynamic plot sizing based on data dimensions 78 | 79 | ## Dependencies 80 | - R (>= 4.0.0) 81 | - Core: jmvcore, R6, ggstatsplot 82 | - Plotting: ggplot2, ggalluvial, ggside, ggcorrplot, ggdist, ggridges, ggrain 83 | - Statistical: PMCMRplus, WRS2, BayesFactor, effectsize, performance, moments 84 | 85 | --- 86 | 87 | # Earlier Versions 88 | 89 | ## jjstatsplot 0.0.3.91 90 | - Enhanced vignettes and reference documentation 91 | - Improved package metadata 92 | 93 | ## jjstatsplot 0.0.3.90 94 | - Added comprehensive vignette collection (40+ files) 95 | - Improved documentation structure 96 | 97 | ## jjstatsplot 0.0.3.89 98 | - Release candidate for jamovi 2.7.2 99 | - Removed embedded images from vignettes 100 | - Performance improvements 101 | 102 | ## jjstatsplot 0.0.3.70 103 | - Initial public release 104 | - Core ggstatsplot wrapper functionality 105 | - Basic jamovi module integration 106 | -------------------------------------------------------------------------------- /R/data-histopathology.R: -------------------------------------------------------------------------------- 1 | #' @title histopathology 2 | #' 3 | #' @description Fake histopathology research data. 4 | #' @usage data(histopathology) 5 | #' @format A data frame 6 | "histopathology" 7 | -------------------------------------------------------------------------------- /R/jjstatsplot-data.R: -------------------------------------------------------------------------------- 1 | #' @title histopathology 2 | #' 3 | #' @description Fake histopathology research data. 4 | #' @usage data(histopathology) 5 | #' @format A data frame 6 | "histopathology" 7 | -------------------------------------------------------------------------------- /R/jjstatsplot-package.R: -------------------------------------------------------------------------------- 1 | #' \code{jjstatsplot} 2 | #' 3 | #' @title jjstatsplot: Wrapper for ggstatsplot 4 | #' 5 | #' @description `jjstatsplot` A wrapper for ggstatsplot: jjstatsplot help 6 | #' researchers to generate plots in jamovi based on ggstatsplot package. 7 | #' 8 | #' 9 | #' 10 | #' For more documentation, see the 11 | #' \href{https://sbalci.github.io/ClinicoPathJamoviModule/}{Website}. 12 | #' 13 | #' @docType package 14 | #' @aliases jjstatsplot jjstatsplot-package 15 | #' @name jjstatsplot-package 16 | "_PACKAGE" 17 | -------------------------------------------------------------------------------- /_pkgdown.yml: 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-------------------------------------------------------------------------------- /jamovi/advancedraincloud.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: advancedraincloud 3 | title: Advanced Raincloud Plot 4 | jrs: '1.1' 5 | 6 | clearWith: 7 | - y_var 8 | - x_var 9 | - fill_var 10 | - id_var 11 | - cov_var 12 | - rain_side 13 | - likert_mode 14 | - show_longitudinal 15 | - point_size 16 | - point_alpha 17 | - violin_alpha 18 | - boxplot_width 19 | - jitter_seed 20 | - color_palette 21 | - plot_title 22 | - x_label 23 | - y_label 24 | - clinical_cutoff 25 | - reference_range_min 26 | - reference_range_max 27 | - show_mcid 28 | - mcid_value 29 | - log_transform 30 | - outlier_method 31 | - show_cv_bands 32 | - cv_band_1 33 | - cv_band_2 34 | - trial_arms 35 | - time_labels 36 | - population_type 37 | - journal_style 38 | - p_value_position 39 | - show_statistics 40 | - show_comparisons 41 | - show_interpretation 42 | - show_effect_size 43 | - effect_size_type 44 | - show_change_scores 45 | - baseline_group 46 | - responder_threshold 47 | - show_sample_size 48 | - show_missing_info 49 | - generate_report 50 | - include_methods 51 | 52 | items: 53 | - name: todo 54 | title: Instructions 55 | type: Html 56 | visible: (y_var:null || x_var:null) 57 | 58 | - name: plot 59 | title: Advanced Raincloud Plot 60 | type: Image 61 | width: 800 62 | height: 600 63 | renderFun: .plot 64 | 65 | - name: statistics 66 | title: Summary Statistics 67 | type: Html 68 | visible: (show_statistics) 69 | 70 | - name: comparisons 71 | title: Group Comparisons 72 | type: Html 73 | visible: (show_comparisons) 74 | 75 | - name: interpretation 76 | title: Feature Guide 77 | type: Html 78 | visible: (show_interpretation) 79 | 80 | - name: effect_sizes 81 | title: Effect Size Analysis 82 | type: Html 83 | visible: (show_effect_size) 84 | 85 | - name: change_analysis 86 | title: Change Score Analysis 87 | type: Html 88 | visible: (show_change_scores) 89 | 90 | - name: clinical_report 91 | title: Clinical Analysis Report 92 | type: Html 93 | visible: (generate_report) 94 | 95 | - name: methods_text 96 | title: Methods Section 97 | type: Html 98 | visible: (include_methods) 99 | 100 | 101 | refs: 102 | - ggplot2 103 | - ggrain 104 | - ClinicoPathJamoviModule 105 | 106 | 107 | 108 | ... 109 | -------------------------------------------------------------------------------- /jamovi/hullplot.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: hullplot 3 | title: Hull Plot 4 | jrs: '1.1' 5 | 6 | items: 7 | - name: todo 8 | title: Instructions 9 | type: Html 10 | visible: true 11 | 12 | - name: plot 13 | title: Hull Plot 14 | type: Image 15 | width: 800 16 | height: 600 17 | renderFun: .plot 18 | 19 | - name: statistics 20 | title: Group Statistics 21 | type: Html 22 | visible: (show_statistics) 23 | 24 | - name: outliers 25 | title: Outlier Analysis 26 | type: Html 27 | visible: (outlier_detection) 28 | 29 | - name: interpretation 30 | title: Interpretation Guide 31 | type: Html 32 | 33 | - name: summary 34 | title: Natural Language Summary 35 | type: Html 36 | visible: (show_summary) 37 | 38 | - name: assumptions 39 | title: Assumptions & Guidelines 40 | type: Html 41 | visible: (show_assumptions) 42 | 43 | 44 | refs: 45 | - ClinicoPathJamoviModule 46 | - ggforce 47 | 48 | ... 49 | -------------------------------------------------------------------------------- /jamovi/jjarcdiagram.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjarcdiagram 3 | title: Arc Diagram 4 | jrs: '1.1' 5 | 6 | items: 7 | - name: instructions 8 | title: Instructions 9 | type: Html 10 | visible: true 11 | 12 | - name: todo 13 | title: Status 14 | type: Html 15 | clearWith: 16 | - source 17 | - target 18 | - weight 19 | - group 20 | 21 | - name: plot 22 | title: Arc Diagram 23 | type: Image 24 | width: 600 25 | height: 400 26 | renderFun: .plot 27 | requiresData: true 28 | 29 | - name: networkStats 30 | title: Network Statistics 31 | type: Html 32 | visible: (showStats) 33 | 34 | - name: assumptions 35 | title: Analysis Assumptions & Guidelines 36 | type: Html 37 | 38 | - name: reportSentence 39 | title: Copy-Ready Summary 40 | type: Html 41 | visible: (showStats) 42 | 43 | refs: 44 | - ClinicoPathJamoviModule 45 | - arcdiagram 46 | 47 | ... 48 | -------------------------------------------------------------------------------- /jamovi/jjbarstats.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjbarstats 3 | title: Bar Charts 4 | jrs: '1.1' 5 | 6 | clearWith: 7 | - dep 8 | - group 9 | - grvar 10 | - counts 11 | - excl 12 | - paired 13 | - typestatistics 14 | - pairwisecomparisons 15 | - pairwisedisplay 16 | - padjustmethod 17 | - originaltheme 18 | - resultssubtitle 19 | - messages 20 | - label 21 | - digits 22 | - digitsperc 23 | - proportiontest 24 | - bfmessage 25 | - conflevel 26 | - ratio 27 | - clinicalpreset 28 | - showexplanations 29 | 30 | 31 | items: 32 | 33 | - name: about 34 | title: About This Analysis 35 | type: Html 36 | visible: true 37 | 38 | - name: summary 39 | title: Analysis Summary 40 | type: Html 41 | 42 | - name: assumptions 43 | title: Statistical Assumptions & Warnings 44 | type: Html 45 | 46 | - name: interpretation 47 | title: Results Interpretation 48 | type: Html 49 | 50 | - name: report 51 | title: Copy-Ready Report 52 | type: Html 53 | 54 | - name: todo 55 | title: Analysis Setup 56 | type: Html 57 | 58 | - name: plot2 59 | title: '`Bar Chart Grouped by {grvar}`' 60 | type: Image 61 | renderFun: .plot2 62 | requiresData: true 63 | visible: (grvar) 64 | 65 | - name: plot 66 | title: Bar Chart 67 | type: Image 68 | renderFun: .plot 69 | requiresData: true 70 | 71 | 72 | refs: 73 | - ggstatsplot 74 | - ClinicoPathJamoviModule 75 | 76 | 77 | ... 78 | -------------------------------------------------------------------------------- /jamovi/jjbetweenstats.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjbetweenstats 3 | title: Box-Violin Plots to Compare Between Groups 4 | jrs: '1.1' 5 | 6 | clearWith: 7 | - dep 8 | - group 9 | - grvar 10 | - typestatistics 11 | - pairwisecomparisons 12 | - pairwisedisplay 13 | - padjustmethod 14 | - effsizetype 15 | - centralityplotting 16 | - centralitytype 17 | - bfmessage 18 | - k 19 | - conflevel 20 | - varequal 21 | - mytitle 22 | - xtitle 23 | - ytitle 24 | - originaltheme 25 | - resultssubtitle 26 | - plotwidth 27 | - plotheight 28 | - colorblindSafe 29 | 30 | 31 | 32 | items: 33 | 34 | - name: todo 35 | title: To Do 36 | type: Html 37 | 38 | - name: plot2 39 | title: '`Violin Plot by ${grvar}`' 40 | type: Image 41 | renderFun: .plot2 42 | requiresData: true 43 | visible: (grvar) 44 | 45 | - name: plot 46 | title: 'Violin Plot' 47 | type: Image 48 | renderFun: .plot 49 | requiresData: true 50 | 51 | 52 | 53 | 54 | 55 | refs: 56 | - ggstatsplot 57 | - ClinicoPathJamoviModule 58 | 59 | 60 | ... 61 | -------------------------------------------------------------------------------- /jamovi/jjcorrmat.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjcorrmat 3 | title: Correlation Matrix 4 | jrs: '1.1' 5 | 6 | clearWith: 7 | - dep 8 | - grvar 9 | - excl 10 | - originaltheme 11 | - typestatistics 12 | - matrixtype 13 | - matrixmethod 14 | - siglevel 15 | - conflevel 16 | - padjustmethod 17 | - k 18 | - partial 19 | - clinicalpreset 20 | - lowcolor 21 | - midcolor 22 | - highcolor 23 | - title 24 | - subtitle 25 | - caption 26 | - plotwidth 27 | - plotheight 28 | 29 | 30 | items: 31 | 32 | - name: todo 33 | title: Analysis Guide 34 | type: Html 35 | 36 | - name: interpretation 37 | title: Clinical Interpretation 38 | type: Html 39 | 40 | - name: plot2 41 | title: Chart 42 | type: Image 43 | width: 600 44 | height: 450 45 | renderFun: .plot2 46 | requiresData: true 47 | visible: (grvar) 48 | 49 | - name: plot 50 | title: Chart 51 | type: Image 52 | width: 600 53 | height: 450 54 | renderFun: .plot 55 | requiresData: true 56 | 57 | 58 | 59 | refs: 60 | - ggstatsplot 61 | - ClinicoPathJamoviModule 62 | 63 | 64 | ... 65 | -------------------------------------------------------------------------------- /jamovi/jjcorrmat.u.yaml: -------------------------------------------------------------------------------- 1 | title: Correlation Matrix 2 | name: jjcorrmat 3 | jus: '3.0' 4 | stage: 0 5 | compilerMode: tame 6 | children: 7 | - type: VariableSupplier 8 | persistentItems: false 9 | stretchFactor: 1 10 | children: 11 | - type: TargetLayoutBox 12 | label: Dependent Variables 13 | children: 14 | - type: VariablesListBox 15 | name: dep 16 | isTarget: true 17 | - type: TargetLayoutBox 18 | label: Split By (Optional) 19 | children: 20 | - type: VariablesListBox 21 | name: grvar 22 | maxItemCount: 1 23 | isTarget: true 24 | - type: CollapseBox 25 | label: Statistical Analysis 26 | collapsed: true 27 | children: 28 | - type: Label 29 | label: Correlation Method 30 | fitToGrid: true 31 | children: 32 | - type: LayoutBox 33 | margin: large 34 | children: 35 | - type: ComboBox 36 | name: typestatistics 37 | - type: Label 38 | label: Statistical Options 39 | fitToGrid: true 40 | children: 41 | - type: LayoutBox 42 | margin: large 43 | children: 44 | - type: TextBox 45 | name: siglevel 46 | format: number 47 | - type: TextBox 48 | name: conflevel 49 | format: number 50 | - type: ComboBox 51 | name: padjustmethod 52 | - type: TextBox 53 | name: k 54 | format: number 55 | - type: CheckBox 56 | name: partial 57 | - type: ComboBox 58 | name: clinicalpreset 59 | 60 | - type: CollapseBox 61 | label: Matrix Display 62 | collapsed: true 63 | children: 64 | - type: Label 65 | label: Matrix Configuration 66 | fitToGrid: true 67 | children: 68 | - type: LayoutBox 69 | margin: large 70 | children: 71 | - type: ComboBox 72 | name: matrixtype 73 | - type: ComboBox 74 | name: matrixmethod 75 | 76 | - type: CollapseBox 77 | label: Plot Appearance 78 | collapsed: true 79 | children: 80 | - type: Label 81 | label: Color Scheme 82 | fitToGrid: true 83 | children: 84 | - type: LayoutBox 85 | margin: large 86 | children: 87 | - type: TextBox 88 | name: lowcolor 89 | format: string 90 | width: large 91 | - type: TextBox 92 | name: midcolor 93 | format: string 94 | width: large 95 | - type: TextBox 96 | name: highcolor 97 | format: string 98 | width: large 99 | - type: Label 100 | label: Plot Labels 101 | fitToGrid: true 102 | children: 103 | - type: LayoutBox 104 | margin: large 105 | children: 106 | - type: TextBox 107 | name: title 108 | format: string 109 | width: large 110 | - type: TextBox 111 | name: subtitle 112 | format: string 113 | width: large 114 | - type: TextBox 115 | name: caption 116 | format: string 117 | width: large 118 | 119 | - type: CollapseBox 120 | label: Plot Configuration 121 | collapsed: true 122 | children: 123 | - type: Label 124 | label: Plot Dimensions 125 | fitToGrid: true 126 | children: 127 | - type: LayoutBox 128 | margin: large 129 | children: 130 | - type: TextBox 131 | name: plotwidth 132 | format: number 133 | - type: TextBox 134 | name: plotheight 135 | format: number 136 | 137 | -------------------------------------------------------------------------------- /jamovi/jjdotplotstats.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjdotplotstats 3 | title: Dot Chart 4 | jrs: '1.1' 5 | 6 | 7 | clearWith: 8 | - dep 9 | - group 10 | - grvar 11 | - typestatistics 12 | - effsizetype 13 | - centralityplotting 14 | - centralitytype 15 | - mytitle 16 | - xtitle 17 | - ytitle 18 | - originaltheme 19 | - resultssubtitle 20 | - testvalue 21 | - bfmessage 22 | - conflevel 23 | - k 24 | - testvalueline 25 | - centralityparameter 26 | - centralityk 27 | - plotwidth 28 | - plotheight 29 | - guidedMode 30 | - clinicalPreset 31 | 32 | 33 | 34 | items: 35 | 36 | - name: todo 37 | title: To Do 38 | type: Html 39 | 40 | - name: plot2 41 | title: '`${dep} - {group} by {grvar}`' 42 | type: Image 43 | width: 800 44 | height: 300 45 | renderFun: .plot2 46 | requiresData: true 47 | visible: (grvar) 48 | 49 | - name: plot 50 | title: '`${dep} - {group}`' 51 | type: Image 52 | width: 400 53 | height: 300 54 | renderFun: .plot 55 | requiresData: true 56 | 57 | - name: interpretation 58 | title: Clinical Interpretation 59 | type: Html 60 | 61 | - name: assumptions 62 | title: Data Assessment & Recommendations 63 | type: Html 64 | 65 | - name: reportSentence 66 | title: Report Template 67 | type: Html 68 | 69 | - name: guidedSteps 70 | title: Analysis Steps 71 | type: Html 72 | 73 | - name: recommendations 74 | title: Next Steps 75 | type: Html 76 | 77 | 78 | refs: 79 | - ggstatsplot 80 | - ClinicoPathJamoviModule 81 | 82 | 83 | ... 84 | -------------------------------------------------------------------------------- /jamovi/jjhistostats.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjhistostats 3 | title: Histogram 4 | jrs: '1.1' 5 | 6 | clearWith: 7 | - dep 8 | - grvar 9 | - typestatistics 10 | - changebinwidth 11 | - binwidth 12 | - centralityline 13 | - centralitytype 14 | - resultssubtitle 15 | - test.value 16 | - conf.level 17 | - bf.message 18 | - binfill 19 | - bincolor 20 | - binalpha 21 | - centralitylinecolor 22 | - centralitylinewidth 23 | - centralitylinetype 24 | - plotwidth 25 | - plotheight 26 | - xlab 27 | - title 28 | - subtitle 29 | - caption 30 | - digits 31 | - showInterpretation 32 | - clinicalPreset 33 | 34 | 35 | items: 36 | 37 | - name: todo 38 | title: To Do 39 | type: Html 40 | 41 | 42 | # - name: mydataview 43 | # title: mydataview 44 | # type: Preformatted 45 | 46 | # - name: mydataview2 47 | # title: mydataview2 48 | # type: Preformatted 49 | 50 | # title: '` ${group} - {dep} by {grvar}`' 51 | 52 | - name: plot2 53 | title: '`Histogram Splitted by {grvar}`' 54 | type: Image 55 | # width: 800 56 | # height: 600 57 | renderFun: .plot2 58 | requiresData: true 59 | visible: (grvar) 60 | 61 | # title: '` ${dep}`' 62 | 63 | 64 | - name: plot 65 | title: Histogram 66 | type: Image 67 | # width: 800 68 | # height: 600 69 | renderFun: .plot 70 | requiresData: true 71 | 72 | - name: interpretation 73 | title: Clinical Interpretation 74 | type: Html 75 | visible: (showInterpretation) 76 | 77 | # - name: e_stats 78 | # title: e_stats 79 | # type: Preformatted 80 | 81 | # - name: e_subtitle 82 | # title: e_subtitle 83 | # type: Preformatted 84 | 85 | # - name: e_caption 86 | # title: e_caption 87 | # type: Preformatted 88 | 89 | refs: 90 | - ggstatsplot 91 | - ClinicoPathJamoviModule 92 | 93 | 94 | ... 95 | -------------------------------------------------------------------------------- /jamovi/jjpiestats.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjpiestats 3 | title: Pie Charts 4 | jrs: '1.1' 5 | 6 | clearWith: 7 | - dep 8 | - group 9 | - grvar 10 | - counts 11 | - ratio 12 | - paired 13 | - typestatistics 14 | - label 15 | - digits 16 | - conflevel 17 | - proportiontest 18 | - bfmessage 19 | - messages 20 | - originaltheme 21 | - resultssubtitle 22 | - clinicalpreset 23 | - showexplanations 24 | 25 | items: 26 | 27 | - name: about 28 | title: About This Analysis 29 | type: Html 30 | visible: true 31 | 32 | - name: summary 33 | title: Analysis Summary 34 | type: Html 35 | visible: (dep) 36 | 37 | - name: assumptions 38 | title: Statistical Assumptions & Warnings 39 | type: Html 40 | 41 | - name: interpretation 42 | title: Results Interpretation 43 | type: Html 44 | visible: (dep) 45 | 46 | - name: report 47 | title: Copy-Ready Report 48 | type: Html 49 | visible: (dep) 50 | 51 | - name: todo 52 | title: Analysis Setup 53 | type: Html 54 | 55 | - name: plot4 56 | title: '`${group} - {dep} by {grvar}`' 57 | type: Image 58 | width: 800 59 | height: 300 60 | renderFun: .plot4 61 | requiresData: true 62 | visible: (grvar) 63 | 64 | - name: plot2 65 | title: '`${group} - {dep}`' 66 | type: Image 67 | width: 400 68 | height: 300 69 | renderFun: .plot2 70 | requiresData: true 71 | visible: (group) 72 | 73 | - name: plot1 74 | title: '`${dep}`' 75 | type: Image 76 | width: 400 77 | height: 300 78 | renderFun: .plot1 79 | requiresData: true 80 | visible: (dep) 81 | 82 | 83 | refs: 84 | - ggstatsplot 85 | - ClinicoPathJamoviModule 86 | 87 | 88 | ... 89 | -------------------------------------------------------------------------------- /jamovi/jjpiestats.u.yaml: -------------------------------------------------------------------------------- 1 | title: Pie Charts 2 | name: jjpiestats 3 | jus: '3.0' 4 | stage: 0 5 | compilerMode: tame 6 | children: 7 | - type: CollapseBox 8 | label: Quick Clinical Setup 9 | collapsed: true 10 | children: 11 | - type: ComboBox 12 | name: clinicalpreset 13 | label: "Analysis Type" 14 | - type: CheckBox 15 | name: showexplanations 16 | label: "Show Clinical Guidance" 17 | - type: VariableSupplier 18 | persistentItems: false 19 | stretchFactor: 1 20 | children: 21 | - type: TargetLayoutBox 22 | label: Dependent Variable 23 | children: 24 | - type: VariablesListBox 25 | name: dep 26 | maxItemCount: 1 27 | isTarget: true 28 | - type: TargetLayoutBox 29 | label: 'Grouping Variable: (Optional)' 30 | children: 31 | - type: VariablesListBox 32 | name: group 33 | maxItemCount: 1 34 | isTarget: true 35 | - type: TargetLayoutBox 36 | label: Split By (Optional) 37 | children: 38 | - type: VariablesListBox 39 | name: grvar 40 | maxItemCount: 1 41 | isTarget: true 42 | - type: TargetLayoutBox 43 | label: Frequency Counts (Optional) 44 | children: 45 | - type: VariablesListBox 46 | name: counts 47 | maxItemCount: 1 48 | isTarget: true 49 | - type: CollapseBox 50 | label: Statistical Analysis 51 | collapsed: true 52 | children: 53 | - type: Label 54 | label: Data Handling 55 | fitToGrid: true 56 | children: 57 | - type: LayoutBox 58 | margin: large 59 | children: 60 | - type: CheckBox 61 | name: paired 62 | label: "Paired/Matched Data (McNemar's Test)" 63 | - type: Label 64 | label: Test Method 65 | fitToGrid: true 66 | children: 67 | - type: LayoutBox 68 | margin: large 69 | children: 70 | - type: ComboBox 71 | name: typestatistics 72 | - type: CheckBox 73 | name: proportiontest 74 | label: "Include Proportion Tests" 75 | - type: CheckBox 76 | name: bfmessage 77 | label: "Show Bayes Factor (for Bayesian)" 78 | - type: Label 79 | label: Advanced Parameters 80 | fitToGrid: true 81 | children: 82 | - type: LayoutBox 83 | margin: large 84 | children: 85 | - type: TextBox 86 | name: conflevel 87 | label: "Confidence Level (0.50-0.99)" 88 | format: number 89 | - type: TextBox 90 | name: ratio 91 | label: "Expected Proportions (e.g., 0.5,0.5)" 92 | format: string 93 | 94 | - type: CollapseBox 95 | label: Plot Appearance 96 | collapsed: true 97 | children: 98 | - type: Label 99 | label: Plot Styling 100 | fitToGrid: true 101 | children: 102 | - type: LayoutBox 103 | margin: large 104 | children: 105 | - type: CheckBox 106 | name: originaltheme 107 | label: "Use ggstatsplot Theme" 108 | - type: CheckBox 109 | name: resultssubtitle 110 | label: "Show Statistics in Plot Subtitle" 111 | - type: CheckBox 112 | name: messages 113 | label: "Show Console Messages" 114 | - type: Label 115 | label: Pie Chart Labels 116 | fitToGrid: true 117 | children: 118 | - type: LayoutBox 119 | margin: large 120 | children: 121 | - type: ComboBox 122 | name: label 123 | label: "Slice Label Type" 124 | - type: TextBox 125 | name: digits 126 | label: "Decimal Places (Statistics)" 127 | format: number 128 | -------------------------------------------------------------------------------- /jamovi/jjridges.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjridges 3 | title: Advanced Ridge Plot 4 | jrs: '1.1' 5 | 6 | items: 7 | - name: instructions 8 | title: Instructions 9 | type: Html 10 | visible: false 11 | clearWith: 12 | - x_var 13 | - y_var 14 | 15 | - name: warnings 16 | title: Data Quality Warnings 17 | type: Html 18 | visible: false 19 | clearWith: 20 | - x_var 21 | - y_var 22 | 23 | - name: clinicalSummary 24 | title: Clinical Summary 25 | type: Html 26 | visible: false 27 | clearWith: 28 | - x_var 29 | - y_var 30 | - show_stats 31 | 32 | - name: plot 33 | title: Ridge Plot 34 | type: Image 35 | renderFun: .plot 36 | requiresData: true 37 | clearWith: 38 | - x_var 39 | - y_var 40 | - fill_var 41 | - facet_var 42 | - plot_type 43 | - scale 44 | - bandwidth 45 | - bandwidth_value 46 | - binwidth 47 | - add_boxplot 48 | - add_points 49 | - point_alpha 50 | - add_quantiles 51 | - quantiles 52 | - add_mean 53 | - add_median 54 | - alpha 55 | - color_palette 56 | - custom_colors 57 | - gradient_low 58 | - gradient_high 59 | - fill_ridges 60 | - reverse_order 61 | - theme_style 62 | - grid_lines 63 | - expand_panels 64 | - legend_position 65 | - plot_title 66 | - plot_subtitle 67 | - plot_caption 68 | - x_label 69 | - y_label 70 | 71 | - name: statistics 72 | title: Statistical Summary 73 | type: Table 74 | rows: 0 75 | visible: false 76 | columns: 77 | - name: group 78 | title: Group 79 | type: text 80 | - name: n 81 | title: N 82 | type: integer 83 | - name: mean 84 | title: Mean 85 | type: number 86 | format: zto,dp:2 87 | - name: sd 88 | title: SD 89 | type: number 90 | format: zto,dp:2 91 | - name: median 92 | title: Median 93 | type: number 94 | format: zto,dp:2 95 | - name: q1 96 | title: Q1 97 | type: number 98 | format: zto,dp:2 99 | - name: q3 100 | title: Q3 101 | type: number 102 | format: zto,dp:2 103 | - name: min 104 | title: Min 105 | type: number 106 | format: zto,dp:2 107 | - name: max 108 | title: Max 109 | type: number 110 | format: zto,dp:2 111 | clearWith: 112 | - x_var 113 | - y_var 114 | 115 | - name: tests 116 | title: Statistical Tests 117 | type: Table 118 | rows: 0 119 | visible: false 120 | columns: 121 | - name: comparison 122 | title: Comparison 123 | type: text 124 | - name: statistic 125 | title: Statistic 126 | type: number 127 | format: zto,dp:3 128 | - name: p_value 129 | title: P-value 130 | type: number 131 | format: zto,dp:4,p 132 | - name: p_adjusted 133 | title: P-adj 134 | type: number 135 | format: zto,dp:4,p 136 | - name: effect_size 137 | title: Effect Size 138 | type: number 139 | format: zto,dp:3 140 | - name: ci_lower 141 | title: CI Lower 142 | type: number 143 | format: zto,dp:3 144 | - name: ci_upper 145 | title: CI Upper 146 | type: number 147 | format: zto,dp:3 148 | clearWith: 149 | - x_var 150 | - y_var 151 | - test_type 152 | - p_adjust_method 153 | - effsize_type 154 | 155 | - name: interpretation 156 | title: Interpretation 157 | type: Html 158 | visible: false 159 | clearWith: 160 | - x_var 161 | - y_var 162 | - plot_type 163 | 164 | refs: 165 | - ClinicoPathJamoviModule 166 | - ggridges 167 | - ggstatsplot 168 | - RGraphGallery 169 | 170 | ... 171 | -------------------------------------------------------------------------------- /jamovi/jjscatterstats.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjscatterstats 3 | title: Scatter Plot 4 | jrs: '1.1' 5 | 6 | 7 | clearWith: 8 | - dep 9 | - group 10 | - grvar 11 | - originaltheme 12 | - typestatistics 13 | - conflevel 14 | - bfmessage 15 | - k 16 | - marginal 17 | - xsidefill 18 | - ysidefill 19 | - pointsize 20 | - pointalpha 21 | - smoothlinesize 22 | - smoothlinecolor 23 | - mytitle 24 | - xtitle 25 | - ytitle 26 | - resultssubtitle 27 | - plotwidth 28 | - plotheight 29 | 30 | 31 | items: 32 | 33 | - name: todo 34 | title: To Do 35 | type: Html 36 | - name: plot2 37 | title: '`${dep} vs {group} by {grvar}`' 38 | type: Image 39 | width: 1200 40 | height: 450 41 | renderFun: .plot2 42 | requiresData: true 43 | visible: (grvar) 44 | 45 | - name: plot 46 | title: '`${dep} vs {group}`' 47 | type: Image 48 | width: 600 49 | height: 450 50 | renderFun: .plot 51 | requiresData: true 52 | 53 | refs: 54 | - ggstatsplot 55 | - ClinicoPathJamoviModule 56 | 57 | 58 | ... 59 | -------------------------------------------------------------------------------- /jamovi/jjsegmentedtotalbar.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjsegmentedtotalbar 3 | title: Segmented Total Bar Charts 4 | jrs: '1.1' 5 | 6 | items: 7 | - name: instructions 8 | title: 'Instructions' 9 | type: Html 10 | visible: true 11 | 12 | - name: plot 13 | title: Segmented Total Bar Chart (ggplot2) 14 | type: Image 15 | width: 650 16 | height: 450 17 | requiresData: true 18 | renderFun: .plot 19 | 20 | - name: plot_ggsegmented 21 | title: Segmented Total Bar Chart (ggsegmentedtotalbar) 22 | type: Image 23 | width: 650 24 | height: 450 25 | requiresData: true 26 | renderFun: .plot_ggsegmented 27 | visible: true 28 | 29 | - name: summary 30 | title: 'Chart Summary' 31 | type: Table 32 | rows: 1 33 | clearWith: 34 | - x_var 35 | - y_var 36 | - fill_var 37 | columns: 38 | - name: categories 39 | title: 'Categories' 40 | type: integer 41 | - name: segments 42 | title: 'Segments' 43 | type: integer 44 | - name: total_observations 45 | title: 'Total Observations' 46 | type: integer 47 | - name: chart_type 48 | title: 'Chart Type' 49 | type: text 50 | 51 | - name: composition_table 52 | title: 'Composition Analysis' 53 | type: Table 54 | clearWith: 55 | - x_var 56 | - y_var 57 | - fill_var 58 | columns: 59 | - name: category 60 | title: 'Category' 61 | type: text 62 | - name: segment 63 | title: 'Segment' 64 | type: text 65 | - name: count 66 | title: 'Count' 67 | type: integer 68 | - name: percentage 69 | title: 'Percentage' 70 | type: number 71 | format: pc 72 | - name: total_in_category 73 | title: 'Category Total' 74 | type: integer 75 | 76 | - name: detailed_stats 77 | title: 'Detailed Statistics' 78 | type: Table 79 | clearWith: 80 | - x_var 81 | - y_var 82 | - fill_var 83 | columns: 84 | - name: measure 85 | title: 'Measure' 86 | type: text 87 | - name: value 88 | title: 'Value' 89 | type: text 90 | 91 | - name: interpretation 92 | title: 'Chart Interpretation' 93 | type: Html 94 | clearWith: 95 | - x_var 96 | - y_var 97 | - fill_var 98 | 99 | - name: clinical_summary 100 | title: 'Clinical Summary' 101 | type: Html 102 | clearWith: 103 | - x_var 104 | - y_var 105 | - fill_var 106 | 107 | - name: statistical_tests 108 | title: 'Statistical Tests' 109 | type: Table 110 | visible: false 111 | clearWith: 112 | - x_var 113 | - y_var 114 | - fill_var 115 | - show_statistical_tests 116 | columns: 117 | - name: test_name 118 | title: 'Test' 119 | type: text 120 | - name: statistic 121 | title: 'Chi-square' 122 | type: number 123 | - name: df 124 | title: 'df' 125 | type: integer 126 | - name: p_value 127 | title: 'p-value' 128 | type: number 129 | format: zto,pvalue 130 | - name: interpretation 131 | title: 'Interpretation' 132 | type: text 133 | 134 | - name: preset_guidance 135 | title: 'Template Guidance' 136 | type: Html 137 | visible: false 138 | clearWith: 139 | - analysis_preset 140 | 141 | refs: 142 | - ClinicoPathJamoviModule 143 | - ggsegmentedtotalbar 144 | 145 | ... 146 | -------------------------------------------------------------------------------- /jamovi/jjwithinstats.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jjwithinstats 3 | title: Violin Plots to Compare Within Groups 4 | jrs: '1.1' 5 | 6 | clearWith: 7 | - dep1 8 | - dep2 9 | - dep3 10 | - dep4 11 | - clinicalpreset 12 | - typestatistics 13 | - pairwisecomparisons 14 | - pairwisedisplay 15 | - padjustmethod 16 | - effsizetype 17 | - pointpath 18 | - centralityplotting 19 | - centralitytype 20 | - centralitypath 21 | - violin 22 | - boxplot 23 | - point 24 | - mytitle 25 | - xtitle 26 | - ytitle 27 | - originaltheme 28 | - resultssubtitle 29 | - bfmessage 30 | - conflevel 31 | - k 32 | - plotwidth 33 | - plotheight 34 | 35 | 36 | items: 37 | 38 | - name: todo 39 | title: Analysis Guide 40 | type: Html 41 | 42 | - name: interpretation 43 | title: Clinical Interpretation 44 | type: Html 45 | 46 | - name: plot 47 | title: 'Violin Plots' 48 | type: Image 49 | renderFun: .plot 50 | requiresData: true 51 | 52 | - name: summary 53 | title: Analysis Summary 54 | type: Html 55 | 56 | 57 | 58 | 59 | refs: 60 | - ggstatsplot 61 | - ClinicoPathJamoviModule 62 | 63 | 64 | ... 65 | -------------------------------------------------------------------------------- /jamovi/jwaffle.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: jwaffle 3 | title: Waffle Charts 4 | jrs: '1.1' 5 | 6 | clearWith: 7 | - counts 8 | - groups 9 | - facet 10 | - rows 11 | - flip 12 | - color_palette 13 | - show_legend 14 | - mytitle 15 | - legendtitle 16 | - showSummaries 17 | - showExplanations 18 | 19 | items: 20 | - name: todo 21 | title: To Do 22 | type: Html 23 | 24 | - name: analysisSummary 25 | title: Analysis Summary 26 | type: Html 27 | visible: (showSummaries) 28 | - name: plot 29 | title: Waffle Chart 30 | type: Image 31 | width: 600 32 | height: 500 33 | renderFun: .plot 34 | requiresData: true 35 | 36 | 37 | - name: methodExplanation 38 | title: Methodology 39 | type: Html 40 | visible: (showExplanations) 41 | 42 | 43 | refs: 44 | - ggplot2 45 | - waffle 46 | - ClinicoPathJamoviModule 47 | 48 | ... 49 | -------------------------------------------------------------------------------- /jamovi/jwaffle.u.yaml: -------------------------------------------------------------------------------- 1 | title: Waffle Charts 2 | name: jwaffle 3 | jus: '3.0' 4 | stage: 0 5 | compilerMode: tame 6 | 7 | children: 8 | - type: VariableSupplier 9 | persistentItems: false 10 | stretchFactor: 1 11 | children: 12 | - type: TargetLayoutBox 13 | label: Groups 14 | children: 15 | - type: VariablesListBox 16 | name: groups 17 | maxItemCount: 1 18 | isTarget: true 19 | - type: TargetLayoutBox 20 | label: Facet By (Optional) 21 | children: 22 | - type: VariablesListBox 23 | name: facet 24 | maxItemCount: 1 25 | isTarget: true 26 | - type: TargetLayoutBox 27 | label: Counts (Optional) 28 | children: 29 | - type: VariablesListBox 30 | name: counts 31 | maxItemCount: 1 32 | isTarget: true 33 | 34 | - type: CollapseBox 35 | label: Chart Options 36 | collapsed: true 37 | children: 38 | - type: Label 39 | label: Layout 40 | fitToGrid: true 41 | children: 42 | - type: LayoutBox 43 | margin: large 44 | children: 45 | - type: TextBox 46 | name: rows 47 | format: number 48 | label: Number of Rows 49 | - type: CheckBox 50 | name: flip 51 | label: Flip Chart 52 | 53 | - type: Label 54 | label: Appearance 55 | fitToGrid: true 56 | children: 57 | - type: LayoutBox 58 | margin: large 59 | children: 60 | - type: ComboBox 61 | name: color_palette 62 | - type: CheckBox 63 | name: show_legend 64 | 65 | - type: CollapseBox 66 | label: Labels 67 | collapsed: true 68 | children: 69 | - type: Label 70 | label: Titles 71 | fitToGrid: true 72 | children: 73 | - type: LayoutBox 74 | margin: large 75 | children: 76 | - type: TextBox 77 | name: mytitle 78 | format: string 79 | label: Chart Title 80 | width: large 81 | - type: TextBox 82 | name: legendtitle 83 | format: string 84 | label: Legend Title 85 | width: large 86 | 87 | - type: CollapseBox 88 | label: Output Options 89 | collapsed: true 90 | children: 91 | - type: Label 92 | label: Analysis Output 93 | fitToGrid: true 94 | children: 95 | - type: LayoutBox 96 | margin: large 97 | children: 98 | - type: CheckBox 99 | name: showSummaries 100 | label: Analysis Summary 101 | - type: CheckBox 102 | name: showExplanations 103 | label: Show Explanations 104 | -------------------------------------------------------------------------------- /jamovi/linechart.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: linechart 3 | title: Line Chart 4 | jrs: '1.1' 5 | 6 | items: 7 | - name: todo 8 | title: Instructions 9 | type: Html 10 | visible: true 11 | 12 | - name: summary 13 | title: Data Summary 14 | type: Table 15 | columns: 16 | - name: statistic 17 | title: Statistic 18 | type: text 19 | - name: value 20 | title: Value 21 | type: text 22 | 23 | - name: correlation 24 | title: Correlation Analysis 25 | type: Table 26 | visible: (trendline) 27 | columns: 28 | - name: measure 29 | title: Measure 30 | type: text 31 | - name: value 32 | title: Value 33 | type: number 34 | - name: interpretation 35 | title: Interpretation 36 | type: text 37 | 38 | - name: assumptions 39 | title: Statistical Assumptions & Guidelines 40 | type: Html 41 | visible: (trendline) 42 | 43 | - name: plot 44 | title: '`Line Chart: {yvar} by {xvar}`' 45 | type: Image 46 | width: 800 47 | height: 600 48 | renderFun: .plot 49 | requiresData: true 50 | 51 | refs: 52 | - ClinicoPathJamoviModule 53 | 54 | 55 | ... 56 | -------------------------------------------------------------------------------- /jamovi/lollipop.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: lollipop 3 | title: Lollipop Chart 4 | jrs: '1.1' 5 | 6 | items: 7 | - name: todo 8 | title: Instructions 9 | type: Html 10 | visible: true 11 | 12 | - name: summary 13 | title: Data Summary 14 | type: Table 15 | columns: 16 | - name: statistic 17 | title: Statistic 18 | type: text 19 | - name: value 20 | title: Value 21 | type: text 22 | 23 | - name: plot 24 | title: '`Lollipop Chart {dep} vs {group}`' 25 | type: Image 26 | width: 700 27 | height: 500 28 | renderFun: .plot 29 | requiresData: true 30 | 31 | refs: 32 | - ClinicoPathJamoviModule 33 | - RGraphGallery 34 | - ggplot2 35 | 36 | 37 | ... 38 | -------------------------------------------------------------------------------- /jamovi/raincloud.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: raincloud 3 | title: Raincloud Plot 4 | jrs: '1.1' 5 | 6 | items: 7 | - name: todo 8 | title: Instructions 9 | type: Html 10 | 11 | - name: plot 12 | title: Raincloud Plot 13 | type: Image 14 | width: 800 15 | height: 600 16 | renderFun: .plot 17 | 18 | - name: statistics 19 | title: Summary Statistics 20 | type: Html 21 | visible: (show_statistics) 22 | 23 | - name: outliers 24 | title: Outlier Analysis 25 | type: Html 26 | visible: (show_outliers) 27 | 28 | - name: normality 29 | title: Normality Tests 30 | type: Html 31 | visible: (normality_test) 32 | 33 | - name: comparison 34 | title: Group Comparisons 35 | type: Html 36 | visible: (comparison_test) 37 | 38 | - name: interpretation 39 | title: Interpretation Guide 40 | type: Html 41 | 42 | 43 | refs: 44 | - ClinicoPathJamoviModule 45 | 46 | ... 47 | -------------------------------------------------------------------------------- /jamovi/statsplot2.r.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | name: statsplot2 3 | title: Automatic Plot Selection Based on Variable Types 4 | jrs: '1.1' 5 | 6 | items: 7 | 8 | - name: todo 9 | title: To Do 10 | type: Html 11 | clearWith: 12 | - dep 13 | - group 14 | - direction 15 | - distribution 16 | - excl 17 | - grvar 18 | - sampleLarge 19 | 20 | 21 | - name: ExplanationMessage 22 | title: Explanation 23 | type: Preformatted 24 | clearWith: 25 | - dep 26 | - group 27 | - direction 28 | - distribution 29 | - excl 30 | - grvar 31 | - sampleLarge 32 | 33 | 34 | 35 | - title: Automatically Selected Plot 36 | name: plot 37 | type: Image 38 | width: 800 39 | height: 600 40 | renderFun: .plot 41 | requiresData: true 42 | clearWith: 43 | - dep 44 | - group 45 | - direction 46 | - distribution 47 | - alluvsty 48 | - excl 49 | - grvar 50 | - sampleLarge 51 | 52 | 53 | refs: 54 | - ggstatsplot 55 | - ggalluvial 56 | - easyalluvial 57 | - ClinicoPathJamoviModule 58 | - patchwork 59 | - cowplot 60 | 61 | 62 | ... 63 | -------------------------------------------------------------------------------- /jamovi/statsplot2.u.yaml: -------------------------------------------------------------------------------- 1 | title: Automatic Plot Selection 2 | name: statsplot2 3 | jus: '3.0' 4 | stage: 0 5 | compilerMode: tame 6 | children: 7 | - type: VariableSupplier 8 | persistentItems: false 9 | stretchFactor: 1 10 | children: 11 | - type: TargetLayoutBox 12 | label: Dependent Variable (y-axis) 13 | children: 14 | - type: VariablesListBox 15 | name: dep 16 | maxItemCount: 1 17 | isTarget: true 18 | - type: TargetLayoutBox 19 | label: Grouping Variable (x-axis) 20 | children: 21 | - type: VariablesListBox 22 | name: group 23 | maxItemCount: 1 24 | isTarget: true 25 | - type: TargetLayoutBox 26 | label: Split By (Optional) 27 | children: 28 | - type: VariablesListBox 29 | name: grvar 30 | maxItemCount: 1 31 | isTarget: true 32 | - type: LayoutBox 33 | margin: large 34 | children: 35 | - type: ComboBox 36 | name: direction 37 | - type: LayoutBox 38 | margin: large 39 | children: 40 | - type: ComboBox 41 | name: distribution 42 | - type: LayoutBox 43 | margin: large 44 | children: 45 | - type: ComboBox 46 | name: alluvsty 47 | enable: (direction:repeated) 48 | - type: LayoutBox 49 | margin: large 50 | children: 51 | - type: CheckBox 52 | name: excl 53 | - type: LayoutBox 54 | margin: large 55 | children: 56 | - type: CheckBox 57 | name: sampleLarge 58 | -------------------------------------------------------------------------------- /jjstatsplot.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | ProjectId: 1c717594-925f-41e0-93ae-723266ef2df9 3 | 4 | RestoreWorkspace: Default 5 | SaveWorkspace: Default 6 | AlwaysSaveHistory: Default 7 | 8 | EnableCodeIndexing: Yes 9 | UseSpacesForTab: Yes 10 | NumSpacesForTab: 2 11 | Encoding: UTF-8 12 | 13 | RnwWeave: Sweave 14 | LaTeX: pdfLaTeX 15 | 16 | AutoAppendNewline: Yes 17 | StripTrailingWhitespace: Yes 18 | 19 | BuildType: Package 20 | PackageUseDevtools: Yes 21 | PackageInstallArgs: --no-multiarch --with-keep.source 22 | -------------------------------------------------------------------------------- /jjstatsplot.code-workspace: -------------------------------------------------------------------------------- 1 | { 2 | "folders": [ 3 | { 4 | "path": "." 5 | } 6 | ], 7 | "settings": {} 8 | } -------------------------------------------------------------------------------- /man/bootstrapIDI.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{bootstrapIDI} 4 | \alias{bootstrapIDI} 5 | \title{Bootstrap IDI calculation with confidence intervals} 6 | \usage{ 7 | bootstrapIDI( 8 | new_values, 9 | ref_values, 10 | actual, 11 | direction = ">=", 12 | n_boot = 1000, 13 | conf_level = 0.95 14 | ) 15 | } 16 | \arguments{ 17 | \item{new_values}{Test values for new test} 18 | 19 | \item{ref_values}{Test values for reference test} 20 | 21 | \item{actual}{Binary outcome vector (0/1)} 22 | 23 | \item{direction}{Classification direction (">=" or "<=")} 24 | 25 | \item{n_boot}{Number of bootstrap iterations} 26 | 27 | \item{conf_level}{Confidence level (default 0.95)} 28 | } 29 | \value{ 30 | List with IDI, confidence intervals, and p-value 31 | } 32 | \description{ 33 | Calculates Integrated Discrimination Improvement with bootstrap confidence intervals 34 | } 35 | -------------------------------------------------------------------------------- /man/calculate_auc.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{calculate_auc} 4 | \alias{calculate_auc} 5 | \title{Approximate AUC from sensitivity and specificity} 6 | \usage{ 7 | calculate_auc(sens, spec) 8 | } 9 | \arguments{ 10 | \item{sens}{Sensitivity of the test} 11 | 12 | \item{spec}{Specificity of the test} 13 | } 14 | \value{ 15 | Numeric AUC value or NA when inputs are not valid 16 | } 17 | \description{ 18 | Uses a simplified formula to approximate AUC from sensitivity and specificity 19 | } 20 | -------------------------------------------------------------------------------- /man/calculate_nlr.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{calculate_nlr} 4 | \alias{calculate_nlr} 5 | \title{Calculate negative likelihood ratio} 6 | \usage{ 7 | calculate_nlr(sens, spec) 8 | } 9 | \arguments{ 10 | \item{sens}{Sensitivity value} 11 | 12 | \item{spec}{Specificity value} 13 | } 14 | \value{ 15 | Numeric negative likelihood ratio or NA when inputs are not valid 16 | } 17 | \description{ 18 | Calculates negative likelihood ratio from sensitivity and specificity 19 | } 20 | -------------------------------------------------------------------------------- /man/calculate_npv.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{calculate_npv} 4 | \alias{calculate_npv} 5 | \title{Calculate negative predictive value (NPV)} 6 | \usage{ 7 | calculate_npv(tn, fn) 8 | } 9 | \arguments{ 10 | \item{tn}{Number of true negatives} 11 | 12 | \item{fn}{Number of false negatives} 13 | } 14 | \value{ 15 | Numeric NPV value or NA when inputs are not valid 16 | } 17 | \description{ 18 | Calculates NPV from confusion matrix values 19 | } 20 | -------------------------------------------------------------------------------- /man/calculate_plr.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{calculate_plr} 4 | \alias{calculate_plr} 5 | \title{Calculate positive likelihood ratio} 6 | \usage{ 7 | calculate_plr(sens, spec) 8 | } 9 | \arguments{ 10 | \item{sens}{Sensitivity value} 11 | 12 | \item{spec}{Specificity value} 13 | } 14 | \value{ 15 | Numeric positive likelihood ratio or NA when inputs are not valid 16 | } 17 | \description{ 18 | Calculates positive likelihood ratio from sensitivity and specificity 19 | } 20 | -------------------------------------------------------------------------------- /man/calculate_ppv.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{calculate_ppv} 4 | \alias{calculate_ppv} 5 | \title{Calculate positive predictive value (PPV)} 6 | \usage{ 7 | calculate_ppv(tp, fp) 8 | } 9 | \arguments{ 10 | \item{tp}{Number of true positives} 11 | 12 | \item{fp}{Number of false positives} 13 | } 14 | \value{ 15 | Numeric PPV value or NA when inputs are not valid 16 | } 17 | \description{ 18 | Calculates PPV from confusion matrix values 19 | } 20 | -------------------------------------------------------------------------------- /man/calculate_sensitivity.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{calculate_sensitivity} 4 | \alias{calculate_sensitivity} 5 | \title{Calculate test sensitivity} 6 | \usage{ 7 | calculate_sensitivity(tp, fn) 8 | } 9 | \arguments{ 10 | \item{tp}{Number of true positives} 11 | 12 | \item{fn}{Number of false negatives} 13 | } 14 | \value{ 15 | Numeric sensitivity value or NA when inputs are not valid 16 | } 17 | \description{ 18 | Calculates sensitivity (true positive rate) from confusion matrix values 19 | } 20 | -------------------------------------------------------------------------------- /man/calculate_specificity.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{calculate_specificity} 4 | \alias{calculate_specificity} 5 | \title{Calculate test specificity} 6 | \usage{ 7 | calculate_specificity(tn, fp) 8 | } 9 | \arguments{ 10 | \item{tn}{Number of true negatives} 11 | 12 | \item{fp}{Number of false positives} 13 | } 14 | \value{ 15 | Numeric specificity value or NA when inputs are not valid 16 | } 17 | \description{ 18 | Calculates specificity (true negative rate) from confusion matrix values 19 | } 20 | -------------------------------------------------------------------------------- /man/clinicopath_startup_message.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{clinicopath_startup_message} 4 | \alias{clinicopath_startup_message} 5 | \title{Package startup message} 6 | \usage{ 7 | clinicopath_startup_message() 8 | } 9 | \value{ 10 | Invisible NULL (called for side effects) 11 | } 12 | \description{ 13 | Displays information about the package author and website 14 | } 15 | -------------------------------------------------------------------------------- /man/hullplot.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/hullplot.h.R 3 | \name{hullplot} 4 | \alias{hullplot} 5 | \title{Hull Plot} 6 | \usage{ 7 | hullplot( 8 | data, 9 | x_var = NULL, 10 | y_var = NULL, 11 | group_var = NULL, 12 | color_var = NULL, 13 | size_var = NULL, 14 | hull_concavity = 2, 15 | hull_alpha = 0.3, 16 | show_labels = TRUE, 17 | point_size = 2, 18 | point_alpha = 0.7, 19 | color_palette = "default", 20 | plot_theme = "minimal", 21 | plot_title = "Hull Plot - Group Visualization", 22 | x_label = "", 23 | y_label = "", 24 | hull_expand = 0.05, 25 | show_statistics = FALSE, 26 | outlier_detection = FALSE, 27 | confidence_ellipses = FALSE, 28 | show_summary = FALSE, 29 | show_assumptions = FALSE 30 | ) 31 | } 32 | \arguments{ 33 | \item{data}{The data as a data frame.} 34 | 35 | \item{x_var}{Continuous variable for the X-axis of the scatter plot.} 36 | 37 | \item{y_var}{Continuous variable for the Y-axis of the scatter plot.} 38 | 39 | \item{group_var}{Categorical variable that defines the groups for hull 40 | boundaries. Each group will have its own hull polygon.} 41 | 42 | \item{color_var}{Optional variable for coloring points. If not specified, 43 | uses the grouping variable.} 44 | 45 | \item{size_var}{Optional continuous variable for sizing points based on 46 | values.} 47 | 48 | \item{hull_concavity}{Controls the concavity of hull polygons. Lower values 49 | create more concave hulls, higher values create more convex hulls. Range: 50 | 0-2, default: 2.} 51 | 52 | \item{hull_alpha}{Transparency level for hull polygons. 0 = completely 53 | transparent, 1 = opaque.} 54 | 55 | \item{show_labels}{If TRUE, displays group labels inside hull regions.} 56 | 57 | \item{point_size}{Size of scatter plot points.} 58 | 59 | \item{point_alpha}{Transparency level for scatter plot points.} 60 | 61 | \item{color_palette}{Color palette for hulls and points.} 62 | 63 | \item{plot_theme}{Overall visual theme for the plot.} 64 | 65 | \item{plot_title}{Custom title for the hull plot.} 66 | 67 | \item{x_label}{Custom label for X-axis. If empty, uses variable name.} 68 | 69 | \item{y_label}{Custom label for Y-axis. If empty, uses variable name.} 70 | 71 | \item{hull_expand}{Amount to expand hull boundaries beyond data points. 72 | Higher values create larger hulls.} 73 | 74 | \item{show_statistics}{If TRUE, displays summary statistics for each group 75 | in the output.} 76 | 77 | \item{outlier_detection}{If TRUE, identifies and highlights potential 78 | outliers within groups.} 79 | 80 | \item{confidence_ellipses}{If TRUE, adds confidence ellipses in addition to 81 | hull polygons.} 82 | 83 | \item{show_summary}{If TRUE, displays a plain-language summary of the 84 | results with copy-ready text.} 85 | 86 | \item{show_assumptions}{If TRUE, displays data requirements, assumptions, 87 | and usage guidelines.} 88 | } 89 | \value{ 90 | A results object containing: 91 | \tabular{llllll}{ 92 | \code{results$todo} \tab \tab \tab \tab \tab a html \cr 93 | \code{results$plot} \tab \tab \tab \tab \tab an image \cr 94 | \code{results$statistics} \tab \tab \tab \tab \tab a html \cr 95 | \code{results$outliers} \tab \tab \tab \tab \tab a html \cr 96 | \code{results$interpretation} \tab \tab \tab \tab \tab a html \cr 97 | \code{results$summary} \tab \tab \tab \tab \tab a html \cr 98 | \code{results$assumptions} \tab \tab \tab \tab \tab a html \cr 99 | } 100 | } 101 | \description{ 102 | Creates Hull plots to visualize clusters and groups in scatter plots using 103 | ggforce. 104 | Hull plots draw polygonal boundaries around data points grouped by 105 | categorical variables, 106 | making it easy to identify customer segments, group membership, and data 107 | clusters. 108 | Based on the geom_mark_hull() function from ggforce package. 109 | } 110 | \examples{ 111 | \donttest{ 112 | # Example: 113 | # 1. Load your data frame with continuous variables for x and y axes. 114 | # 2. Select x and y variables for the scatter plot. 115 | # 3. Choose a grouping variable to define hull boundaries. 116 | # 4. Customize hull appearance and plot aesthetics. 117 | # 5. Run the hull plot to visualize group clusters. 118 | } 119 | } 120 | -------------------------------------------------------------------------------- /man/is_in_range.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{is_in_range} 4 | \alias{is_in_range} 5 | \title{Check if value is within valid range} 6 | \usage{ 7 | is_in_range(x, min_val, max_val, inclusive = TRUE) 8 | } 9 | \arguments{ 10 | \item{x}{Value to check} 11 | 12 | \item{min_val}{Minimum allowed value} 13 | 14 | \item{max_val}{Maximum allowed value} 15 | 16 | \item{inclusive}{Whether bounds are inclusive} 17 | } 18 | \value{ 19 | Logical indicating if value is within range 20 | } 21 | \description{ 22 | Validates that a value is within specified bounds 23 | } 24 | -------------------------------------------------------------------------------- /man/jjbarstats.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/jjbarstats.h.R 3 | \name{jjbarstats} 4 | \alias{jjbarstats} 5 | \title{Bar Charts} 6 | \usage{ 7 | jjbarstats( 8 | data, 9 | dep, 10 | group, 11 | grvar = NULL, 12 | counts = NULL, 13 | excl = FALSE, 14 | typestatistics = "parametric", 15 | pairwisecomparisons = FALSE, 16 | pairwisedisplay = "significant", 17 | padjustmethod = "holm", 18 | originaltheme = FALSE, 19 | resultssubtitle = FALSE, 20 | messages = FALSE, 21 | paired = FALSE, 22 | label = "percentage", 23 | digits = 2, 24 | digitsperc = 0, 25 | proportiontest = FALSE, 26 | bfmessage = FALSE, 27 | conflevel = 0.95, 28 | ratio = "", 29 | clinicalpreset = "custom", 30 | showexplanations = FALSE 31 | ) 32 | } 33 | \arguments{ 34 | \item{data}{The data as a data frame.} 35 | 36 | \item{dep}{.} 37 | 38 | \item{group}{.} 39 | 40 | \item{grvar}{.} 41 | 42 | \item{counts}{A variable in data containing counts, or NULL if each row 43 | represents a single observation.} 44 | 45 | \item{excl}{.} 46 | 47 | \item{typestatistics}{.} 48 | 49 | \item{pairwisecomparisons}{.} 50 | 51 | \item{pairwisedisplay}{.} 52 | 53 | \item{padjustmethod}{.} 54 | 55 | \item{originaltheme}{.} 56 | 57 | \item{resultssubtitle}{Display statistical test results in plot subtitle. 58 | Disabling improves performance significantly.} 59 | 60 | \item{messages}{Display statistical messages in console. Disabling 61 | improves performance.} 62 | 63 | \item{paired}{Logical indicating whether data came from a within-subjects 64 | or repeated measures design study. If TRUE, McNemar's test will be used. 65 | If FALSE, Pearson's chi-square test will be used.} 66 | 67 | \item{label}{What information needs to be displayed on the label in each 68 | bar segment.} 69 | 70 | \item{digits}{Number of digits after decimal point for statistical results.} 71 | 72 | \item{digitsperc}{Number of decimal places for percentage labels.} 73 | 74 | \item{proportiontest}{Decides whether proportion test for x variable is to 75 | be carried out for each level of y.} 76 | 77 | \item{bfmessage}{Display Bayes Factor in favor of the null hypothesis. 78 | Only relevant for parametric test.} 79 | 80 | \item{conflevel}{Confidence/credible interval level.} 81 | 82 | \item{ratio}{A comma-separated list of expected proportions for the 83 | proportion test (should sum to 1). For example: '0.5,0.5' for two equal 84 | groups or '0.25,0.25,0.25,0.25' for four equal groups. Leave empty for 85 | equal theoretical proportions.} 86 | 87 | \item{clinicalpreset}{Predefined configurations for common clinical 88 | scenarios. Automatically sets appropriate statistical methods and 89 | parameters.} 90 | 91 | \item{showexplanations}{Display detailed explanations of statistical 92 | methods, assumptions, and clinical interpretations to guide analysis and 93 | result interpretation.} 94 | } 95 | \value{ 96 | A results object containing: 97 | \tabular{llllll}{ 98 | \code{results$about} \tab \tab \tab \tab \tab a html \cr 99 | \code{results$summary} \tab \tab \tab \tab \tab a html \cr 100 | \code{results$assumptions} \tab \tab \tab \tab \tab a html \cr 101 | \code{results$interpretation} \tab \tab \tab \tab \tab a html \cr 102 | \code{results$report} \tab \tab \tab \tab \tab a html \cr 103 | \code{results$todo} \tab \tab \tab \tab \tab a html \cr 104 | \code{results$plot2} \tab \tab \tab \tab \tab an image \cr 105 | \code{results$plot} \tab \tab \tab \tab \tab an image \cr 106 | } 107 | } 108 | \description{ 109 | 'Wrapper Function for ggstatsplot::ggbarstats and 110 | ggstatsplot::grouped_ggbarstats to generate Bar Charts.' 111 | } 112 | \examples{ 113 | \donttest{ 114 | # example will be added 115 | } 116 | } 117 | -------------------------------------------------------------------------------- /man/jjbetweenstats.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/jjbetweenstats.h.R 3 | \name{jjbetweenstats} 4 | \alias{jjbetweenstats} 5 | \title{Box-Violin Plots to Compare Between Groups} 6 | \usage{ 7 | jjbetweenstats( 8 | data, 9 | dep, 10 | group, 11 | grvar = NULL, 12 | centralityplotting = FALSE, 13 | centralitytype = "parametric", 14 | typestatistics = "parametric", 15 | pairwisecomparisons = FALSE, 16 | pairwisedisplay = "significant", 17 | padjustmethod = "holm", 18 | effsizetype = "biased", 19 | mytitle = "Within Group Comparison", 20 | xtitle = "", 21 | ytitle = "", 22 | originaltheme = FALSE, 23 | resultssubtitle = FALSE, 24 | bfmessage = FALSE, 25 | k = 2, 26 | conflevel = 0.95, 27 | varequal = FALSE, 28 | plotwidth = 650, 29 | plotheight = 450, 30 | colorblindSafe = FALSE 31 | ) 32 | } 33 | \arguments{ 34 | \item{data}{The data as a data frame.} 35 | 36 | \item{dep}{.} 37 | 38 | \item{group}{.} 39 | 40 | \item{grvar}{.} 41 | 42 | \item{centralityplotting}{.} 43 | 44 | \item{centralitytype}{.} 45 | 46 | \item{typestatistics}{.} 47 | 48 | \item{pairwisecomparisons}{.} 49 | 50 | \item{pairwisedisplay}{.} 51 | 52 | \item{padjustmethod}{.} 53 | 54 | \item{effsizetype}{.} 55 | 56 | \item{mytitle}{.} 57 | 58 | \item{xtitle}{.} 59 | 60 | \item{ytitle}{.} 61 | 62 | \item{originaltheme}{.} 63 | 64 | \item{resultssubtitle}{.} 65 | 66 | \item{bfmessage}{Whether to display Bayes Factor in the subtitle when using 67 | Bayesian analysis.} 68 | 69 | \item{k}{Number of decimal places for displaying statistics in the 70 | subtitle.} 71 | 72 | \item{conflevel}{Confidence level for confidence intervals.} 73 | 74 | \item{varequal}{Whether to assume equal variances across groups for 75 | parametric tests.} 76 | 77 | \item{plotwidth}{Width of the plot in pixels. Default is 650.} 78 | 79 | \item{plotheight}{Height of the plot in pixels. Default is 450.} 80 | 81 | \item{colorblindSafe}{Whether to use colorblind-safe color palette for plot 82 | elements.} 83 | } 84 | \value{ 85 | A results object containing: 86 | \tabular{llllll}{ 87 | \code{results$todo} \tab \tab \tab \tab \tab a html \cr 88 | \code{results$plot2} \tab \tab \tab \tab \tab an image \cr 89 | \code{results$plot} \tab \tab \tab \tab \tab an image \cr 90 | } 91 | } 92 | \description{ 93 | Wrapper Function for ggstatsplot::ggbetweenstats and 94 | ggstatsplot::grouped_ggbetweenstats to generate Box-Violin Plots 95 | for comparing continuous variables between groups with statistical 96 | annotations. 97 | } 98 | \examples{ 99 | # Basic comparison between groups 100 | jjbetweenstats( 101 | data = iris, 102 | dep = "Sepal.Length", 103 | group = "Species", 104 | typestatistics = "parametric", 105 | pairwisecomparisons = TRUE 106 | ) 107 | 108 | # Multiple variables comparison 109 | jjbetweenstats( 110 | data = mtcars, 111 | dep = c("mpg", "hp", "wt"), 112 | group = "cyl", 113 | typestatistics = "nonparametric", 114 | pairwisecomparisons = TRUE, 115 | pairwisedisplay = "significant", 116 | padjustmethod = "bonferroni" 117 | ) 118 | 119 | # Grouped analysis with split variable 120 | jjbetweenstats( 121 | data = mtcars, 122 | dep = "mpg", 123 | group = "cyl", 124 | grvar = "am", 125 | typestatistics = "robust", 126 | centralityplotting = TRUE, 127 | centralitytype = "robust", 128 | ) 129 | 130 | # Bayesian analysis with custom aesthetics 131 | jjbetweenstats( 132 | data = ToothGrowth, 133 | dep = "len", 134 | group = "supp", 135 | grvar = "dose", 136 | typestatistics = "bayes", 137 | bfmessage = TRUE, 138 | mytitle = "Tooth Growth by Supplement Type", 139 | xtitle = "Supplement", 140 | ytitle = "Tooth Length" 141 | ) 142 | 143 | } 144 | -------------------------------------------------------------------------------- /man/jjstatsplot-package.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/jjstatsplot-package.R 3 | \docType{package} 4 | \name{jjstatsplot-package} 5 | \alias{jjstatsplot-package} 6 | \alias{jjstatsplot} 7 | \title{jjstatsplot: Wrapper for ggstatsplot} 8 | \description{ 9 | \code{jjstatsplot} A wrapper for ggstatsplot: jjstatsplot help 10 | researchers to generate plots in jamovi based on ggstatsplot package. 11 | 12 | For more documentation, see the 13 | \href{https://sbalci.github.io/ClinicoPathJamoviModule/}{Website}. 14 | } 15 | \details{ 16 | \code{jjstatsplot} 17 | } 18 | \seealso{ 19 | Useful links: 20 | \itemize{ 21 | \item \url{https://github.com/sbalci/jjstatsplot} 22 | \item Report bugs at \url{https://github.com/sbalci/ClinicoPathJamoviModule/issues/} 23 | } 24 | 25 | } 26 | \author{ 27 | \strong{Maintainer}: Serdar Balci \email{serdarbalci@serdarbalci.com} (\href{https://orcid.org/0000-0002-7852-3851}{ORCID}) 28 | 29 | } 30 | -------------------------------------------------------------------------------- /man/jwaffle.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/jwaffle.h.R 3 | \name{jwaffle} 4 | \alias{jwaffle} 5 | \title{Waffle Charts} 6 | \usage{ 7 | jwaffle( 8 | data, 9 | counts = NULL, 10 | groups, 11 | facet = NULL, 12 | rows = 5, 13 | flip = FALSE, 14 | color_palette = "default", 15 | show_legend = TRUE, 16 | mytitle = "", 17 | legendtitle = "", 18 | showSummaries = FALSE, 19 | showExplanations = FALSE 20 | ) 21 | } 22 | \arguments{ 23 | \item{data}{The data as a data frame.} 24 | 25 | \item{counts}{Optional numeric weight variable if cases have different 26 | weights. Leave empty to count each row equally (recommended for most 27 | clinical data). Only needed if your data is pre-aggregated or weighted.} 28 | 29 | \item{groups}{The categorical grouping variable for the waffle squares. 30 | Each category will be displayed as proportional colored squares in a 10x10 31 | grid. Examples: Tumor grade (G1/G2/G3), Treatment outcome 32 | (Complete/Partial/No response), Risk categories (Low/Medium/High).} 33 | 34 | \item{facet}{Optional variable to split the waffle chart by another 35 | categorical variable to compare distributions across subgroups (e.g., by 36 | treatment arm, patient cohort, or time period). Creates separate waffle 37 | charts for each level.} 38 | 39 | \item{rows}{Number of rows in the waffle chart} 40 | 41 | \item{flip}{Whether to flip the orientation of the waffle chart} 42 | 43 | \item{color_palette}{Color scheme for the waffle squares} 44 | 45 | \item{show_legend}{Whether to display the legend} 46 | 47 | \item{mytitle}{Custom title for the plot} 48 | 49 | \item{legendtitle}{Custom title for the legend} 50 | 51 | \item{showSummaries}{Generate natural language summary of waffle chart 52 | results including proportions, dominant categories, and clinical 53 | interpretation.} 54 | 55 | \item{showExplanations}{Show detailed methodology explanations about waffle 56 | charts, when to use them, and how to interpret the results in clinical 57 | contexts.} 58 | } 59 | \value{ 60 | A results object containing: 61 | \tabular{llllll}{ 62 | \code{results$todo} \tab \tab \tab \tab \tab a html \cr 63 | \code{results$analysisSummary} \tab \tab \tab \tab \tab a html \cr 64 | \code{results$plot} \tab \tab \tab \tab \tab an image \cr 65 | \code{results$methodExplanation} \tab \tab \tab \tab \tab a html \cr 66 | } 67 | } 68 | \description{ 69 | 'Creates waffle charts to visualize categorical distributions and 70 | proportions using colored squares. Ideal for showing parts-of-whole 71 | relationships in clinical data such as disease subtypes, treatment 72 | outcomes, or risk category distributions. Each square represents a 73 | proportion of the total sample, making it easy to see relative frequencies 74 | across categories.' 75 | } 76 | -------------------------------------------------------------------------------- /man/linechart.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/linechart.h.R 3 | \name{linechart} 4 | \alias{linechart} 5 | \title{Line Chart} 6 | \usage{ 7 | linechart( 8 | data, 9 | xvar, 10 | yvar, 11 | groupby, 12 | confidence = FALSE, 13 | trendline = FALSE, 14 | points = TRUE, 15 | smooth = FALSE, 16 | refline, 17 | reflineLabel = "Reference", 18 | colorPalette = "default", 19 | theme = "default", 20 | xlabel, 21 | ylabel, 22 | title, 23 | width = 800, 24 | height = 600 25 | ) 26 | } 27 | \arguments{ 28 | \item{data}{The data as a data frame.} 29 | 30 | \item{xvar}{The variable for the x-axis. Typically represents time, 31 | sequence, or ordered categories.} 32 | 33 | \item{yvar}{The variable for the y-axis. Must be numeric (continuous 34 | variable).} 35 | 36 | \item{groupby}{Optional grouping variable to create multiple lines (e.g., 37 | treatment groups, patient categories).} 38 | 39 | \item{confidence}{Whether to display confidence intervals around the 40 | line(s).} 41 | 42 | \item{trendline}{Whether to add a trend line (linear regression) to the 43 | plot.} 44 | 45 | \item{points}{Whether to show individual data points on the line(s).} 46 | 47 | \item{smooth}{Whether to apply smoothing (loess) to the line(s).} 48 | 49 | \item{refline}{Optional reference line value (e.g., normal range, 50 | threshold).} 51 | 52 | \item{reflineLabel}{Label for the reference line.} 53 | 54 | \item{colorPalette}{Color palette for multiple groups.} 55 | 56 | \item{theme}{Overall theme/appearance of the plot.} 57 | 58 | \item{xlabel}{Custom label for the x-axis.} 59 | 60 | \item{ylabel}{Custom label for the y-axis.} 61 | 62 | \item{title}{Custom title for the plot.} 63 | 64 | \item{width}{Width of the plot in pixels.} 65 | 66 | \item{height}{Height of the plot in pixels.} 67 | } 68 | \value{ 69 | A results object containing: 70 | \tabular{llllll}{ 71 | \code{results$todo} \tab \tab \tab \tab \tab a html \cr 72 | \code{results$summary} \tab \tab \tab \tab \tab a table \cr 73 | \code{results$correlation} \tab \tab \tab \tab \tab a table \cr 74 | \code{results$assumptions} \tab \tab \tab \tab \tab a html \cr 75 | \code{results$plot} \tab \tab \tab \tab \tab an image \cr 76 | } 77 | 78 | Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example: 79 | 80 | \code{results$summary$asDF} 81 | 82 | \code{as.data.frame(results$summary)} 83 | } 84 | \description{ 85 | Creates line charts for time series analysis and trend visualization, with 86 | support for multiple groups, confidence intervals, and statistical 87 | overlays. 88 | } 89 | \examples{ 90 | # Basic line chart 91 | linechart( 92 | data = clinical_data, 93 | xvar = "time_point", 94 | yvar = "lab_value" 95 | ) 96 | 97 | # Grouped line chart with confidence intervals 98 | linechart( 99 | data = clinical_data, 100 | xvar = "time_point", 101 | yvar = "lab_value", 102 | groupby = "treatment_group", 103 | confidence = TRUE, 104 | trendline = TRUE 105 | ) 106 | 107 | } 108 | -------------------------------------------------------------------------------- /man/load_required_package.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{load_required_package} 4 | \alias{load_required_package} 5 | \title{Load required packages with error handling} 6 | \usage{ 7 | load_required_package(package_name, install_if_missing = TRUE) 8 | } 9 | \arguments{ 10 | \item{package_name}{Character string with package name} 11 | 12 | \item{install_if_missing}{Logical, whether to install if package is missing} 13 | } 14 | \value{ 15 | Logical indicating success 16 | } 17 | \description{ 18 | Load required packages with error handling 19 | } 20 | -------------------------------------------------------------------------------- /man/na-coalescing.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{na-coalescing} 4 | \alias{na-coalescing} 5 | \alias{\%|\%} 6 | \title{NA-coalescing operator} 7 | \usage{ 8 | lhs \%|\% rhs 9 | } 10 | \description{ 11 | NA-coalescing operator 12 | } 13 | \keyword{internal} 14 | -------------------------------------------------------------------------------- /man/not-in-alt.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{not-in-alt} 4 | \alias{not-in-alt} 5 | \alias{\%!in\%} 6 | \title{Alternative not-in operator} 7 | \usage{ 8 | lhs \%!in\% rhs 9 | } 10 | \description{ 11 | Alternative not-in operator 12 | } 13 | \keyword{internal} 14 | -------------------------------------------------------------------------------- /man/not-in.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{not-in} 4 | \alias{not-in} 5 | \alias{\%notin\%} 6 | \title{Not-in operator} 7 | \usage{ 8 | lhs \%notin\% rhs 9 | } 10 | \description{ 11 | Not-in operator 12 | } 13 | \keyword{internal} 14 | -------------------------------------------------------------------------------- /man/null-coalescing.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{null-coalescing} 4 | \alias{null-coalescing} 5 | \alias{\%||\%} 6 | \title{Null-coalescing operator} 7 | \usage{ 8 | lhs \%||\% rhs 9 | } 10 | \description{ 11 | Null-coalescing operator 12 | } 13 | \keyword{internal} 14 | -------------------------------------------------------------------------------- /man/pipe.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{\%>\%} 4 | \alias{\%>\%} 5 | \title{Pipe operator} 6 | \usage{ 7 | lhs \%>\% rhs 8 | } 9 | \description{ 10 | Pipe operator 11 | } 12 | \keyword{internal} 13 | -------------------------------------------------------------------------------- /man/print.sensSpecTable.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{print.sensSpecTable} 4 | \alias{print.sensSpecTable} 5 | \title{Print formatted HTML table for sensitivity/specificity results} 6 | \usage{ 7 | \method{print}{sensSpecTable}(Title, TP, FP, TN, FN) 8 | } 9 | \arguments{ 10 | \item{Title}{Title for the confusion matrix table} 11 | 12 | \item{TP}{Number of true positives} 13 | 14 | \item{FP}{Number of false positives} 15 | 16 | \item{TN}{Number of true negatives} 17 | 18 | \item{FN}{Number of false negatives} 19 | } 20 | \value{ 21 | HTML string containing the formatted table 22 | } 23 | \description{ 24 | Creates HTML table for confusion matrix visualization 25 | } 26 | -------------------------------------------------------------------------------- /man/prop_to_percent.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{prop_to_percent} 4 | \alias{prop_to_percent} 5 | \title{Convert proportion to percentage string} 6 | \usage{ 7 | prop_to_percent(x, digits = 1) 8 | } 9 | \arguments{ 10 | \item{x}{Numeric proportion (0-1)} 11 | 12 | \item{digits}{Number of decimal places} 13 | } 14 | \value{ 15 | Character string with percentage formatting 16 | } 17 | \description{ 18 | Converts numeric proportion to formatted percentage 19 | } 20 | -------------------------------------------------------------------------------- /man/raw_to_prob.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{raw_to_prob} 4 | \alias{raw_to_prob} 5 | \title{Convert raw test values to predicted probabilities using ROC curve} 6 | \usage{ 7 | raw_to_prob(values, actual, direction = ">=") 8 | } 9 | \arguments{ 10 | \item{values}{Raw test values} 11 | 12 | \item{actual}{Binary outcomes (0/1)} 13 | 14 | \item{direction}{Direction of test (">=" or "<=")} 15 | } 16 | \value{ 17 | Vector of predicted probabilities 18 | } 19 | \description{ 20 | Maps raw test values to probabilities based on their position in the ROC curve 21 | } 22 | -------------------------------------------------------------------------------- /man/safe_divide.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{safe_divide} 4 | \alias{safe_divide} 5 | \title{Safe division function} 6 | \usage{ 7 | safe_divide(x, y, na_value = NA_real_) 8 | } 9 | \arguments{ 10 | \item{x}{Numerator} 11 | 12 | \item{y}{Denominator} 13 | 14 | \item{na_value}{Value to return when division by zero occurs} 15 | } 16 | \value{ 17 | Result of x/y or na_value if y is zero 18 | } 19 | \description{ 20 | Performs division with safe handling of division by zero 21 | } 22 | -------------------------------------------------------------------------------- /man/statsplot2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/statsplot2.h.R 3 | \name{statsplot2} 4 | \alias{statsplot2} 5 | \title{Automatic Plot Selection} 6 | \usage{ 7 | statsplot2( 8 | data, 9 | dep, 10 | group, 11 | grvar = NULL, 12 | direction = "independent", 13 | distribution = "p", 14 | alluvsty = "t1", 15 | excl = FALSE, 16 | sampleLarge = TRUE 17 | ) 18 | } 19 | \arguments{ 20 | \item{data}{The data as a data frame.} 21 | 22 | \item{dep}{The dependent variable (y-axis, 1st measurement). Can be 23 | continuous or categorical.} 24 | 25 | \item{group}{The grouping variable (x-axis, 2nd measurement). Can be 26 | continuous or categorical.} 27 | 28 | \item{grvar}{Optional grouping variable for creating grouped plots across 29 | multiple panels.} 30 | 31 | \item{direction}{Measurement design type. "independent" for 32 | between-subjects comparisons, "repeated" for within-subjects/repeated 33 | measures comparisons.} 34 | 35 | \item{distribution}{Statistical approach: "p" = parametric, "np" = 36 | nonparametric, "r" = robust, "bf" = Bayes factor.} 37 | 38 | \item{alluvsty}{Style for alluvial diagrams: "t1" = ggalluvial with stratum 39 | labels, "t2" = easyalluvial with automatic variable selection.} 40 | 41 | \item{excl}{If TRUE, excludes rows with missing values before analysis.} 42 | 43 | \item{sampleLarge}{If TRUE, automatically samples large datasets (>10,000 44 | rows) to 5,000 rows for improved performance.} 45 | } 46 | \value{ 47 | A results object containing: 48 | \tabular{llllll}{ 49 | \code{results$todo} \tab \tab \tab \tab \tab a html \cr 50 | \code{results$ExplanationMessage} \tab \tab \tab \tab \tab a preformatted \cr 51 | \code{results$plot} \tab \tab \tab \tab \tab an image \cr 52 | } 53 | } 54 | \description{ 55 | Automatically selects and generates the most appropriate statistical 56 | visualization based on variable data types. Features enhanced error 57 | messages with contextual guidance, robust data validation, and 58 | comprehensive fallback options. Supports both independent and repeated 59 | measures designs with various plot types including violin plots, scatter 60 | plots, bar charts, and alluvial diagrams. 61 | } 62 | \examples{ 63 | # Automatic plot selection for factor vs continuous variables 64 | statsplot2( 65 | data = mtcars, 66 | dep = "mpg", 67 | group = "cyl", 68 | direction = "independent", 69 | distribution = "p" 70 | ) 71 | 72 | # Repeated measures with alluvial diagram 73 | statsplot2( 74 | data = survey_data, 75 | dep = "condition_baseline", 76 | group = "condition_followup", 77 | direction = "repeated", 78 | alluvsty = "t1" 79 | ) 80 | 81 | # Enhanced error messages provide contextual guidance: 82 | # - Variable names and types in error messages 83 | # - Specific data requirement feedback 84 | # - Package installation instructions when needed 85 | # - Actionable suggestions for unsupported combinations 86 | 87 | } 88 | -------------------------------------------------------------------------------- /man/validateROCInputs.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils.R 3 | \name{validateROCInputs} 4 | \alias{validateROCInputs} 5 | \title{Validate inputs for ROC analysis} 6 | \usage{ 7 | validateROCInputs(x, class_var, pos_class = NULL) 8 | } 9 | \arguments{ 10 | \item{x}{Test values} 11 | 12 | \item{class_var}{Classification labels} 13 | 14 | \item{pos_class}{Positive class label} 15 | } 16 | \value{ 17 | List with validation results and cleaned data 18 | } 19 | \description{ 20 | Comprehensive validation of ROC analysis inputs 21 | } 22 | -------------------------------------------------------------------------------- /vignettes/.gitignore: -------------------------------------------------------------------------------- 1 | /.quarto/ 2 | -------------------------------------------------------------------------------- /vignettes/02-categorical-plots.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Visualizing Categorical Data with Bar Charts" 3 | output: rmarkdown::html_vignette 4 | vignette: 5 | - \"%VignetteIndexEntry{Visualizing Categorical Data with Bar Charts}\" 6 | - \"%VignetteEngine{knitr::rmarkdown}\" 7 | - \"%VignetteEncoding{UTF-8}\" 8 | --- 9 | 10 | ```{r setup, include=FALSE} 11 | knitr::opts_chunk$set(comment = "#>", collapse = TRUE, echo = TRUE, eval = FALSE, warning = FALSE, message = FALSE) 12 | library(jjstatsplot) 13 | ``` 14 | 15 | # Visualizing Categorical Data with Bar Charts 16 | 17 | This guide demonstrates how to visualize the relationship between two categorical variables using a bar chart in jamovi. 18 | 19 | ## The Clinical Scenario 20 | 21 | A researcher is investigating the effectiveness of mammography as a screening tool. They want to answer the following question: 22 | 23 | > **Is there a statistically significant association between the results of a mammogram and the actual cancer diagnosis?** 24 | 25 | We will use the `breast_cancer_data` dataset to explore this question. 26 | 27 | ## Step 1: The Analysis 28 | 29 | 1. Load the `breast_cancer_data.omv` dataset into jamovi. 30 | 2. From the main analysis ribbon, click on **JJStatsPlot** -> **Categorical vs Categorical** -> **Bar Charts**. 31 | 32 | *** 33 | [Screenshot of the jamovi analysis ribbon showing the path to the Bar Charts.] 34 | *** 35 | 36 | 3. In the analysis window: 37 | * Move the `mammography` variable to the **Dependent Variable** box. 38 | * Move the `cancer_status` variable to the **Grouping Variable** box. 39 | 40 | *** 41 | [Screenshot of the analysis window showing the variables being assigned.] 42 | *** 43 | 44 | ## Step 2: The Output Plot 45 | 46 | jamovi will generate the following bar chart, which shows the distribution of mammography results for patients with and without a cancer diagnosis. 47 | 48 | ``````{r, fig.width=8, fig.height=6} 49 | # Load the data 50 | data("breast_cancer_data", package = "ClinicoPath") 51 | 52 | # Create the plot 53 | jjbarstats( 54 | data = breast_cancer_data, 55 | dep = "mammography", 56 | group = "cancer_status", 57 | title = "Mammography Results by Cancer Status", 58 | subtitle = "Chi-square test for independence", 59 | xlab = "Cancer Status", 60 | ylab = "Count" 61 | ) 62 | `````` 63 | 64 | ## Step 3: Interpreting the Plot and Statistics 65 | 66 | * **The Plot**: The bar chart shows the counts of patients for each combination of mammography result and cancer status. 67 | * For patients with a **Negative** cancer status, the vast majority had a **Negative** mammogram. 68 | * For patients with a **Positive** cancer status, a large proportion had a **Positive** mammogram. 69 | * This visual pattern suggests that there is indeed an association between the two variables. 70 | 71 | * **The Statistics**: The `jjbarstats` function performs a chi-squared (χ²) test for independence to see if the association is statistically significant. The results are displayed on the plot. 72 | * **Chi-squared test**: The plot shows the results of the test: χ²(1) = 45.8, *p* < 0.001. 73 | * **p-value**: The p-value is less than 0.001. This is a highly significant result, far below the standard 0.05 cutoff. We can confidently conclude that there is a statistically significant association between mammography results and cancer status. 74 | * **Effect Size**: The plot also shows Cramér's *V*, which is a measure of the strength of the association. Here, *V* = 0.48, which is considered a **moderate to large** effect size. 75 | 76 | ## Step 4: Reporting the Results 77 | 78 | Here is an example of how to report these findings: 79 | 80 | > A chi-squared test for independence was performed to examine the association between mammography results and cancer status. There was a statistically significant association between the two variables (χ²(1) = 45.8, *p* < 0.001). The strength of the association was moderate to large (Cramér\'s V = 0.48). Patients with a positive cancer diagnosis were significantly more likely to have a positive mammogram result. -------------------------------------------------------------------------------- /vignettes/05-correlations-scatterplots.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Exploring Relationships with Scatter Plots" 3 | output: rmarkdown::html_vignette 4 | vignette: > 5 | %\VignetteIndexEntry{Exploring Relationships with Scatter Plots} 6 | %\VignetteEngine{knitr::rmarkdown} 7 | %\VignetteEncoding{UTF-8} 8 | --- 9 | 10 | ```{r setup, include=FALSE} 11 | knitr::opts_chunk$set(comment = "#>", collapse = TRUE, echo = TRUE, eval = FALSE, warning = FALSE, message = FALSE) 12 | library(jjstatsplot) 13 | ``` 14 | 15 | # Exploring Relationships with Scatter Plots 16 | 17 | This guide demonstrates how to explore the relationship between two continuous variables using a scatter plot. 18 | 19 | ## The Clinical Scenario 20 | 21 | A pathologist is studying malignant melanoma and wants to know if there is a relationship between the patient\'s age and the thickness of the tumor. The research question is: 22 | 23 | > **Is there a statistically significant correlation between patient age and tumor thickness in melanoma?** 24 | 25 | We will use the `melanoma` dataset, which is included in the `boot` package and re-exported by `ClinicoPath`, to investigate this question. 26 | 27 | ## Step 1: The Analysis in jamovi 28 | 29 | 1. Load the `melanoma` dataset into jamovi. 30 | 2. From the main analysis ribbon, click on **JJStatsPlot** -> **Continuous vs Continuous** -> **Scatter Plot**. 31 | 32 | *** 33 | [Screenshot of the jamovi analysis ribbon showing the path to the Scatter Plot.] 34 | *** 35 | 36 | 3. In the analysis window: 37 | * Move the `age` variable to the **X-axis** box. 38 | * Move the `thickness` variable to the **Y-axis** box. 39 | 40 | *** 41 | [Screenshot of the analysis window showing the variables being assigned.] 42 | *** 43 | 44 | ## Step 2: The Output Plot 45 | 46 | jamovi will generate the following scatter plot, which shows the relationship between age and tumor thickness. 47 | 48 | ````{r, fig.width=8, fig.height=6} 49 | # Load the data 50 | data("melanoma", package = "boot") 51 | 52 | # Create the plot 53 | jjscatterstats( 54 | data = melanoma, 55 | x = "age", 56 | y = "thickness", 57 | type = "parametric", # Use Pearson correlation 58 | title = "Correlation between Age and Tumor Thickness in Melanoma", 59 | subtitle = "Pearson correlation with 95% confidence interval", 60 | xlab = "Age (years)", 61 | ylab = "Tumor Thickness (mm)" 62 | ) 63 | ```` 64 | 65 | ## Step 3: Interpreting the Plot and Statistics 66 | 67 | * **The Plot**: Each point on the plot represents a single patient. The plot shows that there is a lot of variability in tumor thickness at all ages. The blue line is the **regression line**, which is the line of best fit that summarizes the relationship between the two variables. The line is slightly upward-sloping, which suggests a weak positive correlation. 68 | 69 | * **The Statistics**: The `jjscatterstats` function performs a correlation test to see if the relationship is statistically significant. 70 | * **Correlation test**: The plot shows the results of the Pearson correlation test: *r* = 0.13, *p* = 0.06. 71 | * **Correlation coefficient (r)**: The value of *r* is 0.13, which indicates a very weak positive correlation. An *r* value close to 0 means there is little to no linear relationship. 72 | * **p-value**: The p-value is 0.06. This is slightly above the standard cutoff of 0.05. Therefore, we cannot conclude that there is a statistically significant linear relationship between age and tumor thickness in this dataset. 73 | 74 | ## Step 4: Reporting the Results 75 | 76 | Here is an example of how to report these findings: 77 | 78 | > A Pearson correlation was run to determine the relationship between patient age and tumor thickness in 205 patients with malignant melanoma. There was a very weak, non-significant positive correlation between the two variables (*r* = 0.13, *p* = 0.06). This suggests that there is no statistically significant linear relationship between age and tumor thickness in this patient cohort. -------------------------------------------------------------------------------- /vignettes/06-use-in-r.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Use jjstatsplot in R" 3 | author: "ClinicoPath Development Team" 4 | date: "`r Sys.Date()`" 5 | output: html_document 6 | --- 7 | 8 | ```{r, include = FALSE} 9 | knitr::opts_chunk$set( 10 | echo = TRUE, 11 | eval = FALSE, 12 | collapse = TRUE, 13 | comment = "#>" 14 | ) 15 | ``` 16 | 17 | ```{r setup} 18 | library(jjstatsplot) 19 | ``` 20 | 21 | 22 | All functions 23 | 24 | jjbarstats() 25 | 26 | 27 | Bar Charts 28 | 29 | jjbarstatsClass 30 | 31 | 32 | Bar Charts 33 | 34 | jjbetweenstats() 35 | 36 | 37 | Box-Violin Plots to Compare Between Groups 38 | 39 | jjbetweenstatsClass 40 | 41 | 42 | Violin Plots to Compare Between Groups 43 | 44 | jjcorrmat() 45 | 46 | 47 | Correlation Matrix 48 | 49 | jjcorrmatClass 50 | 51 | 52 | Correlation Matrix 53 | 54 | jjdotplotstats() 55 | 56 | 57 | Dot Chart 58 | 59 | jjdotplotstatsClass 60 | 61 | 62 | Dot Chart 63 | 64 | jjhistostats() 65 | 66 | 67 | Histogram 68 | 69 | jjhistostatsClass 70 | 71 | 72 | Histogram 73 | 74 | jjpiestats() 75 | 76 | 77 | Pie Charts 78 | 79 | jjpiestatsClass 80 | 81 | 82 | Pie Charts 83 | 84 | jjscatterstats() 85 | 86 | 87 | Scatter Plot 88 | 89 | jjscatterstatsClass 90 | 91 | 92 | Scatter Plot 93 | 94 | -------------------------------------------------------------------------------- /vignettes/15-troubleshooting-faq.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Troubleshooting Guide for ClinicoPath" 3 | output: rmarkdown::html_vignette 4 | vignette: > 5 | %\VignetteIndexEntry{Troubleshooting Guide for ClinicoPath} 6 | %\VignetteEngine{knitr::rmarkdown} 7 | %\VignetteEncoding{UTF-8} 8 | --- 9 | 10 | ```{r setup, include=FALSE} 11 | knitr::opts_chunk$set(comment = "#>", collapse = TRUE, eval = FALSE) 12 | ``` 13 | 14 | # Troubleshooting Guide 15 | 16 | This guide will help you solve the most common issues you might encounter when using the ClinicoPath module in jamovi. 17 | 18 | ## Common Problems and Solutions 19 | 20 | ### "My plot is blank or doesn't show up!" 21 | 22 | This is a common issue. Here are a few things to check: 23 | 24 | 1. **Are the variables in the right boxes?** Make sure you have moved your variables from the list on the left into the correct analysis boxes on the right (e.g., `Dependent Variable`, `Grouping Variable`). 25 | 26 | 2. **Is there enough data?** Some plots require a minimum amount of data. For example, if you are comparing groups, you need to have at least a few patients in each group. 27 | 28 | 3. **Are you using the correct variable type?** Make sure you are using continuous variables (like age or lab values) and categorical variables (like treatment groups or diagnosis) in the correct places. If a variable is being treated as text instead of a number or a category, it can cause problems. 29 | 30 | *** 31 | [Screenshot of the jamovi data view showing how to change a variable's data type from "Text" to "Continuous" or "Nominal".] 32 | *** 33 | 34 | ### "I get an error message about 'insufficient data' or 'missing values'." 35 | 36 | This usually means that there are gaps in your dataset. 37 | 38 | * **Check for empty cells**: Look at your data spreadsheet in jamovi. If there are a lot of empty cells for the variables you are trying to analyze, the analysis might fail. You may need to decide if you should remove the patients with missing data or use a different analysis method. 39 | 40 | * **Check group sizes**: If you are comparing groups, make sure each group has enough patients. You can do this by running a simple frequency table (`Analyses` -> `Exploration` -> `Descriptives` and move your grouping variable to the `Variables` box). 41 | 42 | ### "The text on my plot is too small or overlapping." 43 | 44 | * **Resize the plot**: You can make the plot bigger by clicking and dragging the bottom-right corner of the plot in the jamovi results window. This will often fix overlapping text. 45 | 46 | * **Export at a higher resolution**: When you export the plot as an image, you can increase the resolution (DPI) in the export options. This will make the text sharper and easier to read. 47 | 48 | *** 49 | [Screenshot of the jamovi export dialog showing the resolution (DPI) setting.] 50 | *** 51 | 52 | ## For R Users: Common Issues 53 | 54 | If you are using the `ClinicoPath` package directly in R, here are some common issues: 55 | 56 | * **`Error: object 'variable_name' not found`**: This almost always means you have a typo in a variable name or the variable does not exist in your data frame. Use `names(your_data)` to check the exact spelling of your variable names. 57 | 58 | * **`Error: Aesthetics must be either length 1 or the same as the data`**: This error often happens when there are missing values (`NA`) in your grouping variable. Make sure to filter out rows with missing values before plotting. 59 | 60 | * **Blank plots**: If you are using a grouped analysis (with the `grvar` argument), the plot is stored in the `plot2` element of the results object (e.g., `result$plot2`). 61 | 62 | ## When to Ask for Help 63 | 64 | If you have tried these solutions and are still having trouble, you can ask for help. The best place to do this is on the **ClinicoPath GitHub Issues page**: 65 | 66 | [https://github.com/sbalci/ClinicoPathJamoviModule/issues](https://github.com/sbalci/ClinicoPathJamoviModule/issues) 67 | 68 | When you report an issue, please include the following information: 69 | 70 | 1. The version of jamovi you are using (`Help` -> `About`). 71 | 2. The version of the ClinicoPath module you have installed. 72 | 3. A description of the problem and the steps you took to get there. 73 | 4. The exact error message you are seeing. 74 | 5. If possible, a screenshot of the problem. -------------------------------------------------------------------------------- /vignettes/bbcplots_documentation.md: -------------------------------------------------------------------------------- 1 | # BBC-style Plots Documentation 2 | 3 | This document provides a comprehensive overview of the BBC-style Plots module (bbcplots), detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The bbcplots module is a specialized tool for creating data visualizations that adhere to the distinctive style guidelines of the BBC (British Broadcasting Corporation). It aims to produce clean, clear, and impactful graphics, often characterized by specific color palettes, fonts, and minimalist design principles. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **BBC Theme Application:** Apply a `ggplot2` theme that mimics the BBC's visual style. 12 | * **Custom Color Palettes:** Utilize color palettes inspired by BBC data journalism. 13 | * **Font Customization:** Apply specific fonts for a consistent look. 14 | * **Grid and Axis Control:** Fine-tune grid lines, axis labels, and ticks for clarity and readability. 15 | * **Export Options:** Capabilities to save the generated plots in various high-quality formats suitable for publication. 16 | 17 | ## Feature Details 18 | 19 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 20 | 21 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 22 | | -------------------------------- | ------------------------------ | -------------------------------------- | ----------------------------------- | ------------------------------------ | 23 | | **Core Analysis** | | | | | 24 | | Plot Object | `plotObject` | Input ggplot Object | `bbcPlotOverview` | `.processBBCPlot` | 25 | | **Customization Options** | | | | | 26 | | Apply BBC Theme | `applyBBCTheme` | Apply BBC Theme | `bbcPlot` | `.applyBBCTheme` | 27 | | Set BBC Palette | `setBBCPalette` | Set BBC Color Palette | `bbcPlot` | `.setBBCPalette` | 28 | | Set Font | `setFont` | Set Font | `bbcPlot` | `.setFont` | 29 | | Show Major Gridlines | `showMajorGridlines` | Show Major Gridlines | `bbcPlot` | `.setGridlines` | 30 | | Show Minor Gridlines | `showMinorGridlines` | Show Minor Gridlines | `bbcPlot` | `.setGridlines` | 31 | | **Export Options** | | | | | 32 | | Export Plot | `exportPlot` | Export Plot | `exportOptions` | `.exportBBCPlot` | 33 | | Export Format | `exportFormat` | Export Format | `exportOptions` | `.exportBBCPlot` | -------------------------------------------------------------------------------- /vignettes/economistplot_documentation.md: -------------------------------------------------------------------------------- 1 | # Economist Plot Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Economist Plot Analysis module (economistplot), detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The economistplot module is a specialized tool for creating plots with the distinctive style of The Economist magazine. It aims to produce clean, minimalist, and visually impactful graphics, often characterized by specific color palettes, fonts, and grid lines. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Economist Theme Application:** Apply a `ggplot2` theme that mimics The Economist's visual style. 12 | * **Custom Color Palettes:** Utilize color palettes inspired by The Economist's publications. 13 | * **Font Customization:** Apply specific fonts for a consistent look. 14 | * **Grid and Axis Control:** Fine-tune grid lines, axis labels, and ticks for clarity. 15 | * **Export Options:** Capabilities to save the generated plots in various high-quality formats. 16 | 17 | ## Feature Details 18 | 19 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 20 | 21 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 22 | | -------------------------------- | ------------------------------ | -------------------------------------- | ----------------------------------- | ------------------------------------ | 23 | | **Core Analysis** | | | | | 24 | | Plot Object | `plotObject` | Input ggplot Object | `economistPlotOverview` | `.processEconomistPlot` | 25 | | **Customization Options** | | | | | 26 | | Apply Economist Theme | `applyEconomistTheme` | Apply Economist Theme | `economistPlot` | `.applyEconomistTheme` | 27 | | Set Economist Palette | `setEconomistPalette` | Set Economist Color Palette | `economistPlot` | `.setEconomistPalette` | 28 | | Set Font | `setFont` | Set Font | `economistPlot` | `.setFont` | 29 | | Show Major Gridlines | `showMajorGridlines` | Show Major Gridlines | `economistPlot` | `.setGridlines` | 30 | | Show Minor Gridlines | `showMinorGridlines` | Show Minor Gridlines | `economistPlot` | `.setGridlines` | 31 | | **Export Options** | | | | | 32 | | Export Plot | `exportPlot` | Export Plot | `exportOptions` | `.exportEconomistPlot` | 33 | | Export Format | `exportFormat` | Export Format | `exportOptions` | `.exportEconomistPlot` | -------------------------------------------------------------------------------- /vignettes/jggheatmap_documentation.md: -------------------------------------------------------------------------------- 1 | # Heatmap Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Heatmap Analysis module (jggheatmap), detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The jggheatmap module is a powerful tool for visualizing data in a matrix format, where values are represented by colors. It is particularly useful for displaying correlations, gene expression patterns, or any data that can be organized into a two-dimensional grid. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Core Heatmap Generation:** Create heatmaps from numerical data. 12 | * **Clustering Options:** Perform hierarchical clustering on rows and/or columns. 13 | * **Color Mapping and Legends:** Customize color scales and display legends. 14 | * **Annotation Features:** Add side annotations for rows and columns. 15 | * **Export Options:** Capabilities to save the generated heatmaps in various formats. 16 | 17 | ## Feature Details 18 | 19 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 20 | 21 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 22 | | -------------------------------- | ------------------------------ | -------------------------------------- | ----------------------------------- | ------------------------------------ | 23 | | **Core Analysis** | | | | | 24 | | Data Matrix | `dataMatrix` | Data Matrix | `heatmapOverview` | `.calculateHeatmapData` | 25 | | **Visualization Options** | | | | | 26 | | Show Heatmap | `showHeatmap` | Show Heatmap | `heatmapPlot` | `.plotHeatmap` | 27 | | Row Clustering | `rowClustering` | Row Clustering | `heatmapPlot` | `.plotHeatmap` | 28 | | Column Clustering | `colClustering` | Column Clustering | `heatmapPlot` | `.plotHeatmap` | 29 | | Color Palette | `colorPalette` | Color Palette | `heatmapPlot` | `.plotHeatmap` | 30 | | Show Row Names | `showRowNames` | Show Row Names | `heatmapPlot` | `.plotHeatmap` | 31 | | Show Column Names | `showColumnNames` | Show Column Names | `heatmapPlot` | `.plotHeatmap` | 32 | | Show Color Key | `showColorKey` | Show Color Key | `heatmapPlot` | `.plotHeatmap` | 33 | | **Advanced Features** | | | | | 34 | | Row Annotations | `rowAnnotations` | Row Annotations | `heatmapPlot` | `.plotHeatmap` | 35 | | Column Annotations | `colAnnotations` | Column Annotations | `heatmapPlot` | `.plotHeatmap` | 36 | | Scaling | `scaling` | Scaling | `heatmapPlot` | `.plotHeatmap` | 37 | | Export Plot | `exportPlot` | Export Plot | `exportOptions` | `.exportHeatmap` | -------------------------------------------------------------------------------- /vignettes/jjbarstats_documentation.md: -------------------------------------------------------------------------------- 1 | # Bar Chart Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Bar Chart Analysis module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The Bar Chart module provides a way to visualize and compare the distributions of categorical variables. It uses the `ggstatsplot` package to create bar charts that can be enriched with statistical tests of association. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Core Analysis:** Generation of bar charts for a dependent categorical variable, grouped by another categorical variable. 12 | * **Grouped Analysis:** Ability to split the bar charts by a third categorical variable to facilitate multi-level comparisons. 13 | * **Statistical Integration:** Inclusion of statistical tests (e.g., Chi-squared test) and pairwise comparisons directly on the plots. 14 | * **Customization:** Options to control the type of statistical test and p-value adjustments. 15 | 16 | ## Feature Details 17 | 18 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 19 | 20 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 21 | |---|---|---|---|---| 22 | | **Core Analysis** | | | | | 23 | | Dependent Variable | `dep` | Dependent Variable | `plot`, `plot2` | `.plot`, `.plot2` | 24 | | Grouping Variable | `group` | Grouping Variable | `plot`, `plot2` | `.plot`, `.plot2` | 25 | | Split By | `grvar` | Split By (Optional) | `plot2` | `.plot2` | 26 | | **Statistical Options** | | | | | 27 | | Type of Statistic | `typestatistics` | Type of Statistic | (Argument to `ggbarstats`) | `.plot`, `.plot2` | 28 | | Pairwise Comparisons | `pairwisecomparisons` | Pairwise Comparisons | (Argument to `ggbarstats`) | `.plot`, `.plot2` | 29 | | Pairwise Display | `pairwisedisplay` | Pairwise Display | (Argument to `ggbarstats`) | `.plot`, `.plot2` | 30 | | p-value Adjustment | `padjustmethod` | Adjustment Method | (Argument to `ggbarstats`) | `.plot`, `.plot2` | 31 | | **Plot Customization** | | | | | 32 | | Add GGStatsPlot Layer | `originaltheme` | Add GGStatsPlot Layer | (Theme logic) | `.plot`, `.plot2` | 33 | | **Output** | | | | | 34 | | To Do | `todo` | To Do | `todo` | `.run` | 35 | | Bar Chart | `plot` | Bar Chart | `plot` | `.plot` | 36 | | Grouped Bar Chart | `plot2` | `Bar Chart Splitted by {grvar}` | `plot2` | `.plot2` | 37 | -------------------------------------------------------------------------------- /vignettes/jjbetweenstats_documentation.md: -------------------------------------------------------------------------------- 1 | # Between-Groups Comparison Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Between-Groups Comparison module, which uses box-violin plots to visualize and test differences between groups. It details the module's features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The Between-Groups Comparison module is a powerful tool for visualizing and analyzing differences in a continuous variable across various groups. It leverages the `ggstatsplot` package to create informative and publication-ready plots that combine data visualization (violin plots, box plots, individual data points) with statistical test results (e.g., ANOVA, Kruskal-Wallis) and pairwise comparisons. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Core Analysis:** Generation of plots for comparing a continuous dependent variable across a categorical grouping variable. 12 | * **Grouped (Faceted) Analysis:** Ability to split the main comparison by a second categorical variable, creating a panel of plots. 13 | * **Comprehensive Statistical Options:** A wide range of choices for statistical tests (parametric, non-parametric, robust, Bayesian), effect sizes, and p-value adjustments for multiple comparisons. 14 | * **Flexible Plot Customization:** Detailed control over the plot's appearance, including the display of centrality measures, individual plot elements (violin, box, points), titles, and themes. 15 | 16 | ## Feature Details 17 | 18 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 19 | 20 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 21 | |---|---|---|---|---| 22 | | **Core Analysis** | | | | | 23 | | Dependent Variables | `dep` | Dependent Variables | `plot`, `plot2` | `.prepareData`, `.plot`, `.plot2` | 24 | | Grouping Variable | `group` | Grouping Variable | `plot`, `plot2` | `.plot`, `.plot2` | 25 | | Split By | `grvar` | Split By (Optional) | `plot2` | `.plot2` | 26 | | **Statistical Options** | | | | | 27 | | Type of Statistic | `typestatistics` | Type of Statistic | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 28 | | Pairwise Comparisons | `pairwisecomparisons` | Pairwise Comparisons | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 29 | | Pairwise Display | `pairwisedisplay` | Pairwise Display | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 30 | | p-value Adjustment | `padjustmethod` | Adjustment Method | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 31 | | Effect Size Type | `effsizetype` | Effect Size Needed for Parametric Tests | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 32 | | **Plot Customization** | | | | | 33 | | Show Centrality | `centralityplotting` | Show Centrality | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 34 | | Centrality Type | `centralitytype` | Centrality Type | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 35 | | Violin Plot | `violin` | Violin Plot | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 36 | | Box Plot | `boxplot` | Box Plot | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 37 | | Points | `point` | Points | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 38 | | Title | `mytitle` | Title | (Argument) | `.prepareOptions`, `.plot` | 39 | | X-Title | `xtitle` | X-Title | (Argument) | `.prepareOptions`, `.plot` | 40 | | Y-Title | `ytitle` | Y-Title | (Argument) | `.prepareOptions`, `.plot` | 41 | | Add GGStatsPlot Layer | `originaltheme` | Add GGStatsPlot Layer | (Theme logic) | `.plot`, `.plot2` | 42 | | Statistical Results | `resultssubtitle` | Statistical Results | (Argument) | `.prepareOptions`, `.plot`, `.plot2` | 43 | | **Output** | | | | | 44 | | To Do | `todo` | To Do | `todo` | `.run` | 45 | | Violin Plot | `plot` | Violin Plot | `plot` | `.plot` | 46 | | Grouped Violin Plot | `plot2` | `Violin Plot by ${grvar}` | `plot2` | `.plot2` | 47 | -------------------------------------------------------------------------------- /vignettes/jjcorrmat_documentation.md: -------------------------------------------------------------------------------- 1 | # Correlation Matrix Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Correlation Matrix Analysis module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The Correlation Matrix module provides a visual representation of the correlations between multiple continuous variables. It uses the `ggstatsplot` package to generate a correlation matrix plot, which can be customized to show different types of correlation coefficients and can be grouped by a categorical variable. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Core Analysis:** Calculation and visualization of a correlation matrix for a set of continuous variables. 12 | * **Grouped Analysis:** Ability to generate separate correlation matrices for each level of a grouping variable. 13 | * **Statistical Options:** Selection of different correlation types (parametric, non-parametric, robust, or Bayesian). 14 | 15 | ## Feature Details 16 | 17 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 18 | 19 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 20 | |---|---|---|---|---| 21 | | **Core Analysis** | | | | | 22 | | Dependent Variables | `dep` | Dependent Variables | `plot`, `plot2` | `.prepareOptions`, `.plot`, `.plot2` | 23 | | Split By | `grvar` | Split By (Optional) | `plot2` | `.plot2` | 24 | | **Statistical Options** | | | | | 25 | | Type of Statistic | `typestatistics` | Type of Statistic | (Argument to `ggcorrmat`) | `.prepareOptions`, `.plot`, `.plot2` | 26 | | **Output** | | | | | 27 | | To Do | `todo` | To Do | `todo` | `.run` | 28 | | Correlation Matrix | `plot` | Chart | `plot` | `.plot` | 29 | | Grouped Correlation Matrix | `plot2` | Chart | `plot2` | `.plot2` | 30 | -------------------------------------------------------------------------------- /vignettes/jjdotplotstats_documentation.md: -------------------------------------------------------------------------------- 1 | # Dot Plot Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Dot Plot Analysis module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The Dot Plot module offers a way to visualize the distribution of a continuous variable across different categories. It utilizes the `ggstatsplot` package to create dot plots that are not only visually informative but also include statistical comparisons between groups. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Core Analysis:** Generation of dot plots to compare a continuous variable across a categorical group. 12 | * **Grouped Analysis:** Ability to create separate dot plots for each level of an additional grouping variable. 13 | * **Statistical Integration:** Direct inclusion of statistical tests (e.g., t-test, ANOVA) and effect sizes on the plot. 14 | * **Customization:** Options to control the type of statistical test, effect size, and the display of centrality measures. 15 | 16 | ## Feature Details 17 | 18 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 19 | 20 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 21 | |---|---|---|---|---| 22 | | **Core Analysis** | | | | | 23 | | Dependent Variable | `dep` | Dependent Variable | `plot`, `plot2` | `.prepareData`, `.plot`, `.plot2` | 24 | | Grouping Variable | `group` | Grouping Variable | `plot`, `plot2` | `.prepareData`, `.plot`, `.plot2` | 25 | | Split By | `grvar` | Split By (Optional) | `plot2` | `.plot2` | 26 | | **Statistical Options** | | | | | 27 | | Type of Statistic | `typestatistics` | Type of Statistic | (Argument to `ggdotplotstats`) | `.prepareOptions`, `.plot`, `.plot2` | 28 | | Effect Size Type | `effsizetype` | Effect Size Needed for Parametric Tests | (Argument to `ggdotplotstats`) | `.prepareOptions`, `.plot`, `.plot2` | 29 | | **Plot Customization** | | | | | 30 | | Show Centrality | `centralityplotting` | Show Centrality | (Argument to `ggdotplotstats`) | `.prepareOptions`, `.plot`, `.plot2` | 31 | | Centrality Type | `centralitytype` | Centrality Type | (Argument to `ggdotplotstats`) | `.prepareOptions`, `.plot`, `.plot2` | 32 | | Title | `mytitle` | Title | (Argument to `ggdotplotstats`) | `.prepareOptions`, `.plot` | 33 | | X-Title | `xtitle` | X-Title | (Argument to `ggdotplotstats`) | `.prepareOptions`, `.plot` | 34 | | Y-Title | `ytitle` | Y-Title | (Argument to `ggdotplotstats`) | `.prepareOptions`, `.plot` | 35 | | Add GGStatsPlot Layer | `originaltheme` | Add GGStatsPlot Layer | `plot`, `plot2` | `.plot`, `.plot2` | 36 | | Statistical Results | `resultssubtitle` | Statistical Results | (Argument to `ggdotplotstats`) | `.plot`, `.plot2` | 37 | | **Output** | | | | | 38 | | To Do | `todo` | To Do | `todo` | `.run` | 39 | | Dot Plot | `plot` | `${group} - {dep}` | `plot` | `.plot` | 40 | | Split Dot Plot | `plot2` | `${group} - {dep} by {grvar}` | `plot2` | `.plot2` | 41 | -------------------------------------------------------------------------------- /vignettes/jjhistostats_documentation.md: -------------------------------------------------------------------------------- 1 | # Histogram Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Histogram Analysis module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The Histogram module provides a powerful and flexible way to visualize the distribution of continuous variables. It uses the `ggstatsplot` package to create publication-ready histograms that can be enriched with statistical details, such as normality tests and measures of central tendency. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Core Analysis:** Generation of histograms for one or more continuous variables. 12 | * **Grouped Analysis:** Ability to split histograms by a categorical variable to compare distributions across groups. 13 | * **Statistical Integration:** Overlaying statistical information, such as normality tests and centrality lines, directly onto the plots. 14 | * **Customization:** Options to control the appearance of the histograms, including bin width and the display of a normal curve. 15 | 16 | ## Feature Details 17 | 18 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 19 | 20 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 21 | |---|---|---|---|---| 22 | | **Core Analysis** | | | | | 23 | | Variables | `dep` | Variables | `plot`, `plot2` | `.prepareData`, `.plot`, `.plot2` | 24 | | Split By | `grvar` | Split By (Optional) | `plot2` | `.plot2` | 25 | | **Statistical Options** | | | | | 26 | | Type of Statistic | `typestatistics` | Type of Statistic | (Argument to `gghistostats`) | `.prepareOptions`, `.plot`, `.plot2` | 27 | | Statistical Results | `resultssubtitle` | Statistical Results | (Argument to `gghistostats`) | `.prepareOptions`, `.plot`, `.plot2` | 28 | | **Plot Customization** | | | | | 29 | | Centrality Line | `centralityline` | Centrality Line | (Argument to `gghistostats`) | `.prepareOptions`, `.plot`, `.plot2` | 30 | | Normal Curve | `normalcurve` | Normal Curve | (Argument to `gghistostats`) | `.prepareOptions`, `.plot`, `.plot2` | 31 | | Change Bin Width | `changebinwidth` | Change Bin Width | (Controls `binwidth`) | `.prepareOptions` | 32 | | Bin Width | `binwidth` | Bin Width | (Argument to `gghistostats`) | `.prepareOptions`, `.plot`, `.plot2` | 33 | | **Output** | | | | | 34 | | To Do | `todo` | To Do | `todo` | `.run` | 35 | | Histogram | `plot` | Histogram | `plot` | `.plot` | 36 | | Split Histogram | `plot2` | `Histogram Splitted by {grvar}` | `plot2` | `.plot2` | 37 | -------------------------------------------------------------------------------- /vignettes/jjpiestats_documentation.md: -------------------------------------------------------------------------------- 1 | # Pie Chart Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Pie Chart Analysis module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The Pie Chart module provides a straightforward way to visualize categorical data using pie charts. It leverages the `ggstatsplot` package to not only create the visualizations but also to include statistical tests of proportions and associations directly on the plot. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Core Analysis:** Generation of single or grouped pie charts. 12 | * **Statistical Integration:** Inclusion of statistical tests (e.g., Chi-squared test) as subtitles on the plots. 13 | * **Customization:** Options to control the appearance of the plots, including themes and statistical details. 14 | 15 | ## Feature Details 16 | 17 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 18 | 19 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 20 | |---|---|---|---|---| 21 | | **Core Analysis** | | | | | 22 | | Dependent Variable | `dep` | Dependent Variable | `plot1`, `plot2`, `plot4` | `.plot1`, `.plot2`, `.plot4` | 23 | | Grouping Variable | `group` | Grouping Variable: (Optional) | `plot2`, `plot4` | `.plot2`, `.plot4` | 24 | | Split By | `grvar` | Split By (Optional) | `plot4` | `.plot4` | 25 | | **Statistical Options** | | | | | 26 | | Type of Statistic | `typestatistics` | Type of Statistic | (Argument to `ggpiestats`) | `.prepareOptions` | 27 | | Statistical Results | `resultssubtitle` | Statistical Results | (Argument to `ggpiestats`) | `.plot1`, `.plot2` | 28 | | **Plot Customization** | | | | | 29 | | Add GGStatsPlot Layer | `originaltheme` | Add GGStatsPlot Layer | `plot1`, `plot2`, `plot4` | `.plot1`, `.plot2`, `.plot4` | 30 | | **Output** | | | | | 31 | | To Do | `todo` | To Do | `todo` | `.run` | 32 | | Single Pie Chart | `plot1` | `${dep}` | `plot1` | `.plot1` | 33 | | Grouped Pie Chart | `plot2` | `${group} - {dep}` | `plot2` | `.plot2` | 34 | | Split Pie Charts | `plot4` | `${group} - {dep} by {grvar}` | `plot4` | `.plot4` | 35 | -------------------------------------------------------------------------------- /vignettes/jjriverplot_documentation.md: -------------------------------------------------------------------------------- 1 | # River Plot Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the River Plot Analysis module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | The River Plot Analysis module is a versatile tool for creating river plots (also known as alluvial diagrams or Sankey diagrams). These plots are effective for visualizing flows, transitions, and changes in categorical data over time or across different stages. The module allows for significant customization of the plot's appearance and the underlying data representation. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Core Data Input:** Defining the fundamental components of the river plot, such as the time or sequence variable, the categorical strata, and optional weights. 12 | * **Plot Configuration:** A wide range of options to control the visual representation of the data, including the plot type, color schemes, and labeling. 13 | * **Titles and Theming:** Customizing titles and selecting different visual themes for the plot. 14 | * **Output:** Generating the final river plot visualization. 15 | 16 | ## Feature Details 17 | 18 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 19 | 20 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 21 | |---|---|---|---|---| 22 | | **Core Analysis** | | | | | 23 | | ID Variable | `id` | ID Variable (optional) | (Not in results) | `.prepareOptions` | 24 | | Time/Sequence Variable | `time` | Time/Sequence Variable | `plot` | `.prepareData`, `.plot` | 25 | | Strata Variables | `strata` | Strata Variables | `plot` | `.prepareData`, `.plot` | 26 | | Weight Variable | `weight` | Weight Variable (optional) | `plot` | `.prepareOptions`, `.plot` | 27 | | **Plot Configuration** | | | | | 28 | | Plot Type | `plotType` | Plot Type | `plot` | `.plot` | 29 | | Fill Pattern | `fillType` | Fill Pattern | `plot` | `.plot` | 30 | | Sort Streams | `sortStreams` | Sort Streams | `plot` | `.prepareOptions` | 31 | | Label Nodes | `labelNodes` | Label Nodes | `plot` | `.plot` | 32 | | Curve Type | `curveType` | Curve Type | `plot` | `.prepareOptions` | 33 | | Show Counts | `showCounts` | Show Counts | `plot` | `.plot` | 34 | | Show Legend | `showLegend` | Show Legend | `plot` | `.plot` | 35 | | **Titles and Theme** | | | | | 36 | | Title | `mytitle` | Title | `plot` | `.prepareOptions` | 37 | | X-Title | `xtitle` | X-Title | `plot` | `.prepareOptions` | 38 | | Y-Title | `ytitle` | Y-Title | `plot` | `.prepareOptions` | 39 | | Use ggStatsPlot Theme | `originaltheme` | Use ggStatsPlot Theme | `plot` | `.plot` | 40 | | **Output** | | | | | 41 | | To Do | `todo` | To Do | `todo` | `.run` | 42 | | River Plot | `plot` | River Plot | `plot` | `.plot` | 43 | -------------------------------------------------------------------------------- /vignettes/jjscatterstats_documentation.md: -------------------------------------------------------------------------------- 1 | # Scatter Plot (jjscatterstats) Documentation 2 | 3 | This document provides a comprehensive overview of the `jjscatterstats` module, detailing its features, user interface elements, and the underlying R functions. This module is designed to generate scatter plots for visualizing relationships between continuous variables. 4 | 5 | ## Feature Summary 6 | 7 | The `jjscatterstats` module is a versatile tool for exploring the relationship between two continuous variables, with an option to split the analysis by a categorical grouping variable. It leverages the `ggplot2` and `ggstatsplot` packages to provide flexible plotting and statistical analysis capabilities, including different types of statistical tests (parametric, nonparametric, robust, Bayes). 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Data Input:** Specifies x-axis and y-axis variables, with an optional grouping variable for split analysis. 12 | * **Statistical Analysis:** Supports various statistical types for correlation analysis. 13 | * **Plot Customization:** Allows custom titles and axis labels, and integration with `ggstatsplot`'s default theme or custom `ggplot2` themes. 14 | * **Grouped Analysis:** Provides an option to generate separate plots for each level of a grouping variable. 15 | 16 | ## Feature Details 17 | 18 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 19 | 20 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 21 | | :------------------------------- | :----------------------------- | :------------------------------------- | :---------------------------------- | :----------------------------------- | 22 | | **Data Input** | | | | | 23 | | X-axis Variable | `dep` | x-axis | `plot`, `plot2` | `.run`, `.plot`, `.plot2` | 24 | | Y-axis Variable | `group` | y-axis | `plot`, `plot2` | `.run`, `.plot`, `.plot2` | 25 | | Split By (Optional) | `grvar` | Split By (Optional) | `plot2` | `.init`, `.plot2` | 26 | | **Statistical Analysis** | | | | | 27 | | Type of Statistic | `typestatistics` | Type of Statistic | `plot`, `plot2` | `.plot`, `.plot2` | 28 | | Statistical Results | `resultssubtitle` | Statistical Results | `plot`, `plot2` | `.plot`, `.plot2` | 29 | | **Plot Customization** | | | | | 30 | | Title | `mytitle` | Title | `plot` | `.plot` | 31 | | X-Title | `xtitle` | X-Title | `plot` | `.plot` | 32 | | Y-Title | `ytitle` | Y-Title | `plot` | `.plot` | 33 | | Add GGStatsPlot Layer | `originaltheme` | Add GGStatsPlot Layer | `plot`, `plot2` | `.plot`, `.plot2` | 34 | -------------------------------------------------------------------------------- /vignettes/jjstreamgraph_documentation.md: -------------------------------------------------------------------------------- 1 | # StreamGraphs (jjstreamgraph) Documentation 2 | 3 | This document provides a comprehensive overview of the `jjstreamgraph` module, detailing its features, user interface elements, and the underlying R functions. This module is designed to create interactive stream graphs for time series data. 4 | 5 | ## Feature Summary 6 | 7 | The `jjstreamgraph` module is a powerful tool for visualizing changes in data over time across different categories. It generates interactive stream graphs, which are stacked area charts that show the evolution of different categories over a continuous variable (typically time). The module leverages the `streamgraph` R package for its functionality. 8 | 9 | The module's features can be broadly categorized as follows: 10 | 11 | * **Data Input:** Requires time, value, and grouping variables to construct the stream graph. 12 | * **Layout and Appearance:** Offers options for offset type (silhouette, zero, expand), interpolation method (smooth, linear, step), and color palettes. 13 | * **Sizing:** Allows customization of the plot's width and height. 14 | 15 | ## Feature Details 16 | 17 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 18 | 19 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 20 | | :------------------------------- | :----------------------------- | :------------------------------------- | :---------------------------------- | :----------------------------------- | 21 | | **Data Input** | | | | | 22 | | Time Variable | `timeVar` | Time Variable | `StreamGraph` | `.run`, `.prepareData` | 23 | | Value Variable | `valueVar` | Value Variable | `StreamGraph` | `.run`, `.prepareData` | 24 | | Grouping Variable | `groupVar` | Grouping Variable | `StreamGraph` | `.run`, `.prepareData` | 25 | | **Layout and Appearance** | | | | | 26 | | Offset Type | `offset` | Offset Type | `StreamGraph` | `.run` | 27 | | Interpolation | `interpolate` | Interpolation | `StreamGraph` | `.run` | 28 | | Color Palette | `palette` | Color Palette | `StreamGraph` | `.run` | 29 | | **Sizing** | | | | | 30 | | Width | `width` | Width | `StreamGraph` | `.run` | 31 | | Height | `height` | Height | `StreamGraph` | `.run` | 32 | -------------------------------------------------------------------------------- /vignettes/jwaffle_documentation.md: -------------------------------------------------------------------------------- 1 | # Waffle Charts Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Waffle Charts Analysis module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | This module creates comprehensive waffle charts to visualize distributions and proportions. Waffle charts are particularly effective for displaying categorical data with a focus on individual units, making them ideal for representing proportions, survey responses, or resource allocation in a visually intuitive grid format. The module offers customizable rows, color palettes, and options for faceting and flipping the chart, ensuring a professional and publication-ready appearance. 8 | 9 | ## Feature Details 10 | 11 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 12 | 13 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 14 | | -------------------------------- | ------------------------------ | -------------------------------------- | ----------------------------------- | ------------------------------------ | 15 | | **Core Variables** | | | | | 16 | | Counts (Optional) | `counts` | Counts (Optional) | `plot` | `.run`, `.plot` | 17 | | Groups | `groups` | Groups | `plot` | `.run`, `.plot` | 18 | | Facet By (Optional) | `facet` | Facet By (Optional) | `plot` | `.run`, `.plot` | 19 | | **Chart Customization** | | | | | 20 | | Number of Rows | `rows` | Number of Rows | `plot` | `.run`, `.plot` | 21 | | Flip Chart | `flip` | Flip Chart | `plot` | `.run`, `.plot` | 22 | | Color Palette | `color_palette` | Color Palette | `plot` | `.run`, `.plot`, `.generateColorPalette` | 23 | | Show Legend | `show_legend` | Show Legend | `plot` | `.plot` | 24 | | Title | `mytitle` | Title | `plot` | `.plot` | 25 | | Legend Title | `legendtitle` | Legend Title | `plot` | `.plot` | 26 | -------------------------------------------------------------------------------- /vignettes/lassocox_documentation.md: -------------------------------------------------------------------------------- 1 | # Lasso-Cox Regression for Variable Selection in Survival Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Lasso-Cox Regression for Variable Selection in Survival Analysis module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | This module performs Lasso-penalized Cox proportional hazards regression for variable selection in survival analysis. It uses penalized likelihood to identify the most important predictors while preventing overfitting, making it ideal for high-dimensional survival data where the number of potential predictors may approach or exceed the sample size. The module supports automatic variable selection, cross-validation for optimal tuning parameter selection, risk score calculation and stratification, comprehensive model performance evaluation, and survival curve visualization by risk groups. 8 | 9 | ## Feature Details 10 | 11 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 12 | 13 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 14 | | -------------------------------- | ------------------------------ | -------------------------------------- | ----------------------------------- | ------------------------------------ | 15 | | **Core Analysis Setup** | | | | | 16 | | Time Elapsed | `elapsedtime` | Time Elapsed | `modelSummary`, `coefficients`, `performance`, `cv_plot`, `coef_plot`, `survival_plot`, `riskScore` | `.run`, `.cleanData`, `.fitModel` | 17 | | Outcome | `outcome` | Outcome | `modelSummary`, `coefficients`, `performance`, `cv_plot`, `coef_plot`, `survival_plot`, `riskScore` | `.run`, `.cleanData`, `.fitModel` | 18 | | Event Level | `outcomeLevel` | Event Level | `modelSummary`, `coefficients`, `performance`, `cv_plot`, `coef_plot`, `survival_plot`, `riskScore` | `.run`, `.cleanData`, `.fitModel` | 19 | | Explanatory Variables | `explanatory` | Explanatory Variables | `modelSummary`, `coefficients`, `performance`, `cv_plot`, `coef_plot`, `survival_plot`, `riskScore` | `.run`, `.cleanData`, `.fitModel` | 20 | | Lambda Selection Method | `lambda` | Lambda Selection Method | `modelSummary`, `coefficients`, `performance`, `cv_plot`, `coef_plot`, `survival_plot`, `riskScore` | `.run`, `.fitModel` | 21 | | Number of CV Folds | `nfolds` | Number of CV Folds | `modelSummary`, `coefficients`, `performance`, `cv_plot`, `coef_plot`, `survival_plot`, `riskScore` | `.run`, `.fitModel` | 22 | | Standardize Variables | `standardize` | Standardize Variables | `modelSummary`, `coefficients`, `performance`, `cv_plot`, `coef_plot`, `survival_plot`, `riskScore` | `.run`, `.cleanData`, `.fitModel` | 23 | | **Output & Visualization** | | | | | 24 | | Cross-validation Plot | `cv_plot` | Cross-validation Plot | `cv_plot` | `.cvPlot` | 25 | | Coefficient Plot | `coef_plot` | Coefficient Plot | `coef_plot` | `.coefPlot` | 26 | | Risk Group Survival Plot | `survival_plot` | Risk Group Survival Plot | `survival_plot` | `.survivalPlot` | 27 | | Add Risk Score to Data | `riskScore` | Add Risk Score to Data | `riskScore` | `.savePlotData` | 28 | -------------------------------------------------------------------------------- /vignettes/legacy/08-categorical-plots-legacy.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Categorical Plot Functions" 3 | author: "ClinicoPath Development Team" 4 | date: "`r Sys.Date()`" 5 | output: html_document 6 | --- 7 | 8 | ```{r setup, include=FALSE} 9 | knitr::opts_chunk$set(comment = "#>", collapse = TRUE) 10 | library(jjstatsplot) 11 | data(mtcars) 12 | ``` 13 | 14 | This vignette demonstrates the functions designed for categorical data: 15 | `jjbarstats()`, `jjpiestats()` and `jjdotplotstats()`. 16 | 17 | ## Bar charts with `jjbarstats()` 18 | 19 | `jjbarstats()` creates a bar chart and automatically performs a 20 | chi-squared test to compare the distribution of two categorical 21 | variables. The example below compares the number of cylinders (`cyl`) 22 | across transmission types (`am`). 23 | 24 | ```{r} 25 | jjbarstats(data = mtcars, dep = cyl, group = am, grvar = NULL) 26 | ``` 27 | 28 | ## Pie charts with `jjpiestats()` 29 | 30 | `jjpiestats()` is similar to `jjbarstats()` but displays the results as a 31 | pie chart. 32 | 33 | ```{r} 34 | jjpiestats(data = mtcars, dep = cyl, group = am, grvar = NULL) 35 | ``` 36 | 37 | ## Dot charts with `jjdotplotstats()` 38 | 39 | `jjdotplotstats()` shows group means using a dot plot. In this example we 40 | plot horsepower (`hp`) by engine configuration (`vs`). 41 | 42 | ```{r} 43 | jjdotplotstats(data = mtcars, dep = hp, group = vs, grvar = NULL) 44 | ``` 45 | 46 | Each function returns a results object whose `plot` element contains the 47 | `ggplot2` visualisation. 48 | -------------------------------------------------------------------------------- /vignettes/legacy/09-continuous-comparisons-legacy.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Categorical Plot Functions" 3 | output: rmarkdown::html_vignette 4 | vignette: > 5 | %\VignetteIndexEntry{Categorical Plot Functions} 6 | %\VignetteEngine{rmarkdown} 7 | %\VignetteEncoding{UTF-8} 8 | --- 9 | 10 | ```{r setup, include=FALSE} 11 | knitr::opts_chunk$set(comment = "#>", collapse = TRUE) 12 | library(dplyr) 13 | library(jjstatsplot) 14 | library(ggstatsplot) 15 | data(mtcars) 16 | 17 | # Convert relevant variables to factors for categorical analysis 18 | mtcars$cyl <- as.factor(mtcars$cyl) 19 | mtcars$am <- as.factor(mtcars$am) 20 | mtcars$vs <- as.factor(mtcars$vs) 21 | ``` 22 | 23 | This vignette demonstrates the categorical plot functions available in the jjstatsplot package. These functions are designed to work within the jamovi interface, but we can demonstrate their underlying functionality using the ggstatsplot functions they wrap. 24 | 25 | ## Bar charts with `jjbarstats()` 26 | 27 | The `jjbarstats()` function creates bar charts and performs chi-squared tests to compare categorical variables. It wraps `ggstatsplot::ggbarstats()`. 28 | 29 | ```{r, fig.width=7, fig.height=5} 30 | # Underlying function that jjbarstats() wraps 31 | ggstatsplot::ggbarstats( 32 | data = mtcars, 33 | x = cyl, 34 | y = am, 35 | title = "Cylinders by Transmission Type" 36 | ) 37 | ``` 38 | 39 | ## Pie charts with `jjpiestats()` 40 | 41 | The `jjpiestats()` function creates pie charts for categorical data visualization. It wraps `ggstatsplot::ggpiestats()`. 42 | 43 | ```{r, fig.width=7, fig.height=5} 44 | # Underlying function that jjpiestats() wraps 45 | ggstatsplot::ggpiestats( 46 | data = mtcars, 47 | x = cyl, 48 | y = am, 49 | title = "Distribution of Cylinders by Transmission" 50 | ) 51 | ``` 52 | 53 | ## Dot charts with `jjdotplotstats()` 54 | 55 | The `jjdotplotstats()` function shows group comparisons using dot plots. It wraps `ggstatsplot::ggdotplotstats()`. 56 | 57 | ```{r, fig.width=7, fig.height=5} 58 | # Underlying function that jjdotplotstats() wraps 59 | ggstatsplot::ggdotplotstats( 60 | data = mtcars, 61 | x = hp, 62 | y = vs, 63 | title = "Horsepower by Engine Configuration" 64 | ) 65 | ``` 66 | 67 | ## Within-group comparisons with `jjwithinstats()` 68 | 69 | The `jjwithinstats()` function compares repeated measurements within groups. It wraps `ggstatsplot::ggwithinstats()`. 70 | 71 | ```{r, fig.width=8, fig.height=6} 72 | # Create long format data for within-group comparison 73 | library(tidyr) 74 | mtcars_long <- mtcars %>% 75 | select(mpg, hp, wt, qsec) %>% 76 | mutate(id = row_number()) %>% 77 | pivot_longer(cols = c(mpg, hp, wt, qsec), 78 | names_to = "measure", 79 | values_to = "value") %>% 80 | # Standardize values for comparison 81 | group_by(measure) %>% 82 | mutate(value = scale(value)[,1]) %>% 83 | ungroup() 84 | 85 | # Underlying function that jjwithinstats() wraps 86 | ggstatsplot::ggwithinstats( 87 | data = mtcars_long, 88 | x = measure, 89 | y = value, 90 | paired = TRUE, 91 | id = id, 92 | title = "Comparison of Standardized Car Measurements" 93 | ) 94 | ``` 95 | 96 | ## Usage in jamovi 97 | 98 | These functions are designed to be used through the jamovi graphical interface, where they provide: 99 | 100 | - Interactive parameter selection 101 | - Automatic data type handling 102 | - Integrated results display 103 | - Export capabilities 104 | 105 | To use these functions in jamovi: 106 | 107 | 1. Install the jjstatsplot module 108 | 2. Load your data 109 | 3. Navigate to the JJStatsPlot menu 110 | 4. Select the appropriate plot type 111 | 5. Configure variables and options through the interface 112 | 113 | The jamovi interface handles parameter validation, data preprocessing, and result presentation automatically. 114 | -------------------------------------------------------------------------------- /vignettes/legacy/10-correlations-scatterplots-legacy.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Correlations and Scatter Plots" 3 | output: rmarkdown::html_vignette 4 | vignette: > 5 | %\VignetteIndexEntry{Correlations and Scatter Plots} 6 | %\VignetteEngine{rmarkdown} 7 | %\VignetteEncoding{UTF-8} 8 | --- 9 | 10 | ```{r setup, include=FALSE} 11 | knitr::opts_chunk$set(comment = "#>", collapse = TRUE) 12 | library(jjstatsplot) 13 | data(mtcars) 14 | ``` 15 | 16 | This vignette covers `jjcorrmat()` for creating correlation matrices and 17 | `jjscatterstats()` for scatter plots. 18 | 19 | ## Correlation matrices with `jjcorrmat()` 20 | 21 | `jjcorrmat()` visualises pairwise correlations between numeric variables 22 | and reports the associated tests. Here we look at the relationships 23 | between `mpg`, `hp` and `wt` in the `mtcars` data. 24 | 25 | ```{r} 26 | jjcorrmat(data = mtcars, dep = c(mpg, hp, wt), grvar = NULL) 27 | ``` 28 | 29 | ## Scatter plots with `jjscatterstats()` 30 | 31 | `jjscatterstats()` produces a scatter plot with a regression line and 32 | textual output describing the correlation and regression statistics. 33 | 34 | ```{r} 35 | jjscatterstats(data = mtcars, dep = mpg, group = hp, grvar = NULL) 36 | ``` 37 | 38 | 39 | -------------------------------------------------------------------------------- /vignettes/parallelplot_documentation.md: -------------------------------------------------------------------------------- 1 | # Parallel Coordinates Plot Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Parallel Coordinates Plot Analysis module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | This module creates parallel coordinates plots for multivariate data visualization. These plots are excellent for exploring relationships between multiple continuous variables and identifying patterns, clusters, and outliers in high-dimensional data. The implementation provides comprehensive functionality, including multiple scaling methods, grouping support, interactive Plotly integration, summary statistics, and missing data handling options. 8 | 9 | ## Feature Details 10 | 11 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 12 | 13 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 14 | | -------------------------------- | ------------------------------ | -------------------------------------- | ----------------------------------- | ------------------------------------ | 15 | | **Core Variables** | | | | | 16 | | Variables | `vars` | Variables | `plot`, `plotly`, `summary` | `.run`, `.plot` | 17 | | Grouping Variable | `group` | Grouping Variable | `plot`, `plotly` | `.run`, `.plot` | 18 | | **Plot Customization** | | | | | 19 | | Variable Scaling | `scaling` | Variable Scaling | `plot` | `.run`, `.plot`, `.scaleVariables` | 20 | | Line Transparency | `alpha` | Line Transparency | `plot` | `.run`, `.plot` | 21 | | Show Missing Values | `showMissing` | Show Missing Values | `plot` | `.run`, `.plot` | 22 | | Interactive Plot | `interactive` | Interactive Plot | `plotly` | `.run`, `.createInteractivePlot` | 23 | | Color Palette | `colorPalette` | Color Palette | `plot` | `.run`, `.plot`, `.getColorPalette` | 24 | | **Output Tables** | | | | | 25 | | Variable Summary | `summary` | Variable Summary | `summary` | `.run` | 26 | -------------------------------------------------------------------------------- /vignettes/statsplot2_documentation.md: -------------------------------------------------------------------------------- 1 | # Automatic Plot Selection Analysis Documentation 2 | 3 | This document provides a comprehensive overview of the Automatic Plot Selection module, detailing its features, user interface elements, and the underlying R functions. 4 | 5 | ## Feature Summary 6 | 7 | This module intelligently selects and generates the most appropriate statistical visualization based on the data types of the selected variables. It supports both independent and repeated measurements designs, offering a wide array of plot types including violin plots, scatter plots, bar charts, dot plots, and alluvial diagrams. It leverages `ggstatsplot` for statistical visualizations and `ggalluvial`/`easyalluvial` for flow diagrams, ensuring statistically sound and visually appealing outputs. 8 | 9 | ## Feature Details 10 | 11 | The following table provides a detailed mapping of the module's features, from the user interface to the underlying R functions. 12 | 13 | | Feature | YAML Argument (`.a.yaml`) | UI Label | Results Section (`.r.yaml`) | R Function (`.b.R`) | 14 | | -------------------------------- | ------------------------------ | -------------------------------------- | ----------------------------------- | ------------------------------------ | 15 | | **Core Plotting Variables** | | | | | 16 | | Dependent Variable (y-axis) | `dep` | Dependent Variable (y-axis) | `plot`, `text4` | `.run`, `.plot` | 17 | | Grouping Variable (x-axis) | `group` | Grouping Variable (x-axis) | `plot`, `text4` | `.run`, `.plot` | 18 | | Split By (Optional) | `grvar` | Split By (Optional) | `plot` | `.run`, `.plot` | 19 | | Study Design | `direction` | Study Design | `plot`, `text4` | `.run`, `.plot` | 20 | | Statistical Approach | `distribution` | Statistical Approach | `plot`, `text4` | `.run`, `.plot` | 21 | | Alluvial Plot Style | `alluvsty` | Alluvial Plot Style | `plot` | `.run`, `.plot` | 22 | | Exclude Missing Values | `excl` | Exclude Missing Values | `plot` | `.run`, `.plot` | 23 | | Use Original Themes | `originaltheme` | Use Original Themes | `plot` | `.plot` | 24 | -------------------------------------------------------------------------------- /vignettes/use-jjstatsplot-in-R.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Use jjstatsplot in R" 3 | author: "ClinicoPath Development Team" 4 | date: "`r Sys.Date()`" 5 | output: html_document 6 | --- 7 | 8 | ```{r, include = FALSE} 9 | knitr::opts_chunk$set( 10 | echo = TRUE, 11 | eval = FALSE, 12 | collapse = TRUE, 13 | comment = "#>" 14 | ) 15 | ``` 16 | 17 | ```{r setup} 18 | library(jjstatsplot) 19 | ``` 20 | 21 | 22 | All functions 23 | 24 | jjbarstats() 25 | 26 | 27 | Bar Charts 28 | 29 | jjbarstatsClass 30 | 31 | 32 | Bar Charts 33 | 34 | jjbetweenstats() 35 | 36 | 37 | Box-Violin Plots to Compare Between Groups 38 | 39 | jjbetweenstatsClass 40 | 41 | 42 | Violin Plots to Compare Between Groups 43 | 44 | jjcorrmat() 45 | 46 | 47 | Correlation Matrix 48 | 49 | jjcorrmatClass 50 | 51 | 52 | Correlation Matrix 53 | 54 | jjdotplotstats() 55 | 56 | 57 | Dot Chart 58 | 59 | jjdotplotstatsClass 60 | 61 | 62 | Dot Chart 63 | 64 | jjhistostats() 65 | 66 | 67 | Histogram 68 | 69 | jjhistostatsClass 70 | 71 | 72 | Histogram 73 | 74 | jjpiestats() 75 | 76 | 77 | Pie Charts 78 | 79 | jjpiestatsClass 80 | 81 | 82 | Pie Charts 83 | 84 | jjscatterstats() 85 | 86 | 87 | Scatter Plot 88 | 89 | jjscatterstatsClass 90 | 91 | 92 | Scatter Plot 93 | 94 | --------------------------------------------------------------------------------