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"page": "plot.hv_consort", "title": "Render a CONSORT flow diagram", "topics": [ "plot.hv_consort" ] }, { "page": "plot.hv_correlation_matrix", "title": "Plot an hv_correlation_matrix object", "topics": [ "plot.hv_correlation_matrix" ] }, { "page": "plot.hv_eda", "title": "Plot an hv_eda object", "topics": [ "plot.hv_eda" ] }, { "page": "plot.hv_eda_pages", "title": "Plot an hv_eda_pages object", "topics": [ "plot.hv_eda_pages" ] }, { "page": "plot.hv_followup", "title": "Plot an hv_followup object", "topics": [ "plot.hv_followup" ] }, { "page": "plot.hv_followup_panels", "title": "Plot an hv_followup_panels object", "topics": [ "plot.hv_followup_panels" ] }, { "page": "plot.hv_hazard", "title": "Plot an hv_hazard object", "concept": [ "Hazard plot" ], "topics": [ "plot.hv_hazard" ] }, { "page": "plot.hv_longitudinal", "title": "Plot an hv_longitudinal object", "topics": [ "plot.hv_longitudinal" ] }, { "page": "plot.hv_mirror_hist", "title": "Plot an hv_mirror_hist object", "concept": [ "Propensity Score & Matching" ], "topics": [ "plot.hv_mirror_hist" ] }, { "page": "plot.hv_nnt", "title": "Plot an hv_nnt object", "topics": [ "plot.hv_nnt" ] }, { "page": "plot.hv_nonparametric", "title": "Plot an hv_nonparametric object", "concept": [ "Nonparametric curves" ], "topics": [ "plot.hv_nonparametric" ] }, { "page": "plot.hv_ordinal", "title": "Plot an hv_ordinal object", "topics": [ "plot.hv_ordinal" ] }, { "page": "plot.hv_rmst_contrast", "title": "Plot an hv_rmst_contrast object", "concept": [ "Propensity Score & Matching" ], "topics": [ "plot.hv_rmst_contrast" ] }, { "page": "plot.hv_rmst_curves", "title": "Plot an hv_rmst_curves object", "concept": [ "Propensity Score & Matching" ], "topics": [ "plot.hv_rmst_curves" ] }, { "page": "plot.hv_sankey", "title": "Plot an hv_sankey object", "topics": [ "plot.hv_sankey" ] }, { "page": "plot.hv_spaghetti", "title": "Plot an hv_spaghetti object", "concept": [ "Spaghetti plot" ], "topics": [ "plot.hv_spaghetti" ] }, { "page": "plot.hv_stacked", "title": "Plot an hv_stacked object", "topics": [ "plot.hv_stacked" ] }, { "page": "plot.hv_survival", "title": "Plot an hv_survival object", "concept": [ "Kaplan-Meier survival" ], "topics": [ "plot.hv_survival" ] }, { "page": "plot.hv_survival_difference", "title": "Plot an hv_survival_difference object", "topics": [ "plot.hv_survival_difference" ] }, { "page": "plot.hv_trends", "title": "Plot an hv_trends object", "concept": [ "Temporal trends" ], "topics": [ "plot.hv_trends" ] }, { "page": "plot.hv_upset", "title": "Plot an hv_upset object", "topics": [ "plot.hv_upset" ] }, { "page": "plot.hv_venn", "title": "Plot an hv_venn object", "topics": [ "plot.hv_venn" ] }, { "page": "print.hv_alluvial", "title": "Print an hv_alluvial object", "topics": [ "print.hv_alluvial" ] }, { "page": "print.hv_balance", "title": "Print an hv_balance object", "topics": [ "print.hv_balance" ] }, { "page": "print.hv_consort", "title": "Print an hv_consort object", "topics": [ "print.hv_consort" ] }, { "page": "print.hv_consort_tracker", "title": "Print an hv_consort_tracker object", "topics": [ "print.hv_consort_tracker" ] }, { "page": "print.hv_eda", "title": "Print an hv_eda object", "topics": [ "print.hv_eda" ] }, { "page": "print.hv_eda_pages", "title": "Print an hv_eda_pages object", "topics": [ "print.hv_eda_pages" ] }, { "page": "print.hv_followup", "title": "Print an hv_followup object", "topics": [ "print.hv_followup" ] }, { "page": "print.hv_followup_panels", "title": "Print an hv_followup_panels object", "topics": [ "print.hv_followup_panels" ] }, { "page": "print.hv_hazard", "title": "Print an hv_hazard object", "topics": [ "print.hv_hazard" ] }, { "page": "print.hv_longitudinal", "title": "Print an hv_longitudinal object", "topics": [ "print.hv_longitudinal" ] }, { "page": "print.hv_mirror_hist", "title": "Print an hv_mirror_hist object", "topics": [ "print.hv_mirror_hist" ] }, { "page": "print.hv_nnt", "title": "Print an hv_nnt object", "topics": [ "print.hv_nnt" ] }, { "page": "print.hv_nonparametric", "title": "Print an hv_nonparametric object", "topics": [ "print.hv_nonparametric" ] }, { "page": "print.hv_ordinal", "title": "Print an hv_ordinal object", "topics": [ "print.hv_ordinal" ] }, { "page": "print.hv_rmst_contrast", "title": "Print an hv_rmst_contrast object", "topics": [ "print.hv_rmst_contrast" ] }, { "page": "print.hv_rmst_curves", "title": "Print an hv_rmst_curves object", "topics": [ "print.hv_rmst_curves" ] }, { "page": "print.hv_sankey", "title": "Print an hv_sankey object", "topics": [ "print.hv_sankey" ] }, { "page": "print.hv_spaghetti", "title": "Print an hv_spaghetti object", "topics": [ "print.hv_spaghetti" ] }, { "page": "print.hv_stacked", "title": "Print an hv_stacked object", "topics": [ "print.hv_stacked" ] }, { "page": "print.hv_survival", "title": "Print an hv_survival object", "topics": [ "print.hv_survival" ] }, { "page": "print.hv_survival_difference", "title": "Print an hv_survival_difference object", "topics": [ "print.hv_survival_difference" ] }, { "page": "print.hv_trends", "title": "Print an hv_trends object", "topics": [ "print.hv_trends" ] }, { "page": "print.hv_upset", "title": "Print an hv_upset object", "topics": [ "print.hv_upset" ] }, { "page": "print.hv_venn", "title": "Print an hv_venn object", "topics": [ "print.hv_venn" ] }, { "page": "sample_alluvial_data", "title": "Sample Sankey / Alluvial Data", "topics": [ "sample_alluvial_data" ] }, { "page": "sample_cluster_sankey_data", "title": "Sample Cluster Stability Sankey Data", "topics": [ "sample_cluster_sankey_data" ] }, { "page": "sample_consort_data", "title": "Generate a sample CONSORT tracker for demos and testing", "topics": [ "sample_consort_data" ] }, { "page": "sample_correlation_data", "title": "Sample data for hv_correlation_matrix()", "topics": [ "sample_correlation_data" ] }, { "page": "sample_covariate_balance_data", "title": "Generate Sample Covariate Balance Data", "concept": [ "Propensity Score & Matching" ], "topics": [ "sample_covariate_balance_data" ] }, { "page": "sample_eda_data", "title": "Sample EDA Data", "topics": [ "sample_eda_data" ] }, { "page": "sample_goodness_followup_data", "title": "Generate Sample Goodness-of-Follow-Up Data", "topics": [ "sample_goodness_followup_data" ] }, { "page": "sample_hazard_cohort", "title": "Sample Subject-Level Cohort Behind the Hazard Examples", "topics": [ "sample_hazard_cohort" ] }, { "page": "sample_hazard_data", "title": "Sample Parametric Hazard Model Predictions", "topics": [ "sample_hazard_data" ] }, { "page": "sample_hazard_empirical", "title": "Sample Kaplan-Meier Empirical Points for Hazard Plot Overlay", "topics": [ "sample_hazard_empirical" ] }, { "page": "sample_life_table", "title": "Sample Population Life Table Data", "topics": [ "sample_life_table" ] }, { "page": "sample_longitudinal_counts_data", "title": "Sample Longitudinal Counts Data", "topics": [ "sample_longitudinal_counts_data" ] }, { "page": "sample_mirror_histogram_data", "title": "Generate Sample Data for Mirrored Histogram", "topics": [ "sample_mirror_histogram_data" ] }, { "page": "sample_nnt_data", "title": "Sample Number Needed to Treat Data", "topics": [ "sample_nnt_data" ] }, { "page": "sample_nonparametric_curve_data", "title": "Sample Nonparametric Curve Data", "topics": [ "sample_nonparametric_curve_data" ] }, { "page": "sample_nonparametric_curve_points", "title": "Sample Nonparametric Curve Data Points", "topics": [ "sample_nonparametric_curve_points" ] }, { "page": "sample_nonparametric_ordinal_data", "title": "Sample Nonparametric Ordinal Curve Data", "topics": [ "sample_nonparametric_ordinal_data" ] }, { "page": "sample_nonparametric_ordinal_points", "title": "Sample Nonparametric Ordinal Data Points", "topics": [ "sample_nonparametric_ordinal_points" ] }, { "page": "sample_spaghetti_data", "title": "Sample Spaghetti / Profile Plot Data", "topics": [ "sample_spaghetti_data" ] }, { "page": "sample_stacked_histogram_data", "title": "Generate Sample Data for Stacked Histogram", "topics": [ "sample_stacked_histogram_data" ] }, { "page": "sample_survival_data", "title": "Generate Sample Survival Data", "concept": [ "Kaplan-Meier survival" ], "topics": [ "sample_survival_data" ] }, { "page": "sample_survival_difference_data", "title": "Sample Survival Difference (Life-Gained) Data", "topics": [ "sample_survival_difference_data" ] }, { "page": "sample_trends_data", "title": "Sample Temporal Trend Data", "topics": [ "sample_trends_data" ] }, { "page": "sample_upset_data", "title": "Sample Procedure Co-occurrence Data", "topics": [ "sample_upset_data" ] }, { "page": "save_manuscript", "title": "Save a ggplot at HVTI manuscript defaults", "topics": [ "save_manuscript" ] }, { "page": "save_ppt", "title": "Save ggplot Objects to an Editable PowerPoint Presentation", "topics": [ "save_ppt" ] }, { "page": "scale_fill_hv", "title": "Color and fill scales that apply the role rule to each panel", "topics": [ "scale_color_hv", "scale_colour_hv", "scale_fill_hv" ] }, { "page": "summary.hv_data", "title": "Summarize an hv_data object", "topics": [ "summary.hv_data" ] } ], "_readme": "https://github.com/ehrlinger/hvtiPlotR/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "cli", "consort", "cpp11", "digest", "dplyr", "farver", "fastmap", "fontBitstreamVera", "fontLiberation", "fontquiver", "gdtools", "generics", "ggalluvial", "ggplot2", "ggsankey", "ggupset", "ggvenn", "glue", "gtable", "htmltools", "isoband", "jsonlite", "labeling", "lattice", "lazyeval", "lifecycle", "magrittr", "Matrix", "officer", "openssl", "patchwork", "pillar", "pkgconfig", "purrr", "R6", "ragg", "RColorBrewer", "Rcpp", "rlang", "rvg", "S7", "scales", "stringi", "stringr", "survival", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "utf8", "uuid", "vctrs", "viridisLite", "withr", "xml2", "zip" ], "_vignettes": [ { "source": "contributing.qmd", "filename": "contributing.html", "title": "Contributing to hvtiPlotR", "engine": "quarto::html", "headings": [ "Development environment setup", "Prerequisites", "Installing development dependencies", "The development workflow loop", "Track A: Porting a SAS template", "Step 1: Understand the SAS template output", "Step 2: Create the R source file", "The constructor", "The print and plot methods", "Step 3: Add a sample-data generator", "Step 4: Write roxygen documentation", "Step 5: Register in _pkgdown.yml", "Step 6: Add a worked example to the plot-functions vignette", "Step 7: Add a row to the SAS migration guide", "Step 8: Write tests", "Step 9: Update NEWS.md", "Step 10: Final checklist before opening a PR", "Track B: Package infrastructure", "Package structure overview", "Adding a dependency", "Code style and conventions", "File and function naming", "The bare-ggplot pattern", "Tidy evaluation", "Testing", "Test file layout", "Snapshot tests", "Running checks", "What R CMD CHECK validates", "Vignette conventions", "Releasing a new version", "Session info" ], "created": "2026-03-25 18:57:25", "modified": "2026-09-28 17:13:43", "commits": 9 }, { "source": "plot-decorators.qmd", "filename": "plot-decorators.html", "title": "Decorating and Saving hvtiPlotR Plots", "engine": "quarto::html", "headings": [ "The Composition Pattern", "Themes", "Manuscript", "Poster", "Light PowerPoint", "Dark PowerPoint", "One decorator for a whole deck", "Naming the series without a legend", "Designing the slide around the figure", "Color Scales", "Manual colors", "ColorBrewer palettes", "Suppressing legends", "Labels and Annotations", "labs()", "annotate()", "coord_cartesian()", "Saving Figures", "Manuscript PDF", "Poster PDF", "PowerPoint slides", "Single slide", "Multiple slides from a list", "Fixed panel placement across slides", "Multi-panel PDF (EDA batch output)", "Legend Positioning", "Inside the panel", "Outside the panel (explicit sides)", "Suppress all legends", "Legend text and key size", "Theme Overrides", "Axis text size", "Removing minor grid lines", "Rotating x-axis labels", "Adding a plot title and subtitle", "Expanding plot margins", "Multi-panel Figures with patchwork", "Side-by-side plots", "Controlling relative widths and heights", "Stacking a plot above a risk table", "Shared axis labels and panel tags", "Saving a patchwork composite" ], "created": "2026-03-19 15:27:39", "modified": "2026-10-20 15:24:59", "commits": 22 }, { "source": "plot-functions.qmd", "filename": "plot-functions.html", "title": "hvtiPlotR Plot Functions", "engine": "quarto::html", "headings": [ "Template Reference Map", "Mirrored Propensity Score Histogram", "Binary-match mode (SAVR vs. TF-TAVR)", "Bare plot", "Adding scales, labels, and theme", "Weighted IPTW mode (Limited vs. Extended)", "Bare plot", "Adding scales, labels, and theme", "Stacked Histogram", "Count histogram", "Proportion (fill) histogram", "Saving", "Goodness-of-Follow-Up Plot", 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LOESS", "Variable selection and labels (varnames template pattern)", "Several variables to a page", "Saving EDA plots", "Alluvial (Sankey) Plot", "Fill flows by pre-operative grade", "Two-axis before / after comparison", "Cluster Stability Sankey Plot", "Default plot (K = 2 to 9)", "Custom color palette", "Subset of K values", "CONSORT Patient Flow Diagram", "Building a tracker from your own data", "The diagram", "Auditing the cohort", "Hazard Plot", "Survival curve with KM overlay", "Hazard rate curve", "Cumulative hazard", "Stratified by group", "Life-table overlay", "The hv_hazard() object interface", "Survival Difference (Life-Gained) Plot", "Survival difference curve", "Multiple comparisons", "The hv_survival_difference() object interface", "Number Needed to Treat (NNT) Plot", "NNT curve", "Absolute risk reduction", "The hv_nnt() object interface", "Temporal Trend Plot", "Single variable: cases/year", "Single variable: age", "Multiple groups with scale_color_brewer", "Median summary + manual colors (NYHA style)", "With confidence ribbon", "Binary % outcomes (tp.lp.trends.sas)", "Age as x-axis (tp.lp.trends.age.sas)", "Polytomous groups: repair types (tp.lp.trends.polytomous.sas)", "LV mass index (tp.dp.trends.R, plot2)", "Case volume / total surgeries per year (tp.dp.trends.R, plot4)", "Annotated trend: hospital LOS (tp.dp.trends.R, plot5)", "Spaghetti / Profile Plot", "Unstratified: AV mean gradient, full range (plot_1)", "Unstratified: zoomed y-axis (plot_3)", "Stratified by sex: AV mean gradient (plot_2 / plot_4)", "AV area y-scale (plot_5 / plot_6)", "DVI y-scale (plot_7 / plot_8)", "Ordinal y-axis: MV regurgitation grade (plot_9)", "With LOESS smooth overlay", "Nonparametric Temporal Trend Curve", "Single average curve with 68 % CI ribbon", "Two-group comparison (analogous to tp.np.avpkgrad_ozak_ind_mtwt.sas)", "Nonparametric Ordinal Outcome Curve", "Grade probability curves with data summary points", "Combined mild + moderate (p34 = p3 + p4 pattern)", "Longitudinal Participation Counts", "Bar chart", "Numeric table panel", "Two-panel layout with patchwork", "Saving the combined figure", "UpSet Plot", "Default plot", "Custom intersection bar color", "Color bars by era", "Venn diagram (2-3 sets)", "Draft Footnotes", "Draft annotation pattern", "Custom analyst tag", "Saving without the footnote" ], "created": "2026-03-19 15:27:39", "modified": "2026-10-25 14:57:01", "commits": 35 }, { "source": "hvtiPlotR.qmd", "filename": "hvtiPlotR.html", "title": "hvtiPlotR: Generating plot.sas Style in R", "engine": "quarto::html", "headings": [ "Abstract", "About this document", "Introduction", "The plot.sas macro", "SAS → R Quick Reference", "Structure and output", "Axis labels and scales", "Tuple statements: points and error bars", "Tuple statements: lines and ribbons", "Symbols and colors reference", "Device and theme mapping", "Generating ggplot2 graphics", "Importing the data", "Option 1: SAS xport file (recommended when you have SAS access)", "Option 2: CSV export (when SAS is not available)", "Using the bundled example data", "Initialize the figure", "Labels", "Scales", "Points", "Error Bars", "Lines", "Line types", "Shapes", "Colors", "Global Figure Commands", "PowerPoint Figures", "Themes and Decoration", "Saving publication graphics", "Manuscript graphics", "PowerPoint graphics", "Graphics rules to live by", "Manuscript figures", "PowerPoint figures", "Color", "What not to include", "Conclusions", "References", "Affiliation:" ], "created": "2025-10-21 16:03:15", "modified": "2026-10-13 15:19:54", "commits": 30 }, { "source": "sas-migration-guide.qmd", "filename": "sas-migration-guide.html", "title": "SAS Template Migration Guide", "engine": "quarto::html", "headings": [ "Overview", "Key concepts for SAS users", "Template lookup table", "Nonparametric temporal trends (tp.np.*)", "SAS column name mapping", "Average curve: binary outcome", "Continuous outcome", "Multi-group comparison", "Phase decomposition", "Covariate on the x-axis", "Ordinal outcomes", "Ordinal multi-scenario comparison", "Ordinal phase independence", "Ordinal phases", "Survival analysis (tp.ac.dead.*, tp.cp.dead.*)", "SAS → R argument mapping", "Goodness of follow-up (tp.dp.gfup.R)", "Covariate balance (tp.lp.propen.cov_balance.R)", "Alluvial flow (tp.dp.female_bicus_preAR_sankey.R)", "Cluster stability Sankey (PAM analysis)", "SAS/R workflow → R equivalent", "UpSet plot (tp.complexUpset.R)", "Spaghetti / individual trajectories (tp.dp.spaghetti.echo.R)", "Unstratified: AV mean gradient full range (plot_1)", "Unstratified: zoomed y-axis (plot_3)", "Stratified by sex (plot_2 / plot_4)", "AV area y-scale (plot_5 / plot_6)", "DVI y-scale (plot_7 / plot_8)", "Ordinal y-axis: MV regurgitation grade (plot_9)", "Correlation matrix (descriptive/dc.tables.ods.sas)", "Trends over time (tp.*.trends.*)", "tp.rp.trends.sas: cases/year and age (1968–2000 by 4)", "tp.lp.trends.sas: binary % outcomes (1970–2000 by 10, y 0–100 by 10)", 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