Alluvial & Sankey Diagrams

Usage

alluvial3(
  data,
  vars,
  condensationvar,
  excl = FALSE,
  marg = FALSE,
  fill = "first_variable",
  bin = "default",
  orient = "vert",
  usetitle = FALSE,
  mytitle = "Alluvial Plot",
  maxvars = 8,
  custombinlabels = "",
  time,
  id,
  weight,
  sankeyStyle = FALSE,
  curveType = "cubic",
  engine = "easyalluvial",
  labelNodes = TRUE,
  showCounts = FALSE,
  verbose = TRUE,
  diagram_type = "alluvial",
  value_var,
  source_var,
  target_var,
  node_vars,
  grouping_var,
  time_var,
  node_width = 0.5,
  node_spacing = 0.1,
  edge_alpha = 0.6,
  color_palette = "default",
  show_labels = TRUE,
  label_size = 10,
  iterations = 32,
  show_values = TRUE,
  value_format = "raw",
  sort_nodes = "original",
  flow_direction = "left_right",
  plot_title = "",
  plot_subtitle = "",
  theme_style = "default",
  show_statistics = FALSE,
  show_interpretation = TRUE,
  output_format = "plot_only",
  clinical_mode = FALSE,
  clinical_preset = "none",
  enhanced_gradients = FALSE,
  flow_optimization = FALSE,
  advanced_diagnostics = FALSE,
  export_compatibility = "standard"
)

Arguments

data: The data as a data frame.
vars: a string naming the variables from data that contains the values used for the Alluvial Diagram.
condensationvar: The primary variable to be used for condensation.
excl: Exclude missing values from the analysis.
marg: Include marginal plots.
fill: A list for the argument fill for selecting the variable to be represented by color. Default is 'first_variable'.
bin: labels for the bins from low to high
orient: Orientation of the plot. Default is 'vertical'.
usetitle: Use a custom title for the plot.
mytitle: Title for the plot.
maxvars: Maximum number of variables to include in the alluvial plot.
custombinlabels: Custom labels for bins, separated by commas (e.g., "Low,Medium,High"). Leave empty to use bin option defaults.
time: Optional time or sequence variable for time-based flows.
id: Optional ID variable for tracking individual entities.
weight: Optional weight variable for flow thickness.
sankeyStyle: Apply Sankey diagram styling (narrow nodes, sigmoid curves).
curveType: Curve style for flows. Use sigmoid for Sankey-style appearance.
engine: Choose plotting engine: easyalluvial for automatic plots, ggalluvial for manual control.
labelNodes: Show basic node labels. This is the primary label control that works with all plot engines.
showCounts: Display count values on nodes.
verbose: Show detailed information about the plot generation process.
diagram_type: Type of flow diagram to generate.
value_var: Variable containing flow values/weights for source-target format.
source_var: Variable defining source nodes for source-target format.
target_var: Variable defining target nodes for source-target format.
node_vars: Variables for multi-level node definitions in source-target format.
grouping_var: Variable for grouping flows.
time_var: Variable for temporal flow analysis in source-target format.
node_width: Width of nodes in the diagram.
node_spacing: Spacing between nodes.
edge_alpha: Transparency level for edges.
color_palette: Color palette for the diagram.
show_labels: Enable enhanced label styling with custom fonts and positioning. Complements basic labeling.
label_size: Size of node labels.
iterations: Number of iterations for layout optimization.
show_values: Display flow values on diagram.
value_format: Format for displaying flow values.
sort_nodes: Method for sorting nodes.
flow_direction: Direction of flow in the diagram.
plot_title: Advanced plot title (overrides basic title when set).
plot_subtitle: Subtitle for the plot.
theme_style: Theme style for the plot.
show_statistics: Display statistical summary of flows.
show_interpretation: Display interpretation of the diagram.
output_format: Format for output display.
clinical_mode: Enable clinical-specific features and interpretations for medical data analysis.
clinical_preset: Apply predefined settings optimized for common clinical scenarios.
enhanced_gradients: Apply sophisticated color gradients to flow edges for better visual appeal.
flow_optimization: Automatically optimize flow paths to reduce crossings and improve readability.
advanced_diagnostics: Display detailed flow analysis, transition patterns, and data quality metrics.
export_compatibility: Choose output format compatibility for integration with other tools.

Value

A results object containing:

`results$todo`					a html
`results$naturalSummary`					a html
`results$reportSentence`					a html
`results$caveats`					a html
`results$plot`					an image
`results$plot2`					an image
`results$datatab`					a table
`results$stats`					a table
`results$interpretation`					a html
`results$clinical_summary`					a html
`results$diagnostics_report`					a html
`results$flow_metrics`					a table
`results$transition_analysis`					a table

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$datatab$asDF

as.data.frame(results$datatab)