epiworld-model-diagram: Model Diagram

In epiworldR: Fast Agent-Based Epi Models

Model Diagram

Description

Functions described here are helper functions for drawing diagrams from model data. These generate mermaid diagrams from transition probability matrices which can then be rendered using other packages.

Usage

draw_mermaid_from_data(
  states,
  transition_probs,
  output_file = "",
  allow_self_transitions = FALSE
)

draw_mermaid_from_matrix(
  transition_matrix,
  output_file = "",
  allow_self_transitions = FALSE
)

draw_mermaid_from_file(
  transitions_file,
  output_file = "",
  allow_self_transitions = FALSE
)

draw_mermaid_from_files(
  transitions_files,
  output_file = "",
  allow_self_transitions = FALSE
)

Arguments

states	String vector. List of model states.
transition_probs	Numeric vector. Transition probability matrix
output_file	String. Optional path to a file. If provided, the diagram will be written to the file.
allow_self_transitions	Logical. Whether to allow self-transitions, defaults to FALSE.
transition_matrix	Square matrix. Contains states and transition probabilities.
transitions_file	String. Path to file containing the transition probabilities matrix.
transitions_files	String vector. List of files containing transition probabilities matrices from multiple model runs.

Value

• The draw_mermaid_from_data function returns the mermaid diagram as a string.

• The draw_mermaid_from_matrix function returns the mermaid diagram as a string.

• The draw_mermaid_from_file function returns the mermaid diagram as a string.

• The draw_mermaid_from_files function returns the mermaid diagram as a string.

Examples

# Create and run a model
model <- ModelSIRCONN(
  name = "A Virus",
  n = 10000,
  prevalence = .01,
  contact_rate = 4.0,
  transmission_rate = .5,
  recovery_rate = 1.0 / 7.0
)

verbose_off(model)
run(model, ndays = 50, seed = 1912)

# Draw mermaid diagrams from model data
draw_mermaid_from_data(
  states = get_states(model),
  transition_probs = c(get_transition_probability(model))
)

epiworldR documentation built on June 8, 2025, 1:48 p.m.