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Model Diagram

Source: R/ModelDiagram.R
epiworld-model-diagram.Rd

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

# S3 method for class 'epiworld_diagram'
print(x, ...)

# S3 method for class 'epiworld_diagram'
plot(x, ...)

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
)

draw_mermaid(model, output_file = "", allow_self_transitions = FALSE)

Arguments

x

An epiworld_diagram object.

...

Additional arguments passed to DiagrammeR::mermaid().

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.

model

An object of class epiworld_model.

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.

  • The draw_mermaid returns the mermaid diagram as a string.

Details

draw_mermaid generates a mermaid diagram of the model. The diagram is saved in the specified output file (or printed to the standard output if the filename is empty). See draw_mermaid_from_data().

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
diagram <- draw_mermaid_from_data(
  states = get_states(model),
  transition_probs = c(get_transition_probability(model))
)

if (FALSE) { # \dontrun{
# If DiagrammeR is installed, we can plot the diagram
plot(diagram)
} # }

# Draw a mermaid diagram of the transitions
draw_mermaid(model)
#> flowchart TB
#> 	s0[Infected]
#> 	s1[Recovered]
#> 	s2[Susceptible]
#> 	s0 -->|0.143805| s1
#> 	s2 -->|0.175738| s0
#>