epiworldR (version 0.12.0.0)

add_entities_from_dataframe: Add entities to a model according to a data.frame

Description

Helper function that facilities creating entities and adding them to models. It is a wrapper of add_entity().

Usage

add_entities_from_dataframe(model, entities, col_name, col_number, ...)

Value

Inivisible the model with the added entities.

Arguments

model

An epiworld_model object.

entities

A data.frame with the entities to add. It must contain two columns: entity names (character) and size (proportion or integer).

col_name

The name of the column in entities that contains the entity names.

col_number

The name of the column in entities that contains the entity sizes (either as proportions or integers).

...

Further arguments passed to add_entity()

Examples

# Start off creating three entities.
# Individuals will be distributed randomly between the three.
entities <- data.frame(
  name = c("Pop 1", "Pop 2", "Pop 3"),
  size = rep(3e3, 3)
)

# Row-stochastic matrix (rowsums 1)
cmatrix <- c(
  c(0.9, 0.05, 0.05),
  c(0.1, 0.8, 0.1),
  c(0.1, 0.2, 0.7)
) |> matrix(byrow = TRUE, nrow = 3)

flu_model <- ModelSIRMixing(
  name              = "Flu",
  n                 = 9e3,
  prevalence        = 1 / 9e3,
  contact_rate      = 20,
  transmission_rate = 0.1,
  recovery_rate     = 1 / 7,
  contact_matrix    = cmatrix
) |>
  add_entities_from_dataframe(
    entities = entities,
    col_name = "name",
    col_number = "size",
    # This is passed to `add_entity()`
    as_proportion = FALSE
  )