epiworldR (version 0.12.0.0)

epiworld-summaries: Summary counts and probabilities

Description

Functions to extract summary statistics from models, including transition probabilities, active cases, and outbreak sizes.

Usage

get_transition_probability(x)
get_active_cases(x)
get_outbreak_size(x)

Value

• The get_transition_probability function returns an object of class matrix.

• The function get_active_cases returns a data.frame with four columns: date, virus_id, virus, and active_cases indicating the number of active cases (individuals with a virus) at each point in time.

• The function get_outbreak_size returns a data.frame with four columns: date, virus_id, virus, and outbreak_size indicating the outbreak size per virus at each point in time.

Arguments

x

An object of class epiworld_sir, epiworld_seir, etc. (any model).

See Also

Other Summaries: epiworld-hospitalizations

Examples

# SEIR Connected model
seirconn <- ModelSEIRCONN(
  name              = "Disease",
  n                 = 10000,
  prevalence        = 0.1,
  contact_rate      = 2.0,
  transmission_rate = 0.8,
  incubation_days   = 7.0,
  recovery_rate     = 0.3
)

set.seed(937)
run(seirconn, 50)

# Retrieving the transition probability
get_transition_probability(seirconn)

# Get active cases
head(get_active_cases(seirconn))

# Get outbreak size
head(get_outbreak_size(seirconn))