aggregate_contact_matrix: Aggregate a contact matrix

In bernadette-eu/Bernadette: Bayesian Inference and Model Selection for Stochastic Epidemics

Aggregate a contact matrix

Description

Function to aggregate a contact matrix according to user-defined age groups.

Usage

aggregate_contact_matrix(object, lookup_table, age_distr)

Arguments

object	data.frame; a contact matrix. See contact_matrix.
lookup_table	data.frame; a user-defined data.frame which maps the sixteen 5-year age bands to a new set of age bands.
age_distr	data.frame; the aggregated age distribution. See aggregate_contact_matrix.

Value

An object of class data.frame.

Examples

# Import the age distribution for Greece in 2020:
age_distr <- age_distribution(country = "Greece", year = 2020)

# Lookup table:
lookup_table <- data.frame(Initial = age_distr$AgeGrp,
                           Mapping = c(rep("0-39",  8),
                                       rep("40-64", 5),
                                       rep("65+"  , 3)))

# Aggregate the age distribution table:
aggr_age <- aggregate_age_distribution(age_distr, lookup_table)

# Import the projected contact matrix for Greece:
conmat <- contact_matrix(country = "GRC")

# Aggregate the contact matrix:
aggr_cm <- aggregate_contact_matrix(conmat, lookup_table, aggr_age)

# Plot the contact matrix:
plot_contact_matrix(aggr_cm)

bernadette-eu/Bernadette documentation built on July 1, 2024, 9:58 p.m.