autoplot-conmat: Plot setting matrices using ggplot2

In njtierney/conmat: Builds Contact Matrices using GAMs and Population Data

Plot setting matrices using ggplot2

Description

Plot setting matrices using ggplot2

Usage

## S3 method for class 'conmat_age_matrix'
autoplot(object, ..., title = "Contact Matrices")

## S3 method for class 'conmat_setting_prediction_matrix'
autoplot(object, ..., title = "Setting-specific synthetic contact matrices")

## S3 method for class 'transmission_probability_matrix'
autoplot(
  object,
  ...,
  title = "Setting-specific transmission probability matrices"
)

## S3 method for class 'ngm_setting_matrix'
autoplot(object, ..., title = "Setting-specific NGM matrices")

## S3 method for class 'setting_vaccination_matrix'
autoplot(object, ..., title = "Setting-specific vaccination matrices")

Arguments

object	A matrix or a list of square matrices, with row and column names indicating the age groups.
...	Other arguments passed on
title	Title to give to plot setting matrices. Defaults are provided for certain objects

Value

a ggplot visualisation of contact rates

Examples

## Not run: 
if (interactive()) {
  polymod_contact_data <- get_polymod_setting_data()
  polymod_survey_data <- get_polymod_population()

  setting_models <- fit_setting_contacts(
    contact_data_list = polymod_contact_data,
    population = polymod_survey_data
  )

  fairfield <- abs_age_lga("Fairfield (C)")

  fairfield_hh_size <-
    get_abs_per_capita_household_size(lga = "Fairfield (C)")

  synthetic_settings_5y_fairfield_hh <- predict_setting_contacts(
    population = fairfield,
    contact_model = setting_models,
    age_breaks = c(seq(0, 85, by = 5), Inf),
    per_capita_household_size = fairfield_hh_size
  )

  # Plotting synthetic contact matrices across all settings

  autoplot(
    object = synthetic_settings_5y_fairfield_hh,
    title = "Setting specific synthetic contact matrices"
  )

  # Work setting specific synthetic contact matrices
  autoplot(
    object = synthetic_settings_5y_fairfield_hh$work,
    title = "Work"
  )
}

## End(Not run)

njtierney/conmat documentation built on April 17, 2025, 10:27 p.m.