predict_contacts_1y: Predict contact rate to a given population at full 1y...

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

Predict contact rate to a given population at full 1y resolution

Description

Provides a predicted rate of contacts for contact ages. Take an already fitted model of contact rate and predict the estimated contact rate, and standard error, for all combinations of the provided ages in 1 year increments. So if the minimum age is 5, and the maximum age is 10, it will provide the estimated contact rate for all age combinations: 5 and 5, 5 and 6 ... 5 and 10, and so on. This function is used internally within predict_contacts(), and thus predict_setting_contacts() as well, although it can be used by itself. See examples for more details, and details for more information.

Usage

predict_contacts_1y(model, population, age_min = 0, age_max = 100)

Arguments

model	A single fitted model of contact rate (e.g., fit_single_contact_model())
population	a dataframe of age population information, with columns indicating some lower age limit, and population, (e.g., get_polymod_population())
age_min	Age range minimum value. Default: 0
age_max	Age range maximum value, Default: 100

Details

Prediction features are added using add_modelling_features(). These features include the population distribution of contact ages, fraction of population in each age group that attend school/work as well as the offset according to the settings on all combinations of the participant & contact ages.

Value

Data frame with four columns: age_from, age_to, contacts, and se_contacts. This contains the participant & contact ages from the minimum and maximum ages provided along with the predicted rate of contacts and standard error around the prediction.

Examples

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

fairfield

# predict the contact rates in 1 year blocks to Fairfield data

fairfield_contacts_1 <- predict_contacts_1y(
  model = polymod_setting_models$home,
  population = fairfield,
  age_min = 0,
  age_max = 2
)

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