add_modelling_features: Add features required for modelling to the dataset

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

Add features required for modelling to the dataset

Description

This function adds three main groups of features to the data. It is used internally in fit_single_contact_model() and predict_contacts_1y(). It requires columns named age_to and age_from. The three types of features it adds are described below:

1. Population distribution of contact ages from the function add_population_age_to(), which requires a column called "age_to" representing the age of the person who had contact. It creates a column called pop_age_to. add_population_age_to() takes an extra argument for population, which defaults to get_polymod_population(), but needs to be a conmat_population object, which specifies the age and population characteristics, or a data frame with columns, lower.age.limit, and population.

2. School work participation, which is from the function add_school_work_participation(). This requires columns age_to and age_from, but will operate on any column starting with age and adds columns: school_probability, work_probability, school_year_probability, and school_weighted_pop_fraction.

3. Offset is added on to the data using add_offset(). This requires variables school_weighted_pop_fraction (from add_school_work_participation()) and pop_age_to (from add_school_work_participation()). It adds two columns, log_contactable_population_school, and log_contactable_population.

Usage

add_modelling_features(
  contact_data,
  school_demographics = NULL,
  work_demographics = NULL,
  population = get_polymod_population()
)

Arguments

contact_data	contact data with columns age_to and age_from
school_demographics	(optional) defaults to census average proportion at school. You can provide a dataset with columns, "age" (numeric), and "school_fraction" (0-1), if you would like to specify these details. See abs_avg_school for the default values. If you would like to use the original school demographics used in conmat, these are provided in the dataset, conmat_original_school_demographics.
work_demographics	(optional) defaults to census average proportion employed. You can provide a dataset with columns, "age" (numeric), and "work_fraction", if you would like to specify these details. See abs_avg_work for the default values. If you would like to use the original work demographics used in conmat, these are provided in the dataset, conmat_original_work_demographics.
population	the population argument of add_population_age_to()

Value

data frame with 11 extra columns - the contents of contact_data, plus: pop_age_to, school_fraction_age_from, work_fraction_age_from, school_fraction_age_to, work_fraction_age_to, school_probability, work_probability, school_year_probability, school_weighted_pop_fraction, log_contactable_population_school, and log_contactable_population.

Examples

age_min <- 10
age_max <- 15
all_ages <- age_min:age_max
library(tidyr)
example_df <- expand_grid(
  age_from = all_ages,
  age_to = all_ages,
)
add_modelling_features(example_df)
add_modelling_features(
  example_df,
  school_demographics = conmat_original_school_demographics,
  work_demographics = conmat_original_work_demographics
)

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