Add features required for modelling to the dataset — add_modelling

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:

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.
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.
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
)