compile_epi {ATQ}

Compile Epidemic Data

Description

Compiles and processes epidemic data, simulating school absenteeism using epidemic and individual data.

Usage

compile_epi(epidemic, individual_data, lags = 16, inf_period = 4, T = 300)

Arguments

epidemic

A list of simulated epidemic data (output from simepi() or similar function).

individual_data

A data frame of simulated individuals data (output from simulate_households() or similar function).

lags

Maximum number of lags for absenteeism, default = 16 (note that lag of zero is included).

inf_period

Infection period of epidemic, default = 4.

T

Time period, default = 300 days.

Value

A data frame containing compiled epidemic data, including:

Date

Day of the epidemic

ScYr

School year

pct_absent

Percentage of students absent

absent

Number of students absent

absent_sick

Number of students absent due to illness

new_inf

Number of new infections

reported_cases

Number of reported cases

Case

Indicator for lab confirmed flu case that day

sinterm, costerm

Seasonal terms

window

Indicator for "True Alarm" window

ref_date

Indicator for reference date

lag0, lag1, ..., lag15

Lagged absenteeism values

Examples

# Assuming you have previously simulated epidemic and individual data:
epidemic <- ssir(1000, alpha = 0.4)
individual_data <- data.frame(elem_child_ind = sample(0:1, 1000, replace = TRUE),
                              schoolID = sample(1:10, 1000, replace = TRUE))

compiled_data <- compile_epi(epidemic, individual_data)