sim_tree: Simulated transmission tree

Description

This dataset represents a simulated transmission tree. This simulation was generated using the R package o2groups (see https://github.com/CyGei/o2groups for more information). Group HCW is assortative with a gamma coefficient of 2 and group patient is disassortative with a gamma coefficient of 1/1.25. Suceptible group sizes were 100 and 350, respectively. Code to reproduce the data below:

pak::pak("CyGei/o2groups")
set.seed(123)
sim_tree <- o2groups::simulate_groups(
  duration = 100,
  group_n = 2,
  size = c(100, 350), # susceptible group sizes
  name = c("HCW", "patient"),
  gamma = c(2, 0.8), # assortativity coefficients
  intro_n = c(1, 3),
  r0 = c(2, 2),
  generation_time = c(0, 0.1, 0.2, 0.4, 0.2, 0.1, 0),
  incubation_period = sample(1:14, 1000, replace = TRUE)
)

Usage

sim_tree

Arguments

Format

A data frame with 373 rows and 6 columns:

group: Character. The group to which the individual belongs.
id: Character. Unique identifier for each individual in the study.
source: Character. The ID of the individual who was the source of infection, if known. NA indicates an unknown source.
source_group: Character. The group of the source individual. NA for unknown sources.
date_infection: Numeric. The date of infection. Represented as the number of days since the start of the study.
date_onset: Numeric. The date of onset of symptoms. Represented as the number of days since the start of the study.