Simulated transmission tree
sim_tree.RdThis 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:
pacman::p_load_gh("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)
)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.
NAindicates an unknown source.- source_group
Character. The group of the source individual.
NAfor 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.