This function simulates contact data from a transmission tree. The model assumes that all transmission pairs have experienced contact, and that there is no false-positive reporting of contacts. The probability of contact occuring between a non-transmision pair is given by the parameter lambda. The probability of reporting a contact (transmission pair or not) is given by the parameters eps.

sim_ctd(tTree, eps, lambda)

Arguments

tTree

a dataframe or matrix of two columns, with each row providing the ids (numerical or as characters) of a transmission pair

eps

the contact reporting coverage, defined as the probability of reporting a contact (transmission pair or not)

lambda

the non-infectious contact rate, defined as the probability of contact between a non-transmission pair.

Examples

## load data x <- fake_outbreak tTree <- data.frame(from = x$ances, to = seq_along(x$ances)) ## simulate contact data with coverage of 80% and 10% probability of ## contact between non-transmission pairs ctd <- outbreaker2:::sim_ctd(tTree, eps = 0.8, lambda = 0.1) ## inspect contact data head(ctd)
#> i j #> 1 1 2 #> 2 11 21 #> 3 3 5 #> 4 17 7 #> 5 15 5 #> 6 4 7