contact_score: Compute the tracing score of a contact
In reconhub/tracer: Tools for Informing Contact Tracing

Description Usage Arguments Details Value Author(s) Examples

This function compute the tracing score of a contact, i.e. an individual who has had at least one recorded exposure to a case. For a contact, the tracing score is defined as the probability that this individual will show symptoms for the first time on day 't'.

1	contact_score(x, R, lambda, w)

`x`	A vector of integers indicating dates of onset of the cases causing exposure.
`R`	The average effective reproduction number, i.e. the average number of secondar cases seeded by an infected individual.
`lambda`	The average number of contacts (infectious or not) reported by cases.
`w`	The probability mass function of the serial interval, i.e. the delay from primary to secondary symptom onset. We recommend using the `distcrete` package to generate discretized distributions (see details).

See the distcrete package for generating discretized distributions at: http://github.com/reconhub/distcrete.

A function with two arguments:

t: the date for which the score should be computed.
visit_days_ago: the number of days since the last visit to the contact, defaulting to 1, which means that the last visit happened the day before t.

Thibaut Jombart (thibautjombart@gmail.com)

if (require(distcrete)) {
 ## generate serial interval distribution
 SI <- distcrete("gamma", 1L, w = 0, 10, 0.65)$d
 plot(SI, type="h", xlim=c(0,50), xlab = "Days")
 title("Serial interval distribution")

 ## get tracing score function for:
 ## - exposure to cases with onsets: 1, 10, 25
 ## - R = 2.1
 ## - lambda = 3.5
 f <- contact_score(c(1,10,25), R = 2.1, lambda = 3.5, SI)

 ## score for various days
 f(0) # day 0
 f(10) # day 10
 f(10:20)

 ## plot score for various days
 plot(f, type = "h", xlim = c(0,60), col = pal1(100),
      xlab = "Date", ylab = "P(new symptoms)")
 title("Contact score over time")
}