thin: Thin data to retain matching linelist / contacts

In reconhub/epicontacts: Handling, Visualisation and Analysis of Epidemiological Contacts

Thin data to retain matching linelist / contacts

Description

This function can be used to remove ('thin') data from epicontacts objects to ensure stricter matching of linelists and contacts. It has two behaviours, triggered by the argument what: either it thins data from $linelist, keeping only cases that are in $contacts (thin = "linelist", default), or the converse, i.e. removing contacts which are not fully documented in the linelist.

Usage

thin(x, what = "linelist")

Arguments

x	An epicontacts object.
what	A character string or integer determining which type of data is removed ('thinned'). "linelist" / 1 indicates that only cases appearing in $contacts are kept in $linelist. "contacts / 2" indicates that only cases appearing in $linelist are kept in $contacts.

Author(s)

Thibaut Jombart ([e-mail])

Examples

if (require(outbreaks)) {
## build data
x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts,
                       id = "case_id", to = "case_id", from = "infector",
                       directed = TRUE)

## keep contacts from a specific case '916d0a'
x <- x[j = "916d0a", contacts = "from"]

}

reconhub/epicontacts documentation built on Feb. 28, 2024, 3:15 p.m.