get.individuals: Retrieve individual identifiers

In thibautjombart/OutbreakTools: Basic Tools for the Analysis of Disease Outbreaks

Description

get.individuals is a generic function with a method for obkData, obkSequences and obkContacts objects. It can be used to retrieve individuals identifiers stored in the object.

Usage

get.individuals(x, ...)

get.nindividuals(x, ...)

## S4 method for signature 'obkData'
get.individuals(x,
    data=c("all", "individuals", "records", "contacts", "dna"), ...)

## S4 method for signature 'obkData'
get.nindividuals(x,
    data=c("all", "individuals", "records", "contacts", "dna"), ...)

## S4 method for signature 'obkSequences'
get.individuals(x, ...)

## S4 method for signature 'obkSequences'
get.nindividuals(x, ...)

## S4 method for signature 'obkContacts'
get.individuals(x, ...)

## S4 method for signature 'obkContacts'
get.nindividuals(x, ...)

Arguments

x	an input object to seek individuals from.
data	a character string indicating the name of the data field to look for. It can be 'all'(default), 'individuals', 'records' or 'context'.
...	currently not used.

Author(s)

Thibaut Jombart, Lulla Opatowski, Simon Frost.

Examples

## LOAD DATA ##
data(ToyOutbreak)

## VARIOUS USE OF GET.INDIVIDUALS ##
get.individuals(ToyOutbreak)

get.nindividuals(ToyOutbreak, "records")
get.individuals(ToyOutbreak, "records")

get.nindividuals(ToyOutbreak, "contacts")
get.individuals(ToyOutbreak, "contacts")

thibautjombart/OutbreakTools documentation built on Oct. 26, 2019, 10:56 p.m.