estimateRi: Estimates individual-level reproductive numbers

In nbTransmission: Naive Bayes Transmission Analysis

Description

The function estimateRi uses relative transmission probabilities to estimate the individual-level reproductive number.

Usage

estimateRi(df, indIDVar, dateVar, pVar)

Arguments

df	The name of the dateset with transmission probabilities
indIDVar	The variable name (in quotes) of the individual ID varaibles (data frame df must have variables called <indIDVar>.1 and <indIDVar>.2).
dateVar	The variable name (in quotes) of the dates that the individuals are observed (data frame df must have variables called <dateVar>.1 and <dateVar>.2).
pVar	The variable name (in quotes) of the transmission probabilities.

Details

This function is meant to be called by estimateR which estimates the individual-level, time-level, and average reproductive numbers, but it can also be run directly.

Value

A data frame with the individual-level reproductive numbers. Column names:

• <indIDVar> - the individual ID with name specified.

• <dateVar> - the date the individual was observed with name specified.

• Ri - the individual-level reproductive number.

• nInfectees - the number of possible infectees for this individual.

See Also

estimateR estimateRt estimateRtAvg

nbTransmission documentation built on Jan. 7, 2021, 1:07 a.m.