Estimates individual-level reproductive numbers

Source: R/calcR.R

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

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.

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.

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.