From 5802a8d248c4f02187b4fcd6a405cfa1ed916b81 Mon Sep 17 00:00:00 2001 From: Naeem Model Date: Fri, 23 Jun 2023 01:38:27 +0000 Subject: Normalize line endings --- R/IDEA.R | 116 +++++++++++++++++++++++++++++++-------------------------------- 1 file changed, 58 insertions(+), 58 deletions(-) (limited to 'R/IDEA.R') diff --git a/R/IDEA.R b/R/IDEA.R index 20a9401..854acd7 100644 --- a/R/IDEA.R +++ b/R/IDEA.R @@ -1,58 +1,58 @@ -#' IDEA method -#' -#' This function implements a least squares estimation method of R0 due to Fisman et al. (PloS One, 2013). -#' See details for implementation notes. -#' -#' This method is closely related to that implemented in \code{ID}. The method is based on an incidence decay model. -#' The estimate of R0 is the value which minimizes the sum of squares between observed case counts and cases counts -#' expected under the model. -#' -#' This method is based on an approximation of the SIR model, which is most valid at the beginning of an epidemic. -#' The method assumes that the mean of the serial distribution (sometimes called the serial interval) is known. -#' The final estimate can be quite sensitive to this value, so sensitivity testing is strongly recommended. -#' Users should be careful about units of time (e.g., are counts observed daily or weekly?) when implementing. -#' -#' @param NT Vector of case counts. -#' @param mu Mean of the serial distribution. This needs to match case counts in time units. For example, if case counts -#' are weekly and the serial distribution has a mean of seven days, then \code{mu} should be set to one. If case -#' counts are daily and the serial distribution has a mean of seven days, then \code{mu} should be set to seven. -#' -#' @return \code{IDEA} returns a single value, the estimate of R0. -#' -#' @examples -#' ## ===================================================== ## -#' ## Illustrate on weekly data ## -#' ## ===================================================== ## -#' -#' NT <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) -#' ## obtain Rhat when serial distribution has mean of five days -#' IDEA(NT=NT, mu=5/7) -#' ## obtain Rhat when serial distribution has mean of three days -#' IDEA(NT=NT, mu=3/7) -#' -#' ## ========================================================= ## -#' ## Compute Rhat using only the first five weeks of data ## -#' ## ========================================================= ## -#' -#' IDEA(NT=NT[1:5], mu=5/7) # serial distribution has mean of five days -#' -#' @export -IDEA <- function(NT, mu) { - if (length(NT) < 2) - print("Warning: length of NT should be at least two.") - else { - NT <- as.numeric(NT) - TT <- length(NT) - s <- (1:TT) / mu - - y1 <- log(NT) / s - y2 <- s^2 - y3 <- log(NT) - - IDEA1 <- sum(y2) * sum(y1) - sum(s) * sum(y3) - IDEA2 <- TT * sum(y2) - sum(s)^2 - IDEA <- exp(IDEA1 / IDEA2) - - return(IDEA) - } -} +#' IDEA method +#' +#' This function implements a least squares estimation method of R0 due to Fisman et al. (PloS One, 2013). +#' See details for implementation notes. +#' +#' This method is closely related to that implemented in \code{ID}. The method is based on an incidence decay model. +#' The estimate of R0 is the value which minimizes the sum of squares between observed case counts and cases counts +#' expected under the model. +#' +#' This method is based on an approximation of the SIR model, which is most valid at the beginning of an epidemic. +#' The method assumes that the mean of the serial distribution (sometimes called the serial interval) is known. +#' The final estimate can be quite sensitive to this value, so sensitivity testing is strongly recommended. +#' Users should be careful about units of time (e.g., are counts observed daily or weekly?) when implementing. +#' +#' @param NT Vector of case counts. +#' @param mu Mean of the serial distribution. This needs to match case counts in time units. For example, if case counts +#' are weekly and the serial distribution has a mean of seven days, then \code{mu} should be set to one. If case +#' counts are daily and the serial distribution has a mean of seven days, then \code{mu} should be set to seven. +#' +#' @return \code{IDEA} returns a single value, the estimate of R0. +#' +#' @examples +#' ## ===================================================== ## +#' ## Illustrate on weekly data ## +#' ## ===================================================== ## +#' +#' NT <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) +#' ## obtain Rhat when serial distribution has mean of five days +#' IDEA(NT=NT, mu=5/7) +#' ## obtain Rhat when serial distribution has mean of three days +#' IDEA(NT=NT, mu=3/7) +#' +#' ## ========================================================= ## +#' ## Compute Rhat using only the first five weeks of data ## +#' ## ========================================================= ## +#' +#' IDEA(NT=NT[1:5], mu=5/7) # serial distribution has mean of five days +#' +#' @export +IDEA <- function(NT, mu) { + if (length(NT) < 2) + print("Warning: length of NT should be at least two.") + else { + NT <- as.numeric(NT) + TT <- length(NT) + s <- (1:TT) / mu + + y1 <- log(NT) / s + y2 <- s^2 + y3 <- log(NT) + + IDEA1 <- sum(y2) * sum(y1) - sum(s) * sum(y3) + IDEA2 <- TT * sum(y2) - sum(s)^2 + IDEA <- exp(IDEA1 / IDEA2) + + return(IDEA) + } +} -- cgit v1.2.3