Remove old Shiny UI and server files

[Rnaught] / R / id.R

diff --git a/R/id.R b/R/id.R
index 7e8a04d46796b4cacb74675b8525b3590ac11eec..5277591fc2cb92591c8d702cdec554b15910fbfd 100644 (file)
--- a/R/id.R
+++ b/R/id.R
@@ -1,11 +1,11 @@
-#' ID method
+#' Incidence Decay (ID)

 #'
 #' This function implements a least squares estimation method of R0 due to
 #' Fisman et al. (PloS One, 2013). See details for implementation notes.
 #'
 #' The method is based on a straightforward incidence decay model. The estimate
 #' of R0 is the value which minimizes the sum of squares between observed case
 #'
 #' This function implements a least squares estimation method of R0 due to
 #' Fisman et al. (PloS One, 2013). See details for implementation notes.
 #'
 #' The method is based on a straightforward 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.
+#' 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
 #'
 #' 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


@@ -14,33 +14,32 @@
 #' is strongly recommended. Users should be careful about units of time (e.g.,
 #' are counts observed daily or weekly?) when implementing.
 #'
 #' 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.
+#' @param cases Vector of case counts. The vector must be non-empty and only
+#'   contain positive integers.
+#' @param mu Mean of the serial distribution. This must be a positive number.
+#'   The value should match the case counts in time units. For example, if case
+#'   counts are weekly and the serial distribution has a mean of seven days,
+#'   then `mu` should be set to `1`. If case counts are daily and the serial
+#'   distribution has a mean of seven days, then `mu` should be set to `7`.

 #'
 #'

-#' @return \code{ID} returns a single value, the estimate of R0.
+#' @return An estimate of the basic reproduction number (R0).
+#'
+#' @references [Fisman et al. (PloS One, 2013)](
+#'   https://doi.org/10.1371/journal.pone.0083622)
+#'
+#' @seealso [idea()] for a similar method.
+#'
+#' @export

 #'
 #' @examples
 #'
 #' @examples

-#' # Weekly data:
-#' NT <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4)
+#' # Weekly data.
+#' cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4)

 #'
 #' # Obtain R0 when the serial distribution has a mean of five days.
 #'
 #' # Obtain R0 when the serial distribution has a mean of five days.

-#' ID(NT, mu = 5 / 7)
+#' id(cases, mu = 5 / 7)

 #'
 #' # Obtain R0 when the serial distribution has a mean of three days.
 #'
 #' # Obtain R0 when the serial distribution has a mean of three days.

-#' ID(NT, mu = 3 / 7)
-#'
-#' @export
-ID <- function(NT, mu) {
-  NT <- as.numeric(NT)
-  TT <- length(NT)
-  s <- (1:TT) / mu
-  y <- log(NT) / s
-
-  R0_ID <- exp(sum(y) / TT)
-
-  return(R0_ID)
+#' id(cases, mu = 3 / 7)
+id <- function(cases, mu) {
+  exp(sum((log(cases) * mu) / seq_along(cases)) / length(cases))

 }
 }