Update docs

[Rnaught] / R / wp.R

diff --git a/R/wp.R b/R/wp.R
index 3448911de0cfa33d0cd693b16131cca7fe449500..16b4bbb3730df97919b75737f4022f85c4ba7ce1 100644 (file)
--- a/R/wp.R
+++ b/R/wp.R
@@ -37,14 +37,15 @@
 #'
 #' @param cases Vector of case counts. The vector must be of length at least two
 #'   and only contain positive integers.
 #'
 #' @param cases Vector of case counts. The vector must be of length at least two
 #'   and only contain positive integers.

-#' @param mu Mean of the serial distribution. This must be a positive number or
-#'   `NA`. If a number is specified, 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`.
+#' @param mu Mean of the serial distribution (defaults to `NA`). This must be a
+#'   positive number or `NA`. If a number is specified, 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`.

 #' @param serial Whether to return the estimated serial distribution in addition
 #' @param serial Whether to return the estimated serial distribution in addition

-#'   to the estimate of R0. This must be a value identical to `TRUE` or `FALSE`.
+#'   to the estimate of R0 (defaults to `FALSE`). This must be a value identical
+#'   to `TRUE` or `FALSE`.

 #' @param grid_length The length of the grid in the grid search (defaults to
 #'   100). This must be a positive integer. It will only be used if `mu` is set
 #'   to `NA`. The grid search will go through all combinations of the shape and
 #' @param grid_length The length of the grid in the grid search (defaults to
 #'   100). This must be a positive integer. It will only be used if `mu` is set
 #'   to `NA`. The grid search will go through all combinations of the shape and


@@ -71,9 +72,8 @@
 #'   Otherwise, if `serial` is identical to `FALSE`, only the estimate of R0 is
 #'   returned.
 #'
 #'   Otherwise, if `serial` is identical to `FALSE`, only the estimate of R0 is
 #'   returned.
 #'

-#' @references
-#' [White and Pagano (Statistics in Medicine, 2008)](
-#' https://doi.org/10.1002/sim.3136)
+#' @references [White and Pagano (Statistics in Medicine, 2008)](
+#'   https://doi.org/10.1002/sim.3136)

 #'
 #' @seealso `vignette("wp_serial", package="Rnaught")` for examples of using the
 #'   serial distribution.
 #'
 #' @seealso `vignette("wp_serial", package="Rnaught")` for examples of using the
 #'   serial distribution.


@@ -152,9 +152,8 @@ wp <- function(cases, mu = NA, serial = FALSE,
 #'   * `pmf` - the probability mass function of the estimated serial
 #'     distribution
 #'
 #'   * `pmf` - the probability mass function of the estimated serial
 #'     distribution
 #'

-#' @references
-#' [White and Pagano (Statistics in Medicine, 2008)](
-#' https://doi.org/10.1002/sim.3136)
+#' @references [White and Pagano (Statistics in Medicine, 2008)](
+#'   https://doi.org/10.1002/sim.3136)

 #'
 #' @seealso [wp()] for the function in which this grid search is called.
 #'
 #'
 #' @seealso [wp()] for the function in which this grid search is called.
 #'


@@ -207,9 +206,8 @@ wp_search <- function(cases, grid_length, max_shape, max_scale) {
 #'
 #' @return The sum inside the function `mu(t)` of the log likelihood.
 #'
 #'
 #' @return The sum inside the function `mu(t)` of the log likelihood.
 #'

-#' @references
-#' [White and Pagano (Statistics in Medicine, 2008)](
-#' https://doi.org/10.1002/sim.3136)
+#' @references [White and Pagano (Statistics in Medicine, 2008)](
+#'   https://doi.org/10.1002/sim.3136)

 #'
 #' @seealso [wp()] and [wp_search()] for the functions which require this sum.
 #'
 #'
 #' @seealso [wp()] and [wp_search()] for the functions which require this sum.
 #'