From e1c16cc937f241da2adc99c38ad7c9f09d204f9b Mon Sep 17 00:00:00 2001
From: Naeem Model <me@nmode.ca>
Date: Tue, 13 Feb 2024 08:22:47 +0000
Subject: Update documentation

---
 R/id.R        |  3 +--
 R/idea.R      |  3 +--
 R/seq_bayes.R |  3 +--
 R/wp.R        | 18 +++++++++---------
 4 files changed, 12 insertions(+), 15 deletions(-)

(limited to 'R')

diff --git a/R/id.R b/R/id.R
index eef66d6..91fa5ca 100644
--- a/R/id.R
+++ b/R/id.R
@@ -24,8 +24,7 @@
 #'
 #' @return An estimate of the basic reproduction number (R0).
 #'
-#' @references
-#' [Fisman et al. (PloS One, 2013)](
+#' @references [Fisman et al. (PloS One, 2013)](
 #' https://doi.org/10.1371/journal.pone.0083622)
 #'
 #' @seealso [idea()] for a similar method.
diff --git a/R/idea.R b/R/idea.R
index 0549527..53ba98a 100644
--- a/R/idea.R
+++ b/R/idea.R
@@ -25,8 +25,7 @@
 #'
 #' @return An estimate of the basic reproduction number (R0).
 #'
-#' @references
-#' [Fisman et al. (PloS One, 2013)](
+#' @references [Fisman et al. (PloS One, 2013)](
 #' https://doi.org/10.1371/journal.pone.0083622)
 #'
 #' @seealso [id()] for a similar method.
diff --git a/R/seq_bayes.R b/R/seq_bayes.R
index 59b7b4b..4284419 100644
--- a/R/seq_bayes.R
+++ b/R/seq_bayes.R
@@ -51,8 +51,7 @@
 #'   returned. Note that the estimate is equal to `sum(supp * pmf)` (i.e., the
 #'   posterior mean).
 #'
-#' @references
-#' [Bettencourt and Riberio (PloS One, 2008)](
+#' @references [Bettencourt and Riberio (PloS One, 2008)](
 #' https://doi.org/10.1371/journal.pone.0002185)
 #'
 #' @seealso `vignette("seq_bayes_post", package = "Rnaught")` for examples of
diff --git a/R/wp.R b/R/wp.R
index 3448911..428f366 100644
--- 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 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
-#'   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
@@ -71,8 +72,7 @@
 #'   Otherwise, if `serial` is identical to `FALSE`, only the estimate of R0 is
 #'   returned.
 #'
-#' @references
-#' [White and Pagano (Statistics in Medicine, 2008)](
+#' @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
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