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authorNaeem Model <me@nmode.ca>2024-02-13 08:22:47 +0000
committerNaeem Model <me@nmode.ca>2024-02-13 08:22:47 +0000
commite1c16cc937f241da2adc99c38ad7c9f09d204f9b (patch)
treeaa1d67d4a6d78614320555ba63d536866beb9bfe /R
parentcbe66a70a063988f5436e5e617a0ef6aeed0f166 (diff)
Update documentation
Diffstat (limited to 'R')
-rw-r--r--R/id.R3
-rw-r--r--R/idea.R3
-rw-r--r--R/seq_bayes.R3
-rw-r--r--R/wp.R18
4 files changed, 12 insertions, 15 deletions
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