Update docs

diff --git a/R/id.R b/R/id.R
index 91fa5cab727b43681cb14713333389640a5a1f7e..5277591fc2cb92591c8d702cdec554b15910fbfd 100644 (file)
--- a/R/id.R
+++ b/R/id.R
@@ -25,7 +25,7 @@
 #' @return An estimate of the basic reproduction number (R0).
 #'
 #' @references [Fisman et al. (PloS One, 2013)](
 #' @return An estimate of the basic reproduction number (R0).
 #'
 #' @references [Fisman et al. (PloS One, 2013)](

-#' https://doi.org/10.1371/journal.pone.0083622)
+#'   https://doi.org/10.1371/journal.pone.0083622)

 #'
 #' @seealso [idea()] for a similar method.
 #'
 #'
 #' @seealso [idea()] for a similar method.
 #'

diff --git a/R/idea.R b/R/idea.R
index 53ba98aa5f9181781765ae8edaceba17badee366..14ba838bc5e363244d6b0f7793dfda3fe1cafe36 100644 (file)
--- a/R/idea.R
+++ b/R/idea.R
@@ -26,7 +26,7 @@
 #' @return An estimate of the basic reproduction number (R0).
 #'
 #' @references [Fisman et al. (PloS One, 2013)](
 #' @return An estimate of the basic reproduction number (R0).
 #'
 #' @references [Fisman et al. (PloS One, 2013)](

-#' https://doi.org/10.1371/journal.pone.0083622)
+#'   https://doi.org/10.1371/journal.pone.0083622)

 #'
 #' @seealso [id()] for a similar method.
 #'
 #'
 #' @seealso [id()] for a similar method.
 #'

diff --git a/R/seq_bayes.R b/R/seq_bayes.R
index 428441939686e43a723eda6ceeb7766e0a5b069d..d486d2b8e439e34436fb3919345a56c79066f543 100644 (file)
--- a/R/seq_bayes.R
+++ b/R/seq_bayes.R
@@ -52,7 +52,7 @@
 #'   posterior mean).
 #'
 #' @references [Bettencourt and Riberio (PloS One, 2008)](
 #'   posterior mean).
 #'
 #' @references [Bettencourt and Riberio (PloS One, 2008)](

-#' https://doi.org/10.1371/journal.pone.0002185)
+#'   https://doi.org/10.1371/journal.pone.0002185)

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

diff --git a/R/wp.R b/R/wp.R
index 428f3667f80edd892b44f84d995383d48c345829..16b4bbb3730df97919b75737f4022f85c4ba7ce1 100644 (file)
--- a/R/wp.R
+++ b/R/wp.R
@@ -73,7 +73,7 @@
 #'   returned.
 #'
 #' @references [White and Pagano (Statistics in Medicine, 2008)](
 #'   returned.
 #'
 #' @references [White and Pagano (Statistics in Medicine, 2008)](

-#' https://doi.org/10.1002/sim.3136)
+#'   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.
 #'