diff options
| -rw-r--r-- | R/id.R | 3 | ||||
| -rw-r--r-- | R/idea.R | 3 | ||||
| -rw-r--r-- | R/seq_bayes.R | 3 | ||||
| -rw-r--r-- | R/wp.R | 18 | ||||
| -rw-r--r-- | man/wp.Rd | 19 |
5 files changed, 24 insertions, 22 deletions
@@ -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. @@ -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 @@ -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 @@ -17,15 +17,16 @@ wp( \item{cases}{Vector of case counts. The vector must be of length at least two and only contain positive integers.} -\item{mu}{Mean of the serial distribution. This must be a positive number or -\code{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 \code{mu} should be set to \code{1}. If -case counts are daily and the serial distribution has a mean of seven days, -then \code{mu} should be set to \code{7}.} +\item{mu}{Mean of the serial distribution (defaults to \code{NA}). This must be a +positive number or \code{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 \code{mu} should be set +to \code{1}. If case counts are daily and the serial distribution has a mean of +seven days, then \code{mu} should be set to \code{7}.} \item{serial}{Whether to return the estimated serial distribution in addition -to the estimate of R0. This must be a value identical to \code{TRUE} or \code{FALSE}.} +to the estimate of R0 (defaults to \code{FALSE}). This must be a value identical +to \code{TRUE} or \code{FALSE}.} \item{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 \code{mu} is set @@ -126,3 +127,7 @@ estimate$pmf \references{ \href{https://doi.org/10.1002/sim.3136}{White and Pagano (Statistics in Medicine, 2008)} } +\seealso{ +\code{vignette("wp_serial", package="Rnaught")} for examples of using the +serial distribution. +} |