diff options
Diffstat (limited to 'R')
| -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 |
4 files changed, 12 insertions, 15 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 |