diff options
Diffstat (limited to 'R/WP.R')
| -rw-r--r-- | R/WP.R | 29 |
1 files changed, 14 insertions, 15 deletions
@@ -19,7 +19,7 @@ source("WP_unknown.R") #' is strongly recommended. If the serial distribution is unknown (i.e., \code{mu} is \code{NA}), the #' likelihood function can be flat near the maximum, resulting in numerical instability of the optimizer. #' When \code{mu} is \code{NA}, the implementation takes considerably longer to run. Users should be careful -#' about units of time (e.g. are counts observed daily or weekly?) when implementing. +#' about units of time (e.g., are counts observed daily or weekly?) when implementing. #' #' The model developed in White and Pagano (2008) is discrete, and hence the serial distribution is finite #' discrete. In our implementation, the input value \code{mu} is that of a continuous distribution. The @@ -28,27 +28,26 @@ source("WP_unknown.R") #' user notices that the input \code{mu} and output mean of \code{SD} are different, this is to be expected, #' and is caused by the discretization. #' -#' @param NT Vector of case counts +#' @param NT Vector of case counts. #' @param mu Mean of the serial distribution (needs to match 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 one). The default value of \code{mu} is set to \code{NA}. -#' @param search List of default values for the grid search algorithm; the list includes three elements: the -#' first is \code{B} which is the length of the grid in one dimension, the second is -#' \code{scale.max} which is the largest possible value of the scale parameter, and the third is -#' \code{shape.max} which is the largest possible value of the shape parameter; defaults to +#' @param search List of default values for the grid search algorithm. The list includes three elements: the +#' first is \code{B}, which is the length of the grid in one dimension; the second is +#' \code{scale.max}, which is the largest possible value of the scale parameter; and the third +#' is \code{shape.max}, which is the largest possible value of the shape parameter. Defaults to #' \code{B=100, scale.max=10, shape.max=10}. For both shape and scale, the smallest possible -#' value is 1/\code{B}. +#' value is 1/\code{B}. #' @param tol Cutoff value for cumulative distribution function of the pre-discretization gamma serial -#' distribution, defaults to 0.999 (i.e. in the discretization, the maximum is chosen such that the +#' distribution. Defaults to 0.999 (i.e. in the discretization, the maximum is chosen such that the #' original gamma distribution has cumulative probability of no more than 0.999 at this maximum). #' -#' @return WP returns a list containing the following components: \code{Rhat} is the estimate of R0, \code{SD} -#' is either the discretized serial distribution (if \code{mu} is not \code{NA}) or the estimated -#' discretized serial distribution (if \code{mu} is \code{NA}), and \code{inputs} is a list of the -#' original input variables \code{NT, mu, method, search, tol}. The list also returns the variable -#' \code{check}, which is equal to the number of non-unique maximum likelihood estimators. The serial -#' distribution \code{SD} is returned as a list made up of \code{supp} the support of the distribution -#' and \code{pmf} the probability mass function. +#' @return \code{WP} returns a list containing the following components: \code{Rhat} is the estimate of R0, +#' and \code{SD} is either the discretized serial distribution (if \code{mu} is not \code{NA}), or the +#' estimated discretized serial distribution (if \code{mu} is \code{NA}). The list also returns the +#' variable \code{check}, which is equal to the number of non-unique maximum likelihood estimators. +#' The serial distribution \code{SD} is returned as a list made up of \code{supp} (the support of +#' the distribution) and \code{pmf} (the probability mass function). #' #' @examples #' ## ===================================================== ## |