diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/WP.R | 4 | ||||
| -rw-r--r-- | R/WP_internal.R | 8 | ||||
| -rw-r--r-- | R/seqB.R | 4 |
3 files changed, 8 insertions, 8 deletions
@@ -43,8 +43,8 @@ #' \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}. +#' \code{B = 100, scale.max = 10, shape.max = 10}. For both shape +#' and scale, the smallest possible 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 diff --git a/R/WP_internal.R b/R/WP_internal.R index 420d0c0..dd10d29 100644 --- a/R/WP_internal.R +++ b/R/WP_internal.R @@ -9,7 +9,7 @@ #' #' @return The function returns the maximum likelihood estimator of R0. #' -#' @keywords internal +#' @noRd WP_known <- function(NT, p) { k <- length(p) TT <- length(NT) - 1 @@ -54,7 +54,7 @@ WP_known <- function(NT, p) { #' #' @importFrom stats pgamma qgamma #' -#' @keywords internal +#' @noRd WP_unknown <- function(NT, B = 100, shape.max = 10, scale.max = 10, tol = 0.999) { shape <- seq(0, shape.max, length.out = B + 1) @@ -91,14 +91,14 @@ WP_unknown <- function(NT, B = 100, shape.max = 10, scale.max = 10, #' This is a background/internal function called by \code{WP}. It computes the #' log-likelihood. #' -#' @param NT Vector of case counts. #' @param p Discretized version of the serial distribution. +#' @param NT Vector of case counts. #' @param R0 Basic reproductive ratio. #' #' @return This function returns the log-likelihood at the input variables and #' parameters. #' -#' @keywords internal +#' @noRd computeLL <- function(p, NT, R0) { k <- length(p) TT <- length(NT) - 1 @@ -11,7 +11,7 @@ #' posterior distribution. The prior distribution is the initial belief of the #' distribution of R0, which is the uninformative uniform distribution with #' values between zero and \code{kappa}. Users can change the value of -#' /code{kappa} only (i.e., the prior distribution cannot be changed from the +#' \code{kappa} only (i.e., the prior distribution cannot be changed from the #' uniform). As more case counts are observed, the influence of the prior #' distribution should lessen on the final estimate \code{Rhat}. #' @@ -41,7 +41,7 @@ #' \code{Rhat} is the estimate of R0 (the posterior mean), #' \code{posterior} is the posterior distribution of R0 from which #' alternate estimates can be obtained (see examples), and \code{group} -#' is an indicator variable (if \code{group=TRUE}, zero values of NT +#' is an indicator variable (if \code{group == TRUE}, zero values of NT #' were input and grouping was done to obtain \code{Rhat}). The variable #' \code{posterior} is returned as a list made up of \code{supp} (the #' support of the distribution) and \code{pmf} (the probability mass |