X-Git-Url: https://git.nmode.ca/Rnaught/blobdiff_plain/9c1a5668803e735f034700c55028ffc0146f1e93..5f4889d4df5e94f194ef7f8b839496db04b17f4e:/R/WP_unknown.R

diff --git a/R/WP_unknown.R b/R/WP_unknown.R
index c5b0a35..f339836 100644
--- a/R/WP_unknown.R
+++ b/R/WP_unknown.R
@@ -5,11 +5,11 @@
 #' The function then implements a simple grid search algorithm to obtain the maximum likelihood estimator
 #' of R0 as well as the gamma parameters.
 #'
-#' @param NT vector of case counts
-#' @param B length of grid for shape and scale (grid search parameter)
-#' @param shape.max maximum shape value (grid search parameter)
-#' @param scale.max maximum scale value (grid search parameter)
-#' @param tol cutoff value for cumulative distribution function of the serial distribution, defaults to 0.999
+#' @param NT Vector of case counts.
+#' @param B Length of grid for shape and scale (grid search parameter).
+#' @param shape.max Maximum shape value (grid \code{search} parameter).
+#' @param scale.max Maximum scale value (grid \code{search} parameter).
+#' @param tol cutoff value for cumulative distribution function of the serial distribution (defaults to 0.999).
 #'
 #' @return The function returns \code{Rhat}, the maximum likelihood estimator of R0, as well as the maximum
 #'         likelihood estimator of the discretized serial distribution given by \code{p} (the probability mass
@@ -17,10 +17,12 @@
 #'         The function also returns \code{resLL} (all values of the log-likelihood) at \code{shape} (grid for
 #'         shape parameter) and at \code{scale} (grid for scale parameter), as well as \code{resR0} (the full
 #'         vector of maximum likelihood estimators), \code{JJ} (the locations for the likelihood for these), and
-#'         \code{J0} (the location for the maximum likelihood estimator \code{Rhat}).  If \code{JJ} and \code{J0}
-#'         are not the same, this means that the maximum likelihood estimator is not unique. 
+#'         \code{J0} (the location for the maximum likelihood estimator \code{Rhat}). If \code{JJ} and \code{J0}
+#'         are not the same, this means that the maximum likelihood estimator is not unique.
 #'
-#' @export
+#' @importFrom stats pgamma qgamma
+#'
+#' @keywords internal
 WP_unknown <- function(NT, B=100, shape.max=10, scale.max=10, tol=0.999) {
 	shape <- seq(0, shape.max, length.out=B+1)
 	scale <- seq(0, scale.max, length.out=B+1)
@@ -36,8 +38,8 @@ WP_unknown <- function(NT, B=100, shape.max=10, scale.max=10, tol=0.999) {
             p <- diff(pgamma(0:range.max, shape=shape[i], scale=scale[j]))
             p <- p / sum(p)
             mle <- WP_known(NT, p)
-            resLL[i,j] <- computeLL(p, NT, mle$R)
-            resR0[i,j] <- mle$R
+            resLL[i,j] <- computeLL(p, NT, mle)
+            resR0[i,j] <- mle
         }
     }