Re-gen docs and prevent genning of internal functions

[Rnaught] / man / WP_unknown.Rd

diff --git a/man/WP_unknown.Rd b/man/WP_unknown.Rd
deleted file mode 100644 (file)
index c3872d6..0000000
--- a/man/WP_unknown.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/WP_unknown.R
-\name{WP_unknown}
-\alias{WP_unknown}
-\title{WP method background function WP_unknown}
-\usage{
-WP_unknown(NT, B = 100, shape.max = 10, scale.max = 10, tol = 0.999)
-}
-\arguments{
-\item{NT}{vector of case counts}
-
-\item{B}{length of grid for shape and scale (grid search parameter)}
-
-\item{shape.max}{maximum shape value (grid search parameter)}
-
-\item{scale.max}{maximum scale value (grid search parameter)}
-
-\item{tol}{cutoff value for cumulative distribution function of the serial distribution, defaults to 0.999}
-}
-\value{
-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 function) and \code{range.max} (the distribution has support on the integers one to \code{range.max}).  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.
-}
-\description{
-This is a background/internal function called by \code{WP}.  It computes the maximum likelihood estimator of R0 assuming that the serial distribution is unknown but comes from a discretized gamma distribution.  The function then implements a simple grid search algorithm to obtain the maximum likelihood estimator of R0 as well as the gamma parameters.
-}