R/lnb.R

In shimlab/riboHMM2: Analysis tool for Ribo-seq

#' lnb
#'
#' \code{lnb} returns the log likelihood f(x), 
#' where x ~ Nb(alpha, beta/(E+beta) )
#'
#' @export
#' @param x      a scalar. A realization from negative binomial distribution.
#' @param alpha  shape parameter in gamma distribution
#' @param beta   rate parameter in gamma distribution
#' @param E     a scalar. Normalizing constant for the observed chain x.
#' @return      Log likelihood f(x)
#' 
#' @examples
#' x <- 50
#' alpha <- 1
#' beta <- 0.1
#' E <- 10
#' lnb(x, alpha, beta, E)

lnb <- function(x, alpha, beta, E){
  p <- beta/(E+beta)
  lf <- dnbinom(x, alpha, p, log=TRUE)
  return(lf)
}