Commit 3580533e by Eric Coissac

rename polynomial to multinomial

parent d9a26bc7
# Generated by roxygen2: do not edit by hand
export(dpolynomialACGT)
export(dmultinomialACGT)
export(error_jc)
export(log_add_exp)
export(log_diff_exp)
......
......@@ -55,7 +55,7 @@ log_diff_exp = function(a, b) {
#' @export
log_sum_exp = function(x) Reduce(logaddexp, x)
#' Density probability function of a polynomial distribution for nucleotides
#' Density probability function of a multinomial distribution for nucleotides
#'
#' Computes the probalility to observe a given number of `A`, `C`, `G`, `T`
#' when probalilities of each nucleotide are `pA`, `pC`, `pG`, `pT`.
......@@ -74,15 +74,15 @@ log_sum_exp = function(x) Reduce(logaddexp, x)
#' of the observations given the probabilities of observation
#'
#' @examples
#' dpolynomialACGT(c(3,4),c(3,6),c(3,2),c(3,5),
#' 0.25,0.25,0.25,0.25)
#' dpolynomialACGT(c(3,4),c(3,6),c(3,2),c(3,5),
#' pA = 0.25, pC = 0.25, pG = 0.25, pT = 0.25,
#' log=TRUE)
#' dmultinomialACGT(c(3,4),c(3,6),c(3,2),c(3,5),
#' 0.25,0.25,0.25,0.25)
#' dmultinomialACGT(c(3,4),c(3,6),c(3,2),c(3,5),
#' pA = 0.25, pC = 0.25, pG = 0.25, pT = 0.25,
#' log=TRUE)
#'
#' @author Eric Coissac
#' @export
dpolynomialACGT = function(A,C,G,T,pA,pC,pG,pT,log=FALSE) {
dmultinomialACGT = function(A,C,G,T,pA,pC,pG,pT,log=FALSE) {
lpcomb =( log(pA) * A
+ log(pC) * C
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/proba.R
\name{dpolynomialACGT}
\alias{dpolynomialACGT}
\title{Density probability function of a polynomial distribution for nucleotides}
\name{dmultinomialACGT}
\alias{dmultinomialACGT}
\title{Density probability function of a multinomial distribution for nucleotides}
\usage{
dpolynomialACGT(A, C, G, T, pA, pC, pG, pT, log = FALSE)
dmultinomialACGT(A, C, G, T, pA, pC, pG, pT, log = FALSE)
}
\arguments{
\item{A}{numeric; number of observed *A* at a given site.}
......@@ -34,11 +34,11 @@ Computes the probalility to observe a given number of `A`, `C`, `G`, `T`
when probalilities of each nucleotide are `pA`, `pC`, `pG`, `pT`.
}
\examples{
dpolynomialACGT(c(3,4),c(3,6),c(3,2),c(3,5),
0.25,0.25,0.25,0.25)
dpolynomialACGT(c(3,4),c(3,6),c(3,2),c(3,5),
pA = 0.25, pC = 0.25, pG = 0.25, pT = 0.25,
log=TRUE)
dmultinomialACGT(c(3,4),c(3,6),c(3,2),c(3,5),
0.25,0.25,0.25,0.25)
dmultinomialACGT(c(3,4),c(3,6),c(3,2),c(3,5),
pA = 0.25, pC = 0.25, pG = 0.25, pT = 0.25,
log=TRUE)
}
\author{
......
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