rename polynomial to multinomial

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
-export(dpolynomialACGT)
+export(dmultinomialACGT)
 export(error_jc)
 export(log_add_exp)
 export(log_diff_exp)

R/proba.R

@@ -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 

man/dpolynomialACGT.Rd → man/dmultinomialACGT.Rd

 % 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{