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permp <- function(x,nperm,n1,n2,total.nperm=NULL,method="auto",twosided=TRUE)
# Exact permutation p-values
# Gordon Smyth and Belinda Phipson
# 16 February 2010. Last modified 17 March 2016.
{
if(any(x<0)) stop("negative x values")
if(any(x>nperm)) stop("x cannot exceed nperm")
if(is.null(total.nperm)) {
total.nperm <- choose((n1+n2),n1)
if(n1==n2 & twosided==TRUE) total.nperm <- total.nperm/2
}
method <- match.arg(method,c("auto","exact","approximate"))
if(method=="auto") if(total.nperm>10000) method <- "approximate" else method <- "exact"
# exact p-value by summation
if(method=="exact") {
p <- (1:total.nperm)/total.nperm
prob <- rep(p,length(x))
x2 <- rep(x,each=total.nperm)
Y <- matrix(pbinom(x2,prob=prob,size=nperm),total.nperm,length(x))
x[] <- colMeans(Y)
}
# integral approximation
else {
z <- gauss.quad.prob(128,l=0,u=0.5/total.nperm)
prob <- rep(z$nodes,length(x))
x2 <- rep(x,each=128)
Y <- matrix(pbinom(x2,prob=prob,size=nperm),128,length(x))
int <- 0.5/total.nperm*colSums(z$weights*Y)
x[] <- (x+1)/(nperm+1)-int
}
x
}
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