Nothing
MC.Xmcupo.statistics <-
function(group.Nrs, numMC=10, pi0, group.pi, group.theta, type="ha", siglev=0.05) {
if(missing(group.theta) || missing(group.Nrs))
stop("group.Nrs and/or group.theta missing.")
if(missing(group.pi) && tolower(type) == "ha")
stop("group.pi missing.")
if(missing(pi0) && tolower(type) == "hnull")
stop("pi0 missing.")
if(tolower(type) != "ha" && tolower(type) != "hnull")
stop(sprintf("Type '%s' not found. Type must be 'ha' for power or 'hnull' for size.\n", as.character(type)))
numGroups <- length(group.Nrs)
# Create the parameters for every group
groupParameter <- vector("list", numGroups)
for (i in 1:numGroups){
if(tolower(type) == "ha"){
numTaxa <- ncol(group.pi)
tempPi <- group.pi[i,]
}else{
numTaxa <- length(pi0)
tempPi <- pi0
}
groupParameter[[i]] <- list(pi=tempPi, theta=group.theta[i], nrs=group.Nrs[[i]])
}
# Get all the Xmcupo values
XmcupoStatVector <- rep(0, numMC)
for(i in 1:numMC)
XmcupoStatVector[i] <- Xmcupo.statistics.Hnull.Ha(groupParameter)
# Get a reference value from the real data
qAlpha <- qchisq(p=(1-siglev), df=length(group.theta)*(numTaxa-1), ncp=0, lower.tail=TRUE)
# Calculate pvalues
pval <- (sum(XmcupoStatVector > qAlpha) + 1)/(length(XmcupoStatVector) + 1)
return(pval)
}
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