Nothing
GatherSynonyms <- function(MyHiers, output=c("detail", "counts")) {
MyHiers <- RemoveNAFiles(MyHiers)
output <- match.arg(output)
syns <- matrix(ncol=3, nrow=0)
colnames(syns) <- c("Taxon", "hierID", "Synonym")
SynCounts <- matrix(nrow=length(MyHiers), ncol=3)
colnames(SynCounts) <- c("Taxon", "hierID", "NumberOfSynonyms")
for(i in sequence(length(MyHiers))){
resOneFile <- OneFileHierarchy(MyHiers[i])
Taxon <- resOneFile[which(resOneFile[,6] == GetHierID(MyHiers[i])), 1]
whichSyn <- c(which(resOneFile[,3] == "Synonym"), which(resOneFile[,3] == "synonym"))
SynCounts[i,] <- c(Taxon, GetHierID(MyHiers[i]), length(whichSyn))
if(length(whichSyn) > 0) {
for(j in sequence(length(whichSyn))) {
syns <- data.frame(rbind(syns, c(Taxon, GetHierID(MyHiers[i]), resOneFile[whichSyn[j], 1])), stringsAsFactors=FALSE)
}
}
}
SynCounts <- data.frame(SynCounts, stringsAsFactors=FALSE)
SynCounts[,3] <- as.numeric(SynCounts[,3])
if(output == "detail")
return(syns)
if(output == "counts")
return(SynCounts)
}
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