Objects must be passed as an argument or generated in the function, right?
On 24/02/2011 9:59 AM, Jk Zheng wrote:
Hi, I'm new to R, and found this code confusing. It is from the bioconductor package "RpsiXML". entryCount<- length(nodes) The "nodes" object is either the argument nor generated in the function. How can R find the "nodes" object? What am I missing here?
Functions in R are more properly called "closures". They are made up of code *and an associated environment*. Normally the environment is the one in which the function is created, e.g. the global environment for functions entered at the command line, the namespace of a package for functions there, or an evaluation frame for a function created within another one. When evaluating a closure, R sets up an evaluation frame with the closure's environment as its parent, so any variables defined in the environment are also visible. Presumably "nodes" was defined in the namespace of RpsiXML, but it's possible that parseXmlEntryNodeSet has a different environment, depending on how it has been created. (Or maybe it's a typo.) Duncan Murdoch
Thanks
Zheng Jk
parseXmlEntryNodeSet<- function(psimi25file, psimi25source, verbose=TRUE) {
psimi25Doc<- xmlTreeParse(psimi25file, useInternalNodes = TRUE)
psimi25NS<- getDefaultNamespace(psimi25Doc)
namespaces<- c(ns = psimi25NS)
entry<- getNodeSet(psimi25Doc, "/ns:entrySet/ns:entry", namespaces)
if(verbose)
statusDisplay(paste(length(entry),"Entries found\n",sep=" "))
entryCount<- length(nodes)
entryList<- list()
for(i in 1:entryCount) {
entryList[[i]]<- parseXmlEntryNode(doc=psimi25Doc, index=i,
namespaces=namespaces,
psimi25source=psimi25source,
verbose=verbose)
}
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