R help - Feb 2011 - Objects must be passed as an argument or generated in the function, right?

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?

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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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)
>    }
>
> 	[[alternative HTML version deleted]]
>
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