[R] getNodeSet - what am I doing wrong?

[Duncan Temple Lang]

Johannes Graumann wrote:
> Thanks!
> but:
> > library(XML)
> > xmlDoc <- xmlTreeParse("http://www.unimod.org/xml/unimod_tables.xml")

You need to xmlParse() or xmlTreeParse(url, useInternalNodes = TRUE)
(which are equivalent) in order to be able to use getNodeSet().

The error you are getting is because you are using xmlTreeParse()
and the result is a tree represented in R rather than internal
C-level data structures on which getNodeSet() can operate.

xmlParse() is faster than xmlTreeParse() 
and one can use XPath to query it.

  D.

> > getNodeSet(xmlDoc,"//x:modifications_row", "x")
> Error in function (classes, fdef, mtable)  : 
>   unable to find an inherited method for function "saveXML", for signature 
> "XMLDocument"
> 
> ?
> 
> Thanks, Joh
> 
> 
> Duncan Temple Lang wrote:
> 
> > 
> > Hi Johannes
> > 
> >  This is a common issue.  The document has a default XML namespace, e.g.
> > the root node is defined as
> > 
> >  <unimod xmlns="http://www.unimod.org/xmlns/schema/unimod_tables_1"...>
> >    .....
> > 
> >  So you need to specify which namespace to match in the XPath expression
> > in getNodeSet().  The XML package  provides a "convenient" facility for
> > this. You need only specify the prefix such as "x" and that will
> > be bound to the default namespace. You need to specify this in
> > two places - where you use it in the XPath expression and
> > in the namespaces argument of getNodeSet()
> > 
> > So
> >    getNodeSet(test, "//x:modifications_row", "x")
> > 
> > gives you probably what you want.
> > 
> >  D.
> > 
> > 
> > 
> > On 8/30/10 8:02 AM, Johannes Graumann wrote:
> >> library(XML)
> >>> test <- xmlTreeParse(
> >>> "http://www.unimod.org/xml/unimod_tables.xml",useInternalNodes=TRUE)
> >>> getNodeSet(test,"//modifications_row")
> 
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-- 
"There are men who can think no deeper than a fact" - Voltaire


Duncan Temple Lang                duncan at wald.ucdavis.edu
Department of Statistics          work:  (530) 752-4782
4210 Mathematical Sciences Bldg.  fax:   (530) 752-7099
One Shields Ave.
University of California at Davis
Davis, CA 95616, USA



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