Working with XML nodes in "R"

Question

Given the following XML file:

<XML>
  <A>
    <B>
      <ID>1</ID>
    </B>
    <C>
      <D>10</D>
      <D>20</D>
    </C>
  </A>
  <A>
    <B>
      <ID>2</ID>
    </B>
    <C>
      <D>30</D>
      <D>50</D>
    </C>
  </A>
</XML>

With the following R code I can read in the XML file:

library(XML)
xmlobj <- xmlTreeParse("my_file.xml", useInternalNodes = TRUE)

First, I would like to get a list of the XML nodes "A". I can do this with

node_a <- xpathSApply(doc = xmlobj, path = "//A", xmlChildren)

and the result (node_a) looks like this:

  [,1] [,2]
B ?    ?   
C ?    ?

In a second step I would like to call a function on each of the XML Nodes in the list extracted in step1 returning a list of XML Nodes "D". I tried to get the children of "C" for the first "A" element in the list from step one:

xmlChildren(asXMLNode(node_a["C",1]))

But the result is:

named list()
attr(,"class")
[1] "XMLNodeList"

Finally, I would like to have the values of D separately for each A (one list of D values for A with ID 1 and one list of D values for A with ID 2).

Or in other words, I want to get a list with the values of all D elements which are part of element A with ID 1 and another list with the values of all D elements which are part of element A with ID 2.

jlhoward · Accepted Answer · 2014-11-28 21:24:45Z

1

Calling the xml text at the beginning of your question xmlText,

library(XML)
xml <- xmlParse(xmlText,asText=T)
lapply(xml["//A//C"],function(node)sapply(xmlElementsByTagName(node,"D"),xmlValue))
# [[1]]
#    D    D 
# "10" "20" 
#
# [[2]]
#    D    D 
# "30" "50"

If you want integers instead of character and you don't want the names,

get.D <- function(node) unname(sapply(xmlElementsByTagName(node,"D"),function(n)as.integer(xmlValue(n))))
lapply(xml["//A//C"],get.D)
# [[1]]
# [1] 10 20
#
# [[2]]
# [1] 30 50

edited Nov 28, 2014 at 21:24

answered Nov 28, 2014 at 21:16

jlhoward

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1 Comment

user1377963 Over a year ago

Thanks a lot, that looks very nice! Maybe it's a stupid question but could you also tell me how to get the XML text from the xml file to the variable "xmlText"?

lawyeR · Accepted Answer · 2014-11-28 13:30:06Z

1

I'm not sure of the intermediate steps you want, but to get the values of D,

node_a <- xpathSApply(doc = xmlobj, path = "//D", xmlValue, trim = TRUE)

> node_a
[1] "10" "20" "30" "50"

answered Nov 28, 2014 at 13:30

lawyeR

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2 Comments

user1377963 Over a year ago

The problem is that I want the values for D splitted by the A in which they are contained. For example, I only want to have the values of D for the first or the second A element (with ID 1 or with ID 2). So I tried the following: node_a <- xpathSApply(doc = xmlobj, path = "//A", xmlChildren) node_c <- xpathSApply(doc = node_a[[1]], path = "//C", xmlChildren) But it doesn't matter if doc=node_a[[1]] or doc=xmlobj. How can I excecute xpathSApply only on a subnode?

Chris S. Over a year ago

Use getNodeSet to return subnodes, then apply functions like sapply(getNodeSet(xmlobj, "//A"), xpathSApply, ".//D", xmlValue)

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