Parse XML data in R

Question

I want to parse a XML file with the following structure:

<?xml version="1.0" encoding="UTF-8"?>
<TopLevel FileFormat = "Config">
    <ObjectList ObjectType = "Type1">
        <o><a>value111</a><b>value121</b><c>value131<c/></o>
        <o><a>value112</a><b>value122</b><c>value132<c/></o>
        ...
    </ObjectList>
    <ObjectList ObjectType = "Type2">
        <o><a>value21</a><b>value22</b><c>value23<c/></o>
        ...
    </ObjectList>
    <ObjectList ObjectType = "Type3">
        <o><a>value31</a><b>value32</b><c>value33<c/></o>
        ...
    </ObjectList>
    ...
    <ObjectList ObjectType = "TypeN">
        <o><a>valueN1</a><b>valueN2</b><c>valueN3<c/></o>
        ...
    </ObjectList>
</TopLevel>

I need only data from one node, e.g. 'ObjectList ObjectType = "Type3"'. It may not be the node in the 3rd position. I have to select it based on its name. Finally, the children of this node (a, b, c) should be stored in a data frame.

How can I retrieve this node?
How can I extract the child data into a data frame?

Any ideas? Thanks in advance!

Simon Urbanek · Accepted Answer · 2016-01-29 16:20:28Z

2

Use the XML package to parse the XML:

library(XML)
### load the XML
d <- xmlTreeParse("test.xml")
top <- xmlRoot(d)

use XPath to query what you need, look for all ObjectList nodes with ObjectType='Type3' attribute:

n <- getNodeSet(top, "//ObjectList[@ObjectType='Type3']")

[[1]]
<ObjectList ObjectType="Type3">
 <o>
  <a>value31</a>
  <b>value32</b>
  <c>value33</c>
 </o>
</ObjectList>

convert the structure inside the object into a matrix

m <- lapply(n, function(o)
       t(sapply(xmlChildren(o),
         function(x) xmlSApply(x, xmlValue))))

> m
[[1]]
  a         b         c        
o "value31" "value32" "value33"

You can combine all of them (i.e. if you have multiple matching ObjectList objects) into a data frame:

d <- as.data.frame(do.call("rbind", m))

> d
        a       b       c
o value31 value32 value33

answered Jan 29, 2016 at 16:20

Simon Urbanek

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1 Comment

Chris Over a year ago

This answer helped me to better understand XML parsing. Thank you!

Chris S. · Accepted Answer · 2016-01-30 00:20:31Z

0

Try xmlToDataFrame

doc <- xmlParse("test.xml")
xmlToDataFrame(doc["//ObjectList[@ObjectType='Type3']/o"])
        a       b       c
1 value31 value32 value33

answered Jan 30, 2016 at 0:20

Chris S.

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1 Comment

Chris Over a year ago

This is a really elegant way! Thank you!

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