[R] Need help extracting info from XML file using XML package

Duncan Temple Lang duncan at wald.ucdavis.edu
Mon Mar 2 14:14:05 CET 2009

Wacek Kusnierczyk wrote:
> Don MacQueen wrote:
>> I have an XML file that has within it the coordinates of some polygons
>> that I would like to extract and use in R. The polygons are nested
>> rather deeply. For example, I found by trial and error that I can
>> extract the coordinates of one of them using functions from the XML
>> package:
>>   doc <- xmlInternalTreeParse('doc.kml')
>>   docroot <- xmlRoot(doc)
>>   pgon <-    
> try
>     lapply(
>        xpathSApply(doc, '//Polygon',
>           xpathSApply, '//coordinates', function(node)
>               strsplit(xmlValue(node), split=',|\\s+')),
>        as.numeric)

Just for the record, I the xpath expression in the
second xpathSApply would need to be
to start searching from the previously matched Polygon node.
Otherwise, the search starts from the top of the document again.

However, it would seem that

   xpathSApply(doc, "//Polygon//coordinates",
                 function(node) strsplit(.....))

would be more direct, i.e. fetch the coordinates nodes in single
XPath expression.


> which should find all polygon nodes, extract the coordinates node for
> each polygon separately, split the coordinates string by comma and
> convert to a numeric vector, and then report a list of such vectors, one
> vector per polygon.
> i've tried it on some dummy data made up from your example below.  the
> xpath patterns may need to be adjusted, depending on the actual
> structure of your xml file, as may the strsplit pattern.
> vQ
>> but this is hardly general!
>> I'm hoping there is some relatively straightforward way to use
>> functions from the XML package to recursively descend the structure
>> and return the text strings representing the polygons into, say, a
>> list with as many elements as there are polygons. I've been looking at
>> several XML documentation files downloaded from
>> http://www.omegahat.org/RSXML/ , but since my understanding of XML is
>> weak at best, I'm having trouble.  I can deal with converting the text
>> strings to an R object suitable for plotting etc.
>> Here's a look at the structure of this file
>> graphics[5]% grep Polygon doc.kml
>>         <Polygon id="15342">
>>         </Polygon>
>>         <Polygon id="1073">
>>         </Polygon>
>>         <Polygon id="16508">
>>         </Polygon>
>>         <Polygon id="18665">
>>         </Polygon>
>>         <Polygon id="32903">
>>         </Polygon>
>>         <Polygon id="5232">
>>         </Polygon>
>> And each of the <Polygon> </Polygon> pairs has <coordinates> as per
>> this example:
>>     <Polygon id="15342">
>>         <outerBoundaryIs>
>>             <LinearRing id="11467">
>>                 <coordinates>
>> -23.679835352296,30.263840290388,5.000000000000001
>> -23.68138782285701,30.264740875186,5.000000000000001
>>    [snip]
>> -23.679835352296,30.263840290388,5.000000000000001
>> -23.679835352296,30.263840290388,5.000000000000001 </coordinates>
>>             </LinearRing>
>>         </outerBoundaryIs>
>>     </Polygon>
>> Thanks!
>> -Don
>> p.s.
>> There is a lot of other stuff in this file, i.e, some points, and
>> attributes of the points such as color, as well as a legend describing
>> what the polygons mean, but I can get by without all that stuff, at
>> least for now.
>> Note also that readOGR() would in principle work, but the underlying
>> OGR libraries have some limitations that this file exceeds. Per info
>> at http://www.gdal.org/ogr/drv_kml.html.
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