Import TCX into R using XML package

Question

I am trying to import GPS running data into R from a TCX file using the XML package. Here is a small sample of the data I have (with only 3 track points instead of ~900)

<?xml version="1.0" encoding="UTF-8"?>
<TrainingCenterDatabase xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.garmin.com/xmlschemas/TrainingCenterDatabase/v2">
<Activities>
    <Activity Sport="Running">
        <Id>2011-10-30T16:05:48Z</Id>
        <Lap StartTime="2011-10-30T16:05:48Z">
            <TotalTimeSeconds>3855.99</TotalTimeSeconds>
            <DistanceMeters>12498.8115</DistanceMeters>
            <MaximumSpeed>4.45662498</MaximumSpeed>
            <Calories>1011</Calories>
            <Intensity>Active</Intensity>
            <TriggerMethod>Manual</TriggerMethod>
            <Track>
                <Trackpoint>
                    <Time>2011-10-30T16:05:48Z</Time>
                    <Position>
                        <LatitudeDegrees>52.33613318</LatitudeDegrees>
                        <LongitudeDegrees>-1.58814317</LongitudeDegrees>
                    </Position>
                    <AltitudeMeters>77.5234375</AltitudeMeters>
                    <DistanceMeters>0.00000000</DistanceMeters>
                </Trackpoint>
                <Trackpoint>
                    <Time>2011-10-30T16:05:49Z</Time>
                    <Position>
                        <LatitudeDegrees>52.33614810</LatitudeDegrees>
                        <LongitudeDegrees>-1.58814283</LongitudeDegrees>
                    </Position>
                    <AltitudeMeters>77.5234375</AltitudeMeters>
                    <DistanceMeters>1.77584004</DistanceMeters>
                </Trackpoint>
                <Trackpoint>
                    <Time>2011-10-30T16:05:54Z</Time>
                    <Position>
                        <LatitudeDegrees>52.33627098</LatitudeDegrees>
                        <LongitudeDegrees>-1.58818323</LongitudeDegrees>
                    </Position>
                    <AltitudeMeters>76.0814209</AltitudeMeters>
                    <DistanceMeters>15.7694969</DistanceMeters>
                </Trackpoint>
            </Track>
        </Lap>
    </Activity>
</Activities>
</TrainingCenterDatabase>

And I am attempting to read the trackpoints using

doc = xmlParse("filetest.tcx")
xmlToDataFrame(nodes = getNodeSet(doc, "//Trackpoint"))

However this fails, and the result is an empty data frame. However I have found that if I remove

 xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.garmin.com/xmlschemas/TrainingCenterDatabase/v2"

from the TrainingCenterDatabase tag at the start of the file, this import runs correctly as anticipated. Ie. using the following data:

<?xml version="1.0" encoding="UTF-8"?>
<TrainingCenterDatabase>
    <Activities>
        <Activity Sport="Running">
            <Id>2011-10-30T16:05:48Z</Id>
            <Lap StartTime="2011-10-30T16:05:48Z">
                <TotalTimeSeconds>3855.99</TotalTimeSeconds>
                <DistanceMeters>12498.8115</DistanceMeters>
                <MaximumSpeed>4.45662498</MaximumSpeed>
                <Calories>1011</Calories>
                <Intensity>Active</Intensity>
                <TriggerMethod>Manual</TriggerMethod>
                <Track>
                    <Trackpoint>
                        <Time>2011-10-30T16:05:48Z</Time>
                        <Position>
                            <LatitudeDegrees>52.33613318</LatitudeDegrees>
                            <LongitudeDegrees>-1.58814317</LongitudeDegrees>
                        </Position>
                        <AltitudeMeters>77.5234375</AltitudeMeters>
                        <DistanceMeters>0.00000000</DistanceMeters>
                    </Trackpoint>
                    <Trackpoint>
                        <Time>2011-10-30T16:05:49Z</Time>
                        <Position>
                            <LatitudeDegrees>52.33614810</LatitudeDegrees>
                            <LongitudeDegrees>-1.58814283</LongitudeDegrees>
                        </Position>
                        <AltitudeMeters>77.5234375</AltitudeMeters>
                        <DistanceMeters>1.77584004</DistanceMeters>
                    </Trackpoint>
                    <Trackpoint>
                        <Time>2011-10-30T16:05:54Z</Time>
                        <Position>
                            <LatitudeDegrees>52.33627098</LatitudeDegrees>
                            <LongitudeDegrees>-1.58818323</LongitudeDegrees>
                        </Position>
                        <AltitudeMeters>76.0814209</AltitudeMeters>
                        <DistanceMeters>15.7694969</DistanceMeters>
                    </Trackpoint>
                </Track>
            </Lap>
        </Activity>
    </Activities>
</TrainingCenterDatabase>

And I get the dataframe I want: (apart from position not being split into the lat and long, but I anticipate that I should be able to deal with that, unless someone can suggest a simpler way to do this directly using XPath?)

> xmlToDataFrame(nodes = getNodeSet(doc, "//Trackpoint"))
                  Time               Position AltitudeMeters DistanceMeters
1 2011-10-30T16:05:48Z 52.33613318-1.58814317     77.5234375     0.00000000
2 2011-10-30T16:05:49Z 52.33614810-1.58814283     77.5234375     1.77584004
3 2011-10-30T16:05:54Z 52.33627098-1.58818323     76.0814209     15.7694969

Obviously I don't want to have to manually remove this from any file I want to import. Is there something I am doing wrong (with XPath perhaps?) which is preventing this from working, or is there a work around to remove the section from the XML data?

Many thanks

Answer 1

It is a namespace issue. Just do this

xmlToDataFrame(nodes <- getNodeSet(doc, "//ns:Trackpoint", "ns"))

To directly obtain position split by latitude and longitude, you could do the following

nodes <- getNodeSet(doc, "//ns:Trackpoint", "ns")
mydf  <- plyr::ldply(nodes, as.data.frame(xmlToList))
setNames(mydf, c('time', 'lat', 'long', 'alt', 'distance'))

It gives

                  time         lat        long        alt   distance
1 2011-10-30T16:05:48Z 52.33613318 -1.58814317 77.5234375 0.00000000
2 2011-10-30T16:05:49Z 52.33614810 -1.58814283 77.5234375 1.77584004
3 2011-10-30T16:05:54Z 52.33627098 -1.58818323 76.0814209 15.7694969