Description Value Methods Note Author(s) Examples
GXL http://www.gupro.de/GXL is "an XML sublanguage designed to be a standard exchange format for graphs". This document describes tools in the graph package for importing GXL data to R and for writing graph data out as GXL.
fromGXL |
currently returns a graphNEL when possible. This
function is based on |
toGXL |
for an input of class "graphNEL", returns an object of class c("XMLInternalDOM", "XMLOutputStream"); see the example for how to convert this to a text stream encoding XML |
dumpGXL |
returns an R list with all the node, edge, and named attribute information specified in the GXL stream |
validateGXL |
returns silently (invisibly returns the parsed tree) for a DTD-compliant stream, or is otherwise very noisy |
con = connection: returns a graphNEL based on a parsing of the GXL stream on the connection
con = connection: returns an R list based on a parsing of the GXL stream on the connection
con = connection: checks the GXL stream against its DTD
object = graphNEL: creates an XMLInternalDOM representing the graph in GXL
At present, toGXL does not return a validating GXL stream
because XML package does not properly handle the dtd and namespaces
arguments to xmlTree. This is being repaired. To fix
the stream, add
<!DOCTYPE gxl SYSTEM "http://www.gupro.de/GXL/gxl-1.0.1.dtd">
as second record in the output.
Some structures in a graphNEL and some tags in GXL may not be handled at this time.
Vince Carey <stvjc@channing.harvard.edu>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | sf <- file(system.file("GXL/simpleExample.gxl", package="graph"))
show(fromGXL(sf))
print(dumpGXL(sf))
close(sf)
#validateGXL(sf)
# bad <- file(system.file("GXL/c2.gxl", package="graph"))
# here's how you can check if the GXL is well-formed, if
# you have a libxml2-based version of R XML package
#
# try( validateGXL(bad) )
#
gR <- graphNEL(nodes=letters[1:4], edgeL=list(
a=list(edges=4), b=list(edges=3), c=list(edges=c(2,1)), d=list(edges=1)),
edgemode="directed")
#
# following requires that you are using XML bound with recent libxml2
#
#an <- as.numeric
#if (an(libxmlVersion()$major)>=2 && an(libxmlVersion()$minor)>=4)
## since toGXL returns an XML object, we need to attach the XML
## package.
library("XML")
cat(saveXML(toGXL(gR)$value()))
wtd <- file(system.file("GXL/kmstEx.gxl", package="graph"))
wtdg <- fromGXL(wtd)
close(wtd)
print(edgeWeights(wtdg))
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