fromGXL-methods

Methods for GXL manipulations in package graph

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.

Keywords
methods, models
Value

fromGXL
currently returns a graphNEL when possible. This function is based on xmlEventParse with handlers defined in the function NELhandler. The dump() element of this handler should emit information on all children of nodes and edges; the asGraphNEL() element will return a graphNEL object with weights if child with name attribute "weights" is present for each edge element.
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

Note

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 as second record in the output.

Some structures in a graphNEL and some tags in GXL may not be handled at this time.

Methods

fromGXL
con = connection: returns a graphNEL based on a parsing of the GXL stream on the connection
dumpGXL
con = connection: returns an R list based on a parsing of the GXL stream on the connection
validateGXL
con = connection: checks the GXL stream against its DTD
toGXL
object = graphNEL: creates an XMLInternalDOM representing the graph in GXL

Aliases
  • fromGXL-methods
  • toGXL-methods
  • GXL
  • dumpGXL-methods
  • dumpGXL
  • fromGXL
  • gxlTreeNEL
  • NELhandler
  • toGXL
  • validateGXL
  • dumpGXL,connection-method
  • fromGXL,connection-method
  • validateGXL,connection-method
Examples
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))
Documentation reproduced from package graph, version 1.50.0, License: Artistic-2.0

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