fromGXL-methods {graph} | R Documentation

## Methods for GXL manipulations in package graph

### Description

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.

### 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 `<attr>` 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

### 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

### 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 `<!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.

### Author(s)

Vince Carey <stvjc@channing.harvard.edu>

### 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))

[Package graph version 1.58.2 Index]