pathfinder.igraph: Creating a Pathfinder network from an igraph object

In comato: Analysis of Concept Maps and Concept Landscapes

Description

pathfinder creates the Pathfinder network from a weighted graph based on pathfinder.matrix. It is a convenience method that can be called on the result of a call to landscape

Usage

## S3 method for class 'igraph'
pathfinder(data, q = 2, r = 1, threshold = 0,
  prune.edges = F, filename = "", ...)

Arguments

data	An igraph object.
q	The parameter q used in the Pathfinder algorithm. The resulting graph will be q-triangular.
r	The parameter r used in the Pathfinder algorithm for the r-metric.
threshold	A numeric value used for pruning the graph before the Pathfinder algorithm. The pruning works in conjunction with the value of prune.edges.
prune.edges	If TRUE, each entry of the weight matrix that is lower than threshold will be set to 0 and columns with a resulting sum of 0 are removed. If FALSE, only columns of the weight matrix with a sum of less than threshold will be removed.
filename	Optional. If specified, the resulting Pathfinder network will be stored in TGF format in the given file.
...	-

Value

An igraph object that represents the Pathfinder network as a weighted graph.

Examples

#Create concept maps from three random graphs
require("igraph")
g1 = set.vertex.attribute(erdos.renyi.game(5, 0.7, type="gnp"), "name", value=1:5)
g2 = set.vertex.attribute(erdos.renyi.game(5, 0.7, type="gnp"), "name", value=1:5)
g3 = set.vertex.attribute(erdos.renyi.game(5, 0.7, type="gnp"), "name", value=1:5)

#Create conceptmaps object from three conceptmap objects
simple_cms = conceptmaps(list(conceptmap(g1), conceptmap(g2), conceptmap(g3)))
pathfinder(landscape(simple_cms, result="graph", mode="undirected"))

Example output

This is package 'modeest' written by P. PONCET.
For a complete list of functions, use 'library(help = "modeest")' or 'help.start()'.

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

IGRAPH b715e4b UNW- 5 9 -- 
+ attr: name (v/c), weight (e/n)
+ edges from b715e4b (vertex names):
[1] 1--2 1--3 1--4 1--5 2--3 2--4 2--5 3--4 3--5

comato documentation built on May 2, 2019, 6:52 a.m.