"Intergraph" is an R package with coercion routines for netowrk data objects. For more information, see
This is a short tutorial showing how to use functions in package "intergraph" using some example network data contained in the package.
To show the data, first load the packages.
library(intergraph)
library(network)
## network: Classes for Relational Data
## Version 1.13.0 created on 2015-08-31.
## copyright (c) 2005, Carter T. Butts, University of California-Irvine
## Mark S. Handcock, University of California -- Los Angeles
## David R. Hunter, Penn State University
## Martina Morris, University of Washington
## Skye Bender-deMoll, University of Washington
## For citation information, type citation("network").
## Type help("network-package") to get started.
library(igraph)
##
## Attaching package: 'igraph'
## The following objects are masked from 'package:network':
##
## %c%, %s%, add.edges, add.vertices, delete.edges,
## delete.vertices, get.edge.attribute, get.edges,
## get.vertex.attribute, is.bipartite, is.directed,
## list.edge.attributes, list.vertex.attributes,
## set.edge.attribute, set.vertex.attribute
## The following objects are masked from 'package:stats':
##
## decompose, spectrum
## The following object is masked from 'package:base':
##
## union
Now, these are the summaries of the "igraph" objects:
summary(exIgraph)
## IGRAPH D--- 15 11 --
## + attr: label (v/c), label (e/c)
summary(exIgraph2)
## IGRAPH U--- 15 11 --
## + attr: label (v/c), label (e/c)
These are the summaries of the "network" objects:
exNetwork
## Network attributes:
## vertices = 15
## directed = TRUE
## hyper = FALSE
## loops = FALSE
## multiple = FALSE
## bipartite = FALSE
## total edges= 11
## missing edges= 0
## non-missing edges= 11
##
## Vertex attribute names:
## label vertex.names
##
## Edge attribute names:
## label
exNetwork2
## Network attributes:
## vertices = 15
## directed = FALSE
## hyper = FALSE
## loops = FALSE
## multiple = FALSE
## bipartite = FALSE
## total edges= 11
## missing edges= 0
## non-missing edges= 11
##
## Vertex attribute names:
## label vertex.names
##
## Edge attribute names:
## label
More information is available in the Appendix.
asNetwork and asIgraphConversion of network objects between classes "network" and "igraph" can be
performed using functions asNetwork and asIgraph.
Converting "network" objects to "igraph" is done by calling function
asIgraph on a "network" object:
# check class of 'exNetwork'
class(exNetwork)
## [1] "network"
# convert to 'igraph'
g <- asIgraph(exNetwork)
# check class of the result
class(g)
## [1] "igraph"
Check if edgelists of the objects are identical
el.g <- get.edgelist(g)
el.n <- as.matrix(exNetwork, "edgelist")
identical( as.numeric(el.g), as.numeric(el.n))
## [1] TRUE
Converting "igraph" objects to "network" is done by calling function
asNetwork on an "igraph" object:
net <- asNetwork(exIgraph)
Note the warning because of a "non-standard" network attribute layout, which
is a function. Printing "network" objects does not handle non-standard
attributes very well. However, all the data and attributes are copied
correctly.
Check if edgelists of the objects are identical
el.g2 <- get.edgelist(exIgraph)
el.n2 <- as.matrix(net, "edgelist")
identical( as.numeric(el.g2), as.numeric(el.n2))
## [1] TRUE
Objects of class "igraph" and "network", apart from storing actual network data (vertexes and edges), allow for adding attributes of vertexes, edges, and attributes of the network as a whole (called "network attributes" or "graph attributes" in the nomenclatures of packages "network" and "igraph" respectively).
Vertex and edge attributes are used by "igraph" and "network" in a largely similar fashion. However, network-level attributes are used differently. Objects of class "network" use network-level attributes to store various metadata, e.g., network size, whether the network is directed, is bipartite, etc. In "igraph" this information is stored separately.
The above difference affects the way the attributes are copied when we convert "network" and "igraph" objects into one another.
Both functions asNetwork and asIgraph have an additional argument attrmap
that is used to specify how vertex, edge, and network attributes are copied.
The attrmap argument requires a data frame. Rows of that data frame specify
rules of copying/renaming different attributes. The data frame should have the
following columns (all of class "character"):
type: one of "network", "vertex" or "edge", whether the rule applies to
network, vertex or edge attribute.fromslc: name of the which we are converting fromfromattr: name of the attribute in the object we are converting fromtocls: name of the class of the object we are converting totoattr: name of the attribute in the object we are converting toThe default rules are returned by a function attrmap(), these are:
attrmap()
## type fromcls fromattr tocls toattr
## 1 network network directed igraph <NA>
## 2 network network bipartite igraph <NA>
## 3 network network loops igraph <NA>
## 4 network network mnext igraph <NA>
## 5 network network multiple igraph <NA>
## 6 network network n igraph <NA>
## 7 network network hyper igraph <NA>
## 8 vertex igraph name network vertex.names
For example, the last row specifies a rule that when an object of class
"igraph" is converted to class "network", then a vertex attribute name in the
"igraph" object will be copied to a vertex attribute called vertex.names in
the resulting object of class "network.
If the column toattr contains an NA, that means that the corresponding
attribute is not copied. For example, the first row specifies a rule that when
an object of class "network" is converted to class "igraph", then a network
attribute directed in the "network" object is not copied to the resulting
object of class "igraph".
Users can customize the rules, or add new ones, by constructing similar
data frames and supplying them through argument attrmap to functions
asIgraph and asNetwork.
As an example let us set the option to always drop the na vertex attribute. First, we need to setup the rule by adding an extra row to the data frame returned by attrmap:
new_rule <- data.frame(type="vertex", fromcls="network", fromattr="na",
tocls="igraph", toattr=NA,
stringsAsFactors=FALSE)
# combine with the default rules
rules <- rbind( attrmap(), new_rule )
rules
## type fromcls fromattr tocls toattr
## 1 network network directed igraph <NA>
## 2 network network bipartite igraph <NA>
## 3 network network loops igraph <NA>
## 4 network network mnext igraph <NA>
## 5 network network multiple igraph <NA>
## 6 network network n igraph <NA>
## 7 network network hyper igraph <NA>
## 8 vertex igraph name network vertex.names
## 9 vertex network na igraph <NA>
Now we can use it with asIgraph:
(ig1 <- asIgraph(exNetwork))
## IGRAPH D--- 15 11 --
## + attr: label (v/c), na (v/l), vertex.names (v/c), label (e/c), na
## | (e/l)
## + edges:
## [1] 2-> 1 3-> 1 4-> 1 5-> 1 6-> 7 8-> 9 10->11 11->12 14->12 12->13
## [11] 13->14
(ig2 <- asIgraph(exNetwork, amap=rules))
## IGRAPH D--- 15 11 --
## + attr: label (v/c), vertex.names (v/c), label (e/c), na (e/l)
## + edges:
## [1] 2-> 1 3-> 1 4-> 1 5-> 1 6-> 7 8-> 9 10->11 11->12 14->12 12->13
## [11] 13->14
# check if "na" was dropped
"na" %in% igraph::list.vertex.attributes(ig1)
## [1] TRUE
"na" %in% igraph::list.vertex.attributes(ig2)
## [1] FALSE
Function asDF can be used to convert network object (of class "igraph" or "network")
to a list of two data frames:
l <- asDF(exIgraph)
str(l)
## List of 2
## $ edges :'data.frame': 11 obs. of 3 variables:
## ..$ V1 : num [1:11] 2 3 4 5 6 8 10 11 12 13 ...
## ..$ V2 : num [1:11] 1 1 1 1 7 9 11 12 13 14 ...
## ..$ label: chr [1:11] "ba" "ca" "da" "ea" ...
## $ vertexes:'data.frame': 15 obs. of 2 variables:
## ..$ intergraph_id: int [1:15] 1 2 3 4 5 6 7 8 9 10 ...
## ..$ label : chr [1:15] "a" "b" "c" "d" ...
The resulting list has two components edges and vertexes. The edges component is essentially
an edge list containing ego and alter ids in the first two columns. The remaining columns store
edge attributes (if any). For our example data it is
l$edges
## V1 V2 label
## 1 2 1 ba
## 2 3 1 ca
## 3 4 1 da
## 4 5 1 ea
## 5 6 7 fg
## 6 8 9 hi
## 7 10 11 jk
## 8 11 12 kl
## 9 12 13 lm
## 10 13 14 mn
## 11 14 12 nl
The vertexes component contains data on vertexes with vertex id (the same
that is used in the first two column of edges) is stored in the first two
columns. The remaining columns store vertex attributes (if any). For our
example data it is:
l$vertexes
## intergraph_id label
## 1 1 a
## 2 2 b
## 3 3 c
## 4 4 d
## 5 5 e
## 6 6 f
## 7 7 g
## 8 8 h
## 9 9 i
## 10 10 j
## 11 11 k
## 12 12 l
## 13 13 m
## 14 14 n
## 15 15 o
Functions asNetwork and asIgraph can also be used to create network objects
from data frames such as those above. The first argument should be an edge list data frame.
Optional argument vertices expectes data frames with vertex data (just like l$vertexes).
Additionally we need to specify whether the edges should be interpreted as directed or not
through the argument directed.
For example, to create an object of class "network" from the dataframes created above from
object exIgraph we can:
z <- asNetwork(l$edges, directed=TRUE, l$vertexes)
z
## Network attributes:
## vertices = 15
## directed = TRUE
## hyper = FALSE
## loops = FALSE
## multiple = FALSE
## bipartite = FALSE
## total edges= 11
## missing edges= 0
## non-missing edges= 11
##
## Vertex attribute names:
## label vertex.names
##
## Edge attribute names:
## label
This is actually what basically happens when we call asNetwork(exIgraph)
Package intergraph contains four example networks:
exNetwork and exIgraph contain the same directed network as objects of class "network" and "igraph" respectively.exNetwork2 and exIgraph2 contain the same undirected network as objects of class "network" and "igraph" respectively.All four datasets contain:
label with vertex labels. These are letters from a to o.label with edge labels. These are pasted letters of the adjecent nodes.We will use them in the examples below.
Networks are shown below using the following code:
layout(matrix(1:4, 2, 2, byrow=TRUE))
op <- par(mar=c(1,1,2,1))
# compute layout
coords <- layout.fruchterman.reingold(exIgraph)
plot(exIgraph, main="exIgraph", layout=coords)
plot(exIgraph2, main="exIgraph2", layout=coords)
plot(exNetwork, main="exNetwork", displaylabels=TRUE, coord=coords)
plot(exNetwork2, main="exNetwork2", displaylabels=TRUE, coord=coords)
par(op)
sessionInfo()
## R Under development (unstable) (2016-12-05 r71733)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux stretch/sid
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] igraph_1.0.1 network_1.13.0 knitr_1.15.1 intergraph_2.0-2
##
## loaded via a namespace (and not attached):
## [1] compiler_3.4.0 magrittr_1.5 markdown_0.7.7 tools_3.4.0
## [5] stringi_1.1.2 highr_0.6 stringr_1.1.0 mime_0.5
## [9] evaluate_0.10