Read a Pajek Project or Network File and Convert to an R 'Network' Object
Return a (list of) network object(s) after reading a
corresponding .net or .paj file. The code accepts ragged array edgelists,
but cannot currently handle 2-mode, multirelational (e.g. KEDS), or networks
with entries for both edges and arcs (e.g. GD-a99m). See network,
statnet, or sna for more information.
read.paj(file, verbose = FALSE, debug = FALSE, edge.name = NULL,
simplify = FALSE, time.format = c("pajekTiming", "networkDynamic"))file |
the name of the file whence the data are to be read. If it does
not contain an absolute path, the file name is relative to the current
working directory (as returned by |
verbose |
logical: Should longer descriptions of the reading and coercion process be printed out? |
debug |
logical: Should very detailed descriptions of the reading and coercion process be printed out? This is typically used to debug the reading of files that are corrupted on coercion. |
edge.name |
optional name for the edge variable read from the file. The default is to use the value in the project file if found. |
simplify |
Should the returned network be simplified as much as
possible and saved? The values specifies the name of the file which the data
are to be stored. If it does not contain an absolute path, the file name is
relative to the current working directory (see |
time.format |
if the network has timing information attached to
edges/vertices, how should it be processed? |
If the *Vertices block includes the optional graphic attributes
(coordinates, shape, size, etc.) they will be read attached to the network
as vertex attributes but values will not be interperted (i.e. Pajek's color
names will not be translated to R color names). Vertex attributes included
in a *Vector block will be attached as vertex attributes.
Edges or Arc weights in the *Arcs or *Edges block are include
in the network as an attribute with the same name as the network. If no
weight is included, a default weight of 1 is used. Optional graphic
attributes or labels will be attached as edge attributes.
If the file contains an empty Arcs block, an undirected network will
be returned. Otherwise the network will be directed, with two edges (one in
each direction) added for every row in the *Edges block.
If the *Vertices, *Arcs or *Edges blocks having timing
information included in the rows (indicated by '[...]' tokens), it will be
attached to the vertices with behavior determined by the time.format
option. If the 'networkDynamic' format is used, times will be
translated to networkDynamic's spell model with the assumtion that
the original Pajek representation was indicating discrete time chunks. For
example "[5-10]" will become the spell [5,11], "[2-*]"
will become [2,Inf] and "[7]" will become [7,8]. See
documentation for networkDynamic's ?activity.attribute for
details.
The *Arcslist, *Edgelist and *Events blocks are not yet
supported.
As there is no known single complete specification for the file format, parsing behavior has been infered from references and examples below.
The structure of the object returned by read.paj depends on
the contents of the file it parses.
if input file contains information about a single 'network' object (i.e .net input file) a single network object is returned with attribute data set appropriately if possible. or a list of networks (for .paj input).
if input file contains multiple sets of relations for a single network, a list of network objects ('network.series') is returned, along with a formula object?.
if input .paj file contains additional information (like partition
information), or multiple *Network definitions a two element list is
returned. The first element is a list of all the network objects created,
and the second is a list of partitions, etc. (how are these matched up)
Dave Schruth dschruth@u.washington.edu, Mark S. Handcock handcock@stat.washington.edu (with additional input from Alex Montgomery ahm@reed.edu), Skye Bender-deMoll skyebend@uw.edu
Batagelj, Vladimir and Mrvar, Andrej (2011) Pajek Reference Manual version 2.05 http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/pajekman.pdf Section 5.3 pp 73-79
Batageli, Vladimir (2008) "Network Analysis Description of Networks" http://vlado.fmf.uni-lj.si/pub/networks/doc/ECPR/08/ECPR01.pdf
Pajek Datasets http://vlado.fmf.uni-lj.si/pub/networks/data/esna/
## Not run:
require(network)
par(mfrow=c(2,2))
test.net.1 <- read.paj("http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net")
plot(test.net.1,main=test.net.1%n%'title')
test.net.2 <- read.paj("http://vlado.fmf.uni-lj.si/pub/networks/data/mix/USAir97.net")
# plot using coordinates from the file in the file
plot(test.net.2,main=test.net.2%n%'title',
coord=cbind(test.net.2%v%'x',
test.net.2%v%'y'),
jitter=FALSE)
# read .paj project file
# notice output has $networks and $partitions
read.paj('https://vlado.fmf.uni-lj.si/vlado/podstat/AO/net/Tina.paj')
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.