% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/fileio.R
\name{read.paj}
\alias{read.paj}
\alias{read.paj.simplify}
\alias{switchArcDirection}
\alias{readAndVectorizeLine}
\title{Read a Pajek Project or Network File and Convert to an R 'Network' Object}
\usage{
read.paj(file, verbose = FALSE, debug = FALSE, edge.name = NULL,
  simplify = FALSE, time.format = c("pajekTiming", "networkDynamic"))
}
\arguments{
\item{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 \code{\link{getwd}}).  \code{file} can
also be a complete URL.}

\item{verbose}{logical: Should longer descriptions of the reading and
coercion process be printed out?}

\item{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.}

\item{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.}

\item{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 \code{\link{getwd}}). If
\code{specify} is TRUE the file name is the name \code{file}.}

\item{time.format}{if the network has timing information attached to
edges/vertices, how should it be processed?  \code{'pajekTiming'} will
attach the timing information unchanged in an attribute named
\code{pajek.timing}. \code{'networkDynamic'} will translate it to a spell
matrix format, attach it as an \code{'activity'} attribute and add the class
\code{'networkDynamic'} -- formating it for use by the \code{networkDynamic}
package.}
}
\value{
The structure of the object returned by \code{read.paj} depends on
the contents of the file it parses. \itemize{ \item 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).  \item 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?.  \item
if input .paj file contains additional information (like partition
information), or multiple \code{*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) }
}
\description{
Return a (list of) \code{\link{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 \code{network},
\code{statnet}, or \code{sna} for more information.
}
\details{
If the \code{*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 \code{*Vector} block will be attached as vertex attributes.

Edges or Arc weights in the \code{*Arcs} or \code{*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 \code{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 \code{*Edges} block.

If the \code{*Vertices}, \code{*Arcs} or \code{*Edges} blocks having timing
information included in the rows (indicated by '[...]' tokens), it will be
attached to the vertices with behavior determined by the \code{time.format}
option.  If the \code{'networkDynamic'} format is used, times will be
translated to \code{networkDynamic}'s spell model with the assumtion that
the original Pajek representation was indicating discrete time chunks.  For
example \code{"[5-10]"} will become the spell \code{[5,11]}, \code{"[2-*]"}
will become \code{[2,Inf]} and \code{"[7]"} will become \code{[7,8]}. See
documentation for \code{networkDynamic}'s \code{?activity.attribute} for
details.

The \code{*Arcslist}, \code{*Edgelist} and \code{*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.
}
\examples{

\dontrun{
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')
}

}
\references{
Batagelj, Vladimir and Mrvar, Andrej (2011) Pajek Reference
Manual version 2.05
\url{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"
\url{http://vlado.fmf.uni-lj.si/pub/networks/doc/ECPR/08/ECPR01.pdf}

Pajek Datasets \url{http://vlado.fmf.uni-lj.si/pub/networks/data/esna/}
}
\seealso{
\code{\link{network}}
}
\author{
Dave Schruth \email{dschruth@u.washington.edu}, Mark S. Handcock
\email{handcock@stat.washington.edu} (with additional input from Alex
Montgomery \email{ahm@reed.edu}), Skye Bender-deMoll
\email{skyebend@uw.edu}
}
\keyword{datasets}
