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\import{mcx.zmm}
\begin{pud::man}{
{name}{mcx clcf}
{html_title}{The mcx clcf manual}
{author}{Stijn van Dongen}
{section}{1}
{synstyle}{long}
{defstyle}{long}
\man_share
}
\${html}{\"pud::man::maketoc"}
\sec{name}{NAME}
\NAME{mcx_clcf}{compute the clustering coefficient of a graph}
\sec{synopsis}{SYNOPSIS}
\par{
\mcx{clcf} [options] [matrix-file]}
\disclaim_mcx{clcf}
\par{
\mcx{clcf}
\synoptopt{-abc}{<fname>}{specify label input}
\synoptopt{-imx}{<fname>}{specify matrix input}
\synoptopt{-tab}{<fname>}{use tab file}
\synoptopt{-o}{<fname>}{write to this file}
\shared_synoptopt{-t}
\shared_synoptopt{-J}
\shared_synoptopt{-j}
\synoptopt{--summary}{return mean clustering coefficient}
\stdsynopt
}
\sec{description}{DESCRIPTION}
\par{
\mcx{clcf} computes the clustering coefficient of a graph.}
\par{
The input graph/matrix, if specified with the \genopt{-imx} option, has to
be in mcl matrix/graph format. You can use label input instead by using the
\genopt{-abc} option.
Refer to \mysib{mcxio} for a description of these two input formats.
By default \mcx{diameter} reads from STDIN \it{and expects matrix format}.
To specify label input from STDIN use \useopt{-abc}{-}.}
\sec{options}{OPTIONS}
\begin{itemize}{\mcx_itemopts}
\item{\defopt{-abc}{<fname>}{label input}}
\car{
The file name for input that is in label format.}
\item{\defopt{-imx}{<fname>}{input matrix}}
\car{
The file name for input. STDIN is assumed if not specified.}
\item{\defopt{-o}{<fname>}{output file}}
\car{
The file name for output. STDOUT is the default output stream.
}
\item{\defopt{-tab}{<fname>}{use tab file}}
\car{
This option causes the output to be printed with the labels
found in the tab file.
With \genopt{-abc} this option will, additionally, construct
a graph only on the labels found in the tab file.
If this option is used in conjunction with \genopt{-imx} the
tab domain and the matrix domain are required to be identical.
}
\item{\defopt{--summary}{return mean clustering coefficient}}
\car{
By the default a 1-column table (with row names included) is output, one row
for each node. This option causes the output of the average clustering
coefficient only.
}
\items{
{\defopt{-t}{<int>}{use <int> threads}}
{\defopt{-J}{<intJ>}{a total of <intJ> jobs are used}}
{\defopt{-j}{<intj>}{this job has index <intj>}}
}
\car{
Computing clustering coefficients is time-intensive
for large graphs. If you have multiple CPUs available consider using as
many threads. Additionally it is possible to spread the computation over
multiple jobs/machines.
These three options are described in the \sibref{clmprotocols} manual page.
The following set of options, if given to as many commands, defines three jobs, each running four threads.
}
\verbatim{-t 4 -J 3 -j 0 -o out.0
-t 4 -J 3 -j 1 -o out.1
-t 4 -J 3 -j 2 -o out.2}
\car{
The output can then be collected with
}
\verbatim{mcx collect --add-column -o out.all out.[0-2]}
\stddefopt
\end{itemize}
\sec{seealso}{SEE ALSO}
\par{
\mysib{mcxio},
and \mysib{mclfamily} for an overview of all the documentation
and the utilities in the mcl family.}
\end{pud::man}
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