File: mcxclcf.azm

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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}