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mcxclcf(1) [debian man page]

mcx clcf(1)							  USER COMMANDS 						       mcx clcf(1)

  NAME
      mcx clcf - compute the clustering coefficient of a graph

  SYNOPSIS
      mcx clcf [options] [matrix-file]

      mcxclcf  is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode clcf.
      The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described  in  the  mcx  manual
      page.

      mcx clcf [-abc <fname> (specify label input)] [-imx <fname> (specify matrix input)] [-tab <fname> (use tab file)] [-o <fname> (write to this
      file)] [-t <int> (use <int> threads)] [-J <intJ> (a total of <intJ> jobs are used)] [-j <intj>  (this  job  has  index  <intj>)]	[--summary
      (return mean clustering coefficient)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)]

  DESCRIPTION
      mcx clcf computes the clustering coefficient of a graph.

      The  input  graph/matrix,  if specified with the -imx option, has to be in mcl matrix/graph format. You can use label input instead by using
      the -abc option.	Refer to mcxio(5) for a description of these two input formats.  By default mcx diameter  reads  from  STDIN  and  expects
      matrix format.  To specify label input from STDIN use -abc -.

  OPTIONS
      -abc <fname> (label input)
	The file name for input that is in label format.

      -imx <fname> (input matrix)
	The file name for input. STDIN is assumed if not specified.

      -o <fname> (output file)
	The file name for output. STDOUT is the default output stream.

      -tab <fname> (use tab file)
	This  option causes the output to be printed with the labels found in the tab file.  With -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 -imx the tab domain and the matrix domain  are
	required to be identical.

      --summary (return mean clustering coefficient)
	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.

      -t <int> (use <int> threads)
      -J <intJ> (a total of <intJ> jobs are used)
      -j <intj> (this job has index <intj>)
	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. Conceptually, each job takes a number of threads from
	the total thread pool. If job control is used (the -J option is used) then the number of jobs should not exceed  the  number  of  threads.
	The  total number of threads divided by the total number of jobs defines the number of threads that will be used by the current job. Addi-
	tionally, the number of threads specified signifies the total added amount of all threads across all machines and must be the same for all
	jobs.  This  number is used by each job to infer its own set of tasks. The following set of options, if given to as many commands, defines
	three jobs, each running four threads.

	-t 12 -G 3 -g 0
	-t 12 -G 3 -g 1
	-t 12 -G 3 -g 2

  SEE ALSO
      mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  mcx clcf 12-068						      8 Mar 2012							 mcx clcf(1)

Check Out this Related Man Page

clm residue(1)							  USER COMMANDS 						    clm residue(1)

  NAME
      clm residue - extend clustering of subgraph to clustering of graph.

      clmresidue  is  not  in  actual fact a program. This manual page documents the behaviour and options of the clm program when invoked in mode
      residue. The options -h, --apropos, --version, -set, --nop are accessible in all clm modes. They are described in the clm manual page.

  SYNOPSIS
      clm residue -icl fname (input clustering) -imx fname (input graph) [-rpm fname (residue projection matrix)]  [-o	fname  (output	clustering
      file)]

  DESCRIPTION
      The cluster file presumably contains a clustering of a subgraph of the graph G contained by the matrix file, implying that the row domain of
      that clustering is a subset of the node domain of the graph. clm residue will compute  a	simple	upwards  projection  of  that  clustering,
      resulting in a clustering of G.

  OPTIONS
      -imx fname (input graph)

      -icl fname (input clustering)

      -rpm fname (residue projection matrix)
	The name for the file in which the residue projection matrix is stored.  It contains for each node and for each cluster in the input clus-
	tering the combined weight of the (edges to the) neighbours of that node in that cluster.  The default output file name is out.rpm.

      -o fname (output clustering file)
	The name for the file in which the majority vote projection clustering is stored. Aka the majority vote projection clustering storage file
	name.

	This  embodies	a very crude approach to distributing the missing nodes in the input clustering onto that same cluster. For each node, the
	cluster is taken for which the residue projection is the largest (see above). The residue (i.e. the set of  missing  nodes)  is  initially
	viewed	as  a  cluster;  the set of nodes for which the projection is largest for the residue itself will form a new cluster, if it is not
	empty.

	By default output is sent to STDOUT.

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  clm residue 12-068						      8 Mar 2012						      clm residue(1)
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