clmresidue(1) [debian 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)

clm imac(1)							  USER COMMANDS 						       clm imac(1)

  NAME
      clm imac - Interpret Matrices (c.q. MCL iterands output by mcl) As Clusterings.

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

  SYNOPSIS
      clm imac -imx <fname> [options]

      clm imac -imx fname (input file) [-o fname (name/stem for output)] [-dag fname (output  DAG)]  [-overlap	str  (overlap  mode)]  [-sort  str
      (size|revsize|lex|none)]	[-strict  num (in 0..1)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version,
      exit)]

  DESCRIPTION
      Use clm imac to interpret matrices (as clusterings) output by mcl using mcl's -dump ite option.

      Use clm imac only if you have a special reason; the normal usage of mcl is to do multiple runs for varying -I parameters and use	the  clus-
      terings output by mcl itself.  One reason is if you are interested in clusterings with overlap; early MCL iterands generally induce cluster-
      ings possessing overlap.	Another reason is to investigate how the cluster structure associated with the MCL process evolves over time.

  OPTIONS
      -imx fname (input file)
	The input file is presumably an MCL iterand resulting from the mcl option -dump ite.

      -strict num (in 0..1)
	Higher values (up until 1) will thin out the DAG constructed by clm imac. The default value is 0.00001, yielding the full DAG.

      -o fname (file name/stem)
	Write to file named fname.

      -dag fname (output DAG)
	Write the DAG (directed acyclic graph) constructed from the input to file. This DAG is constructed according to the  structure	associated
	with  diagonally positive semi-definite matrices as described in the PhD thesis Graph clustering by flow simulation.  Consult mclfamily(7)
	for references.

      -sort str (size|revsize|lex|none)
	Sort the clusters either by increasing size, decreasing size, lexicographically by the indices they contain, or use the clustering exactly
	as obtained from the interpretation routine.

      -overlap mode (overlap mode)
	With  mode  set  to  cut,  remove  any overlap by allocating the nodes in overlap to the first cluster in which they were found. Mode keep
	leaves overlap unchanged, and mode split results in overlapping parts excised and introduced as clusters in their own right.

  AUTHOR
      Stijn van Dongen.

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

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