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 clusterings
      output by mcl itself.  One reason is if you are interested in
      clusterings with overlap; early MCL iterands generally induce
      clusterings 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 1.008, 09-308            4 Nov 2009                       clm imac(1)
