7 Nov 2008 clm imac 1.008, 08-312
clmimac - 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.
clm imac -imx <fname> [options]
clm imac -imx fname (input file) [-o fname (name/stem for output)] [-dag fname (output DAG)] [--enstrict (remove overlap)] [-sort str (size|revsize|lex|none)] [-strict num (in 0..1)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)]
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.
-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 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. | ||
--enstrict (remove overlap) | ||
Remove overlap should it be found, by allocating the nodes in overlap to the first cluster in which they were found. |
Stijn van Dongen.
mclfamily for an overview of all the documentation and the utilities in the mcl family.