mcxalter(1) USER COMMANDS mcxalter(1)
NAME
mcxalter - various network transformations
SYNOPSIS
mcxalter [-imx <fname> (specify matrix input)] [-abc <fname> (specify label input)] [-tab <fname> (use tab file)] [-o <fname> (output)] [-tf
spec (apply tf-spec to input matrix)]
DESCRIPTION
This utility supplies various transformations of networks.
OPTIONS
-abc <fname> (label input)
The file name for input that is in label format.
-imx <fname> (input matrix)
The file name for input that is in mcl native matrix format.
-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.
-tf <tf-spec> (transform input matrix values)
Transform the input matrix values according to the syntax described in mcxio(5).
-o fname (output file)
Output file.
AUTHOR
Stijn van Dongen.
SEE ALSO
mcxio(5), mcx(1), mcxsubs(1), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
mcxalter 12-068 8 Mar 2012 mcxalter(1)
Check Out this Related Man Page
mcx ctty(1) USER COMMANDS mcx ctty(1)
NAME
mcx ctty - compute betweenness centrality for network nodes
SYNOPSIS
mcx ctty [options] [matrix-file]
mcxctty is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode ctty.
The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described in the mcx manual
page.
mcx ctty [-abc <fname> (specify label input)] [-imx <fname> (specify matrix input)] [-extent <int> (only consider paths of length at most
<int>)] [-o <fname> (output file name)] [-tab <fname> (use tab file)] [-t <int> (use <int> threads)] [-J <intJ> (a total of <intJ> jobs are
used)] [-j <intj> (this job has index <intj>)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version,
exit)]
DESCRIPTION
mcx ctty computes betweenness centrality for all nodes in a graph, using the between centrality update algorithm from [1].
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 name)
The name of the file to write output to.
-extent <int> (only consider paths of length at most <int>)
This option will lead to different results. Results will still be informative however, being representative for the local context in which
nodes reside. It does probably not make sense to use values smaller than four or five.
-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.
-t <int> (use <int> threads)
-J <intJ> (a total of <intJ> jobs are used)
-j <intj> (this job has index <intj>)
Computing centrality scores in a graph is time-intensive. If you have multiple CPUs available consider using as many threads. Addition-
ally 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. Addition-
ally, 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
REFERENCES
[1] Ulrik Brandes, A Faster Algorithm for Betweenness Centrality. Journal of Mathematical Sociology 25(2): 163-177, (2001). http://cite-
seerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.11.2024
SEE ALSO
mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
mcx ctty 12-068 8 Mar 2012 mcx ctty(1)