Seriation

Algorithms, implementations, manuscripts, and test cases for iterative deterministic frequency seriation done by agglomeration.

These algorithms are intended to automate and extend the initial, mainly manual implementation of IDSS in Lipo (2001).

commandline:

python ./IDSS.py --inputfile=../testdata/pfg.txt --xyfile=../testdata/pfgXY.txt --largestonly=1 --mst=1 --screen=1

as a module:

import IDSSseriation= IDSS()

args={}args['inputfile'] ="../testdata/pfg.txt"args['xyfile']="../testdata/pfgXY.txt"args['largestonly']=1args['screen']=1args['mst']=1

seriation.seriate(args)

'''''

Directory Structure

• python> Contains python modules for seriation. The perl script has been entirely rewritten into python and this is the version> that we are using for most of the development.
• analysis> Contains R, mathematica, and other scripts aimed at analyzing the basic problem and trial algorithms,> before being implemented in software. Also will contain benchmarks and performance analysis of finished> software versions, to document scaling of the algorithms and optimizations.
• doc> Software documentation, installation instructions, FAQs, todo lists
• java> Main root directory for a Java library implementing the seriation algorithms, for embedding in many types of > systems. May also contain simple UI implementations (CLI, web app) to run seriations.
• manuscripts> Directories containing journal manuscripts describing the algorithm or applying it to data. Each directory> represents a separate paper and is self-contained.
• output> Directory for writing finished seriation solutions for test data sets. This provides common configuration for > software implementations and system tests.
• perl> Perl implementation of the seriation algorithm. This serves as our initial testing ground and way of trying > ideas for optimizations, and it will be useful long-term for small or "normal" data sets.
• testdata> Repository of real and idealized data sets used to test the algorithm and implementations.

Authors

Carl P. Lipo, California State University at Long BeachMark E. Madsen, University of Washington, Seattle

(1) Lipo, Carl P. 2001 Science, Style and the Study of Community Structure: An Example from the Central1317 Mississippi River Valley. British Archaeological Reports, International Series, no. 918. Oxford.

wget https://archive.org/download/github.com-clipo-Seriation_-_2015-04-07_22-44-25/clipo-Seriation_-_2015-04-07_22-44-25.bundle

 git clone clipo-Seriation_-_2015-04-07_22-44-25.bundle 

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