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  About site: http://www.anthro.utah.edu/~rogers/abcml/

Title: Social Sciences/Archaeology/Topics/Zooarchaeology - ABCml: Analysis of Bone Counts by Maximum Likelihood Software that implements a statistical method for analysis of bone counts from archaeological or paleontological sites. Java version of the software and documentation.
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ABCml: Analysis of Bone Counts by Maximum Likelihood

ABCml: Analysis of Bone Counts by Maximum Likelihood

by Alan R. Rogers

Quick links

Launch Java version of ABCml Status of Java version of ABCmlDocumentation

Introduction

ABCml is a computer package that implements a statistical method described by Rogers, Alan R. 2000. Analysis of bone counts by maximum likelihood. Journal of Archaeological Science, 27: 111-125.The method is designed for analysis of bone counts from archaeologicalor paleontological sites. It provides estimates of the fraction ofthe assemblage that was deposited by each of several agents ofdeposition, of the intensity of density-mediated attrition, and of thenumber of animals contributing to the assemblage. It has been used inseveral other publications: Rogers, Alan R. 2000. On the value of soft bones in faunal analysis, Journal of Archaeological Science, 27(7):635-639. Rogers, Alan R. 2000. On equifinality in faunal analysis. American Antiquity, 65(4), In press. Rogers, Alan R. and Jack M. Broughton. 2000. Selective transport of animal parts by ancient hunters: A new statistical method and an application to the Emeryville Shellmound fauna, Journal of Archaeological Science, In press.

Description

Bones may be deposited in an archeological sites in many differentways. They may be washed in by water, or brought there by humans,hyenas, or other predators and scavengers. They may represent thebones that are left after a prey animal has been killed and thevaluable pieces have been carried away. Each of the mechanisms bywhich bones are introduced to the site is called an "agent ofdeposition." The goal of ABCml is to estimate the fraction of thefaunal assemblage that each such agent that has contributed. Bonecounts are affected not only by what was deposited in the site butalso by various forms of attrition. For example, bones may be gnawedbeyond recognition by carnivores or dissolved in acidic sediment.Thus, ABCml also attempts to estimate the intensity of attrition. Itturns out also to be necessary to estimate the number of animals thatwere originally deposited at the site. Thus, ABCml estimates thefollowing parameters:alpha[i]fraction of the animals in the assemblage deposited by theith agent of deposition.betathe intensity of attritionkappathe expected number of animals originally deposited in the site.To accomplish all this, ABCml requires detailed descriptions of thevarious agents of deposition, of the density of each skeletal part,and of the number of each part in a living animal.

How to get the software

The software is distributed in several ways:Java AppletThe Java version of the software can be run from your web browser.After clicking here, the ABCml programwill start. After asking you to paste data into various dialog boxes,the program will analyze your data and show you the results. Beforedoing this, you should read the documentation for the variousinput files and for the ABCml program itself.The Java version of the package is incomplete--it contains only theprogram (also called ABCml) that is used for estimating parameters.If there is sufficient demand for the Java version of this software, Iwill also translate the other parts of the package.Executable filesThese versions contain the entire distribution and are available bothfor Microsoft and Linux operating systems.C source codeThis version of the distribution must be compiled before it can beexecuted. It is covered by the Gnu Public License, whichmeans that you can use it for free and are also allowed to give itaway, but neither you nor anyone you give it to is allowed to sell it.For details about the Gnu Public License, click here.You can download the C version of the software here:C source distribution in gzipped tar (.tgz) format: click here to downloadC source distribution in zip format: click here to downloadYou can also download the C version of the software in executableform. These distributions include executable files only, so you willalso want to download the source distribution (see above) in order toget the documentation. To download the executable files, click on oneof the following:MSDOS executables in zip format:click here to downloadi386 Linux executables in gzipped tar (tgz) format:click here to download

Unpacking the archives

After downloading these files you will need to unpack them. Theprocedure depends on the type of archive you have downloaded.Unpacking archives in gzipped tar formatThis format first packages the files using tar and then compresses theresulting archive. To unpack the compressed archive, you reversethese steps. The files can be uncompressed using gunzip, the Gnudecompression program and then unpacked using any version of theprogram tar. Alternatively, you can use Gnu's version of tar, whichcollapses the two steps into a single command. Gnu's software isfreely available here.I will assume that you are unpacking both the source distribution andalso the Linux executables. If you are using gunzip with a non-Gnuversion of tar, then execute the following unix commands:gunzip abcml-0_16.tgz tar xvf abcml-0_16.targunzip abcml-0_16-linuxexe.tgztar xvf abcml-0_16-linuxexe.tarIf you have Gnu's version of tar, the commands are even simpler:tar zxvf abcml-0_16.tgztar zxvf abcml-0_16-linuxexe.tgzI have not tried either method under MSDOS, so check your manual.Unpacking archives in zip formatZip format is widely used in the PC world and is also available underunix. The MSDOS versions of the pkzip and pkunzip programs areavailable for free from the pkwareweb site.I assume that you have downloaded the source and MSDOS excecutables inzip format, and that you have the pkunzip program running. You shouldthen be able unpack the archives using the following commands from anMSDOS window:pkunzip -d abcml-0_16.zippkunzip -d abcml-0_16-msdosexe.zipThese commands work fine under Windows98, but they would fail underearlier versions that that require short file names.After unpackingAfter unpacking the archive, you will find a sub-directory calledabcml-0_16, which contains the following subdirectories:abcml-0_16/bin executable filesabcml-0_16/doc documentationabcml-0_16/src source codeabcml-0_16/hadza transport data for the Hadzaabcml-0_16/toy data for toy model (see the paper cited above)The bin directory will be empty unless you have downloaded one of theexecutable distributions. If you do have executables, change into therelevant directory and type "./abcml" (unix or linux) or just abcml(MSDOS). The program should produce an error message telling you thatyou have forgotten to provide input.The next step is to copy the executable files into one of thedirectories that your operating system looks in when it is trying tofind executable files. Alternatively, you could change your pathvariable to add the abcml bin directory into the path. (See thedocumentation for the PATH command if you are using a Microsoftoperating system. If you are using some flavor of linux or unix, lookat the man page for the shell that you use (probably bash or ksh) andfind out how to set your PATH variable.) That is all you need to doby way of installation.Next, you need to read the documentation. You can find that online(see below) or in the doc directory of your distribution.

Documentation

 

Software

that

implements

a

statistical

method

for

analysis

of

bone

counts

from

archaeological

or

paleontological

sites.

Java

version

of

the

software

and

documentation.

http://www.anthro.utah.edu/~rogers/abcml/

ABCml: Analysis of Bone Counts by Maximum Likelihood 2008 December

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Software that implements a statistical method for analysis of bone counts from archaeological or paleontological sites. Java version of the software and documentation.

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