# -----------------------------------------------------------------------------
# "A Habitat-based Perspective of Marine Biogeography in Passive and 
#  Convergent Tectonic Settings"
# Bjorn-Gustaf J. Brooks, bjorn@climatemodeling.org, August 6, 2009
# -----------------------------------------------------------------------------

To recreate our methods based on data data downloaded from the 
Paleobiology Database (www.paleodb.org), I have created a simple BASH 
script that makes calls to other scripts and common Linux utilities 
(AWK, BASH, C-shell, PSQL, SED). "build_mdiv.bash" will automatically 
generate the PostgreSQL tables, and produce our analytical results 
using IDL. If you do not have access to IDL, you can re-write our 
scripts in another language with minimal difficulty. You will also 
need access to a k-means clustering program in order to develop 
habitat types from the lithological data. The scripts were developed 
and tested under Fedora Core 6 (x86_64 release) using PostgreSQL 
version 8.1.10.

# -----------------------------------------------------------------------------
# RECREATE OUR ANALYTICAL RESULTS----------------------------------------------
Once you have extracted the compressed tar/zip file, 'cd' into 
the 'supplement' directory. If you are running Linux, PSQL, IDL, 
and have substituted your own k-means clustering routine for lines 
73-80 of build_mdiv.bash, execute the following command:

   ./build_mdiv.bash

This should take less than twenty minutes to populate your database, 
and generate our analytical results. You may want to leave the job 
running in the background on a remote machine:

   (nohup time ./build_mdiv.bash < /dev/null ) >& build_mdiv.log &

After the script is complete the results to various analyses will 
appear in the following locations:

Habitat Type Assignments........mdiv_patch

Diversity Indexes...............mdiv_meso
by Assemblage

Correlations....................Standard Out/build_mdiv.log & 
				PSQL table "mdiv_cen_corr"

# -----------------------------------------------------------------------------
# WHERE TO FIND OUR PAPER -----------------------------------------------------

    http://www.climatemodeling.org/paleo/ecosystem_drift/

# -----------------------------------------------------------------------------
# WHERE TO FIND OUR ROUTINES --------------------------------------------------

    http://www.climatemodeling.org/paleo/ecosystem_drift/supplement.tar.gz
    http://www.climatemodeling.org/paleo/ecosystem_drift/supplement.zip

# -----------------------------------------------------------------------------
# DOCUMENTATION ---------------------------------------------------------------
These methods are described in detail through our Supplementary Information
of 'Habitat and Tectonic Controls of Marine Biogeography', and: 

    http://www.climatemodeling.org/paleo/ecosystem_drift/

Enjoy!