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RE: AI-GEOSTATS: Plant specimen point data: call for help and/or collaboration

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  • Koukoulas, Sotirios
    Dear John, With Arcview you can do a lot of statistical analysis but you must be able to program in Avenue (for the older versions 3.x) or Visual Basic for the
    Message 1 of 2 , Jan 7, 2002
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      Dear John,
      With Arcview you can do a lot of statistical analysis but you must be able
      to
      program in Avenue (for the older versions 3.x) or Visual Basic for the new
      version 8.1. In the newest version (AV.8.1) there is a Geostatistics
      extension with tutorial and sample data. Have a look at:
      http://www.esri.com/software/arcgis/arcgisxtensions/geostatistical/index.htm
      l

      In the older versions there are some extensions developed by individuals and
      you can
      download them from the web http://gis.esri.com/arcscripts/scripts.cfm . Here
      you
      will find many other extensions for statistical analysis (correlation, point
      patterns analysis etc). Generally speaking you might need to do some
      software development (nothing major though)in order to get the best of your
      software. I have developed a link between ArcView and M.Moeur's software
      (Moeur, M., 1995. Ripley's K analysis program, U.S. Dep. of Agriculture,
      Forest Service, Intermountain Research Station, Moscow, Idaho.) in the past
      and I can send it to you if you want. The problem is that I have to dig it
      out from my backups so it will take me some time (you'll have to contact
      Melinda Moeur for the Ripley's K analysis software though).

      If you can't afford ArcView's Geostatistical extension maybe you should look
      at Linux and Grass software
      (http://www.geog.uni-hannover.de/grass/index2.html) with its geostatistics
      package (free with the source code available
      http://www.geog.uni-hannover.de/grass/statsgrass/index.html). Also worth
      looking is the Grass - R interface (ftp://reclus.nhh.no/pub/R/) "R" is a
      statistical program that can do a lot (also free with its source code
      available).

      I hope this helps a bit.
      Best Regards,
      Sotirios


      ------------------------
      Dr Sotirios Koukoulas,
      Research Scientist
      Coastal Resources Centre,
      Environmental Research Institute,
      Geography Dept. building,
      University College Cork,
      Cork, Ireland
      email: s.koukoulas@...
      <http://crc.ucc.ie/>



      -----Original Message-----
      From: Janovec, John [mailto:jjanovec@...]
      Sent: Saturday, January 05, 2002 8:01 PM
      To: 'ai-geostats@...'
      Subject: AI-GEOSTATS: Plant specimen point data: call for help and/or
      collaboration


      Dear Geostats Members:

      I am a botanist at The New York Botanical Garden. My colleagues and I study
      plants, and many of us focus on tropical plant groups. We have six million
      specimens in our collection from all over the world. The emphasis of my
      e-mail message to you today involves plants of tropical America
      (neotropics).

      Two of us here at the garden have been applying multivariate statistical
      procedures in our research to test patterns of species distribution and
      morphological variation. We use these stats to test such things as species
      boundaries, and to figure out which morphological characters are
      contributing to patterns of variation. We use both quantitative and
      qualitative data (i.e., leaf length in cm; presence/absence of leaf
      pubescence-- ordinal data-- 0/1/2).

      On the side, separate from stats, we use ArcView GIS to plot plant
      distributions onto geospatial data layers. Currently I plot specimen
      collection locality points into my ArcView projects. I then bring in
      layers, such as USGS DEMs and other environmental data from ArcAtlas and
      ArcWorld to allow more detailed visualization, presentation, and
      understanding of plant distribution patterns.

      We are now interested in bringing statistics and GIS together in order to
      statistically analyze distribution patterns of plants and display the
      results of this analysis in the GIS presentation system.

      For instance, we have a growing database for our plants. The database
      represents information collected from individual plant specimens, including
      locality, coordinates, habitat, and plant morphology.

      How can we bring regression, correlation, multivariate statistics, and more
      into our GIS work?

      Where does one run the calculations? Can we do that in ArcView? We have
      ArcView Spatial Analyst, but it seems to me that calculations are very
      simple with that extension, i.e., nothing as powerful as a statistics
      package such as SysStat or others.

      Another challenge we have is multiple specimens per locality. Imagine that
      each specimen is represented by the same 50 morphological data points
      (measurements and ordinal scores). If there are 50 specimens at one point
      (i.e., Iquitos, Peru), and each of the specimens has 50 data points, when we
      run a simple grid analysis of one morphological character (i.e., leaf
      length), the resulting grid point system represents only the specimens
      sitting 'on top'. Do you understand? This is one example of problems we
      are facing.

      Is anybody interested in a collaboration that would lead to collaborative
      grants and projects? We're thinking of setting up a model system (or using
      a system that has already been developed) to analyze distribution of our
      specific plant groups (palms, wild nutmeg trees, and Brazil nut trees--
      several thousand species in total). We would want to correlate
      morphological trends with geospatial data to better understand distribution
      patterns.

      Currently we are looking at collections from Mesoamerica (Mex and Central
      America). By simple plotting of points we are already seeing patterns that
      have never been published. There are gaps in distribution that relate to
      historical deforestation, minute and major changes in habitat, changes in
      rainfall, etc. These patterns have significant implications for
      conservation of Mesoamerican habitats and for understanding distribution of
      species, speciation patterns, and diversity patterns.

      We are botanists. That is what we do best. We are not computer experts,
      although they run the show these days in our work. If we spend all of our
      time doing the stats and the geospatial analysis, we'll never have time to
      continue generating the datasets for the plants we study. The datasets are
      built through field and herbarium (botanical museum) work. We're also
      discussing the idea of incorporating molecular data into the 'geospatial
      system', especially population genetics data, but that is another story for
      another day.

      What we need is a collaborative team. Before we can build that team, we need
      some feedback. Perhaps there are folks out there who are looking for
      additional exciting projects from the computer and geospatial side.

      If so, please contact us. We have six million specimens in the herbarium of
      The New York Botanical Garden (www.nybg.org/bsci.htm). The specimens are
      important for understanding species, for identifying species, and for
      vouchering other studies based on these collections (e.g., molecular
      analyses are vouchered by the herbarium specimen of the species being
      analyzed). What we don't see is an effort to take these specimens and make
      geospatial sense out of them.

      We are interested in setting up a model system that will include:

      1. plant specimens
      2. plant species
      3. geospatial data
      4. gis mapping
      5. geospatial analysis
      6. analysis
      7. visualization
      8. presentation through paper publication
      9. presentation through an interactive website at nybg.org

      For the plants, we have plenty of data and some preliminary products. WE
      will post some of the preliminary products to the internet this month. But,
      our preliminary products do not take into account the amazing level of
      resources and analysis that I think are available in the geospatial
      community.

      If this sounds interesting, please contact us through me at:

      John Janovec
      Institute of Systematic Botany
      The New York Botanical Garden
      Bronx, NY 10458

      tele: 718-543-8292

      e-mail: jjanovec@...

      (An e-mail contact is best to start with).

      Thank you for your time! I am anxious to see if this e-mail will help me
      generate some new contacts. I just signed up with this mailing list.

      John Janovec

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