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Advanced Tools for Biodiversity Analysis Workshop

Learn about spatial and temporal biodiversity analysis tools presented in the VertNet Biodiversity Informatics Training Workshop. Activities include macroecology, GIS, digital image processing, and data manipulation. Join to explore niche modeling, field sampling, and spatial data processing.

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Advanced Tools for Biodiversity Analysis Workshop

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  1. Selected tools for the analysis of spatial and temporal biodiversity patterns. Michael Denslow VertNetBiodiversity Informatics Training Workshop (BITW) June 2012

  2. Activities • Spatial and temporal patterns of plants • Macroecology • Biodiversity Informatics • Natural History Collections/Collecting • SERNEC • Teaching • GIS • Digital Image Processing • GeoComputation

  3. Software/Services Others… Web services…

  4. Example 1: Data Manipulation • Data combining and cleaning • Plant occurrences (plots) • Rivers – 3 • Sites – 11, 6, 6 • Years – 8, 4, 2

  5. Example 1: Data Manipulation • Issues • Different files/formats • R functions • Read files • Append site names • Combine datasets sample taxon Adun "a" "spX" "1" "a" "spY" "2" "b" "spZ" "1" "b" "spZ" "3" "b" "spW" "2" "c" "spY" "2" "c" "spZ" "1" spWspXspYspZ a 0 1 2 0 b 2 0 0 3 c 0 0 2 1

  6. Example 2: Read/Write Spatial Data • GDAL (and OGR) • Read/Write geospatial data • Supported formats • Raster > 120 • Vector > 70 • Reproject • R package • rgdal

  7. Example 2: Read/Write Spatial Data • Field sample sites • X, Y coordinates provided by colleague • rgdal used to convert to .gpx • GPS friendly format • Transfer to GPS unit • GPSBabel • Open Source • Cross platform • Command line tools

  8. Example 3: Niche Modeling • Develop potential distribution of exotic species of local concern • Field sampling • Appalachian Trail • 3 plant taxa • Student mentoring

  9. Example 3: Niche Modeling • R – dismo, rgdal, rms • Data cleaning / preparation • Presence data tables to .shp files • Generate background data • Model generation • Coefficients • ArcGIS • ESRI geodatabase for agency • Gather GIS layers • Derive surfaces (e.g., elevation to slope) • Extract values • Final model rasters

  10. Thank you!

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