1 / 12

Selected tools for the analysis of s patial and temporal biodiversity patterns.

Selected tools for the analysis of s patial and temporal biodiversity patterns. Michael Denslow VertNet Biodiversity Informatics Training Workshop (BITW ) June 2012. Activities. Spatial and temporal patterns of plants Macroecology Biodiversity Informatics

rollin
Download Presentation

Selected tools for the analysis of s patial and temporal biodiversity patterns.

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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!

More Related