Selected tools for the analysis of s patial and temporal biodiversity patterns.
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Transcript of Selected tools for the analysis of s patial and temporal biodiversity patterns.
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Selected tools for the analysis of spatial and temporal biodiversity patterns.
Michael Denslow
VertNet Biodiversity Informatics Training Workshop (BITW)
June 2012
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Activities
Spatial and temporal patterns of plants Macroecology
Biodiversity Informatics Natural History Collections/Collecting SERNEC
Teaching GIS Digital Image Processing GeoComputation
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Software/Services
Others…
Web services…
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Example 1: Data Manipulation
Data combining and cleaning
Plant occurrences (plots) Rivers – 3 Sites – 11, 6, 6 Years – 8, 4, 2
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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"
spW spX spY spZa 0 1 2 0b 2 0 0 3c 0 0 2 1
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Example 2: Read/Write Spatial Data
GDAL (and OGR) Read/Write geospatial data Supported formats
Raster > 120 Vector > 70
Reproject R package
rgdal
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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
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Example 3: Niche Modeling
Develop potential distribution of exotic species of local concern Field sampling Appalachian Trail 3 plant taxa
Student mentoring
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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
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Thank you!