Selected tools for the analysis of spatial and temporal biodiversity patterns.

Michael Denslow

VertNet Biodiversity Informatics Training Workshop (BITW)

June 2012

Activities

Spatial and temporal patterns of plants Macroecology

Biodiversity Informatics Natural History Collections/Collecting SERNEC

Teaching GIS Digital Image Processing GeoComputation

Software/Services

Others…

Web services…

Example 1: Data Manipulation

Data combining and cleaning

Plant occurrences (plots) Rivers – 3 Sites – 11, 6, 6 Years – 8, 4, 2

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

Example 2: Read/Write Spatial Data

GDAL (and OGR) Read/Write geospatial data Supported formats

Raster > 120 Vector > 70

Reproject R package

rgdal

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

Example 3: Niche Modeling

Develop potential distribution of exotic species of local concern Field sampling Appalachian Trail 3 plant taxa

Student mentoring

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

Thank you!