Biodiversity Informatics Training Workshop June 2012 Beginner’s GIS Biodiversity Informatics Training Workshop June 2012

Outline What is GIS GIS & Map Fundamentals Spatial Data Types Data Formats Software DEMO/Exercises

Environmental Systems Research Institute (ESRI), 2007 What is GIS? GIS = Geographic Information System(s) GIS is a collection of computer hardware, software, and geographic data for capturing, managing, analyzing, and displaying all forms of geographically referenced information. Environmental Systems Research Institute (ESRI), 2007

An “image” with attribute information What is GIS? An “image” with attribute information

Tool to make complex patterns simple What is GIS? Tool to make complex patterns simple

Environment for integrating diverse data What is GIS? Environment for integrating diverse data

Overview of spatial data Artist credit Philippe Intraligi – Adobe CS5 Raster and vector data collide

Overview of spatial data

Vector data Points, lines, and polygons

Vector data Shapefiles are common vector format of GIS data Shapefiles consist of 3 main components: *.shp – main file stores geometry *.shx – index of geometry *.dbf – database of attributes

Vector data Shapefiles may also have: *.prj – plain text file of projection *.sbn and *.sbx – spatial index of features *.atx – index of attributes *.shp.xml – metadata

Raster Data Resolution e.g. 4 x 4 km

General data issue: spatial scale Spatial scale has two elements: resolution and extent Decrease in resolution Increase in extent Things to consider: Spatial scale/resolution Extent Type of spcies data: presence only or presence/absence? Resolution Extent In practice, resolution and extent tend to be inversely related

Raster Data Resolution= cell size

15 KM pixel

7.5 km per pixel

4.5 km per pixel

1 km per pixel

Raster data - interpolation

Raster data - interpolation Inverse distance weighting Kriging Polynomials Or Spline

Raster data - interpolation Polynomials Or Spline Inverse distance weighting Kriging Using linear-weighted set of samples (greater the distance, the less influence on output raster value) Good for dense sampling Statistical method that fits a function to a radius of points, assuming a spatial correlation in distance or directionality Interpolated surface do not pass through sample sites Many different types Uses a mathematical function to create a minimize overall surface curvature Sample points pass through surface Best for variables like T

Raster data - interpolation

Environmental Data: conversion to raster Weather station records (vector point data) -areas of interpolation not uniform over the world -only has had one update -working on others but is the basis for much of the downscaled future and past climate surfaces also used in this kind of modeling WorldClim Method: Hijmans et al. 2005 Interpolated raster climate surfaces (grid)

Gridded Climate Models are not just for climatologists any more… Specifically developed method for mountainous regions, areas of high complexity climatically (800m)

Prism vs. Worldclim

Prism vs. Worldclim

Raster data - remote sensing

Raster data - remote sensing Ned Horning, Center for Biodiversity and Conservation, AMNH

Raster Data Raster data - remote sensing Passive: Natural EM radiation e.g. Infrared, Aerial light photography Active: Sensor EM radiation e.g. RADAR, LIDAR

Raster Data Common formats: ESRI ASCII (.asc) ESRI Grid Geotiffs (.tif) Any raster file can be used as a GIS grid Also: MrSID netCDF BIL

Raster Data What’s in an ESRI grid? dblbnd.adf hdr.adf sta.adf vat.adf w001001.adf –> actual raster data w001001x.adf prj.adf (opt)

Vector v. Raster Tradeoffs between the 2 types of data

Vector v. Raster Tradeoffs between the 2 types of data

Software

Win Mac GNU/ Linux Unix Web GIS software Win Mac GNU/ Linux Unix Web CARIS Y N Chameleon ERDAS IMAGINE ESRI ArcGIS DIVA-GIS Winebottler GeoServer Java GeoTools GRASS via pyWPS IDRISI ILWIS JUMP GIS LandSerf Manifold System MapInfo MapServer Maptitude Oracle Spatial PostGIS Quantum GIS Smallworld ? SPRING Solaris TatukGIS TransCAD TerraView TNTmips TransModeler

ArcGIS Commercial software, but ESRI Conservation Program grants support non-profits with free licenses ArcGIS is a suite of applications: ArcMap, ArcCatalog, ArcTools Lots of extensions and interacts well with python and R stats with an extension Includes, web server, web services, online GIS, and freeware (ArcExplorer)

DIVA-GIS Free, not open source Designed for niche modeling: Bioclim, Domain

uantum GIS Open source, Functionality from plugins in C+ or python Access to GRASS and R routines

Some GIS Software Resources DIVA-GIS http://www.diva-gis.org/ Quantum GIS http://qgis.org/ Free Geography Tools http://freegeographytools.com/ GISLounge http://gislounge.com/ FreeGIS.org http://freegis.org/

Some GIS Data Resources Climate Data: http://www.worldclim.org/ http://www.prism.oregonstate.edu Global Land Cover Facility http://www.landcover.org/ EarthExplorer (US DEM, LC) http://edcsns17.cr.usgs.gov/NewEarthExplorer/ USGS Seamless Viewer http://seamless.usgs.gov/ Global Administrative Boundaries http://www.gadm.org

Scale / Environmental Variable Dependencies Pearson and Dawson 2003 Global Ecology and Biogeography