arcgis role in maxent modeling - recent proceedings · 2014-07-09 · raster, etc in the...

ArcGIS Role in Maxent Modeling Christopher Woods

Christopher.R.Woods @leidos.com Carpinteria, CA

©2014 LEIDOS. ALL RIGHTS RESERVED.

Modeling

Ñ Remember that all models are wrong; the practical question is how wrong do they have to be to not be useful − Statistician, George E. P. Box

− Empirical Model-Building and Response Surfaces

(1987)


What is Maxent

Ñ Maxent stands for ‘Maximum Entropy’ − Type of inductive modeling that uses presence only

occurrence data along with environmental variables to derive a probability of occurrence or potential suitable habitat.

Ñ Software can be downloaded from • http://www.cs.princeton.edu/~schapire/maxent/

http://www.cs.princeton.edu/%7Eschapire/maxent/


About Maxent

Ñ Runs in a separate application Ñ Inputs:

− CSV file of occurrences − ASCII Grid of Environmental Layers

Ñ Outputs: − ASCII Grid of Potential Suitable Habitat


Why use Maxent?

Ñ Limited Range or Habitat data exists for species of interest

Ñ Occurrence records available Ñ Locates ‘Potential’ Suitable Habitat Ñ Subject Matter Experts needed to ground truth results to

highlight areas needed for more focused study to determine presence or absence


Environmental Layers Used in Maxent PRISM Precipitation

PRISM Temperature

Ruggedness

Aspect

Vegetation

Distance to Water

Soils

• Example of environmental raster layers used in Maxent

• Layers are stacked upon each other within the model


Occurrence Data Used in Maxent Ñ Occurrence data (point locations) are added to the model Ñ Stored in a CSV file containing X,Y positions in the same

coordinate system as environmental layers

Species Observation


Prism Precipitation

Prism Temperature

Ruggedness

Aspect

Occurrence Data Used in Maxent

Ñ Occurrence data (point locations) are added to the model Ñ Stored in a CSV file containing X,Y positions in same

coordinate system as environmental layers Ñ Maxent uses the point occurrence data to look for

relationships within the stack of environmental layers

Species Observation

ArcGIS Role in Maxent Modeling


ArcGIS Role

Ñ Creating Snap Grid for Study Area Ñ Create Environmental Layers Ñ Align Layers to snap grid using the same projection,

pixel size and grid extent Ñ Create CSV of Occurrence Data Ñ Populate Samples with Data (optional) Ñ Convert Environmental Data to ASCII Ñ Convert Results from ASCII to Imagine/Tiff/Grid Ñ Symbolize Results on Map

Using ArcGIS to Create Environmental Layers

Using ArcGIS to Create Environmental Layers Soil, Geology, Vegetation


LANDFIRE Existing Vegetation, Geology, Soils

Ñ LANDFIRE Existing Vegetation type, currently raster dataset (30m cell size resolution) − Extract using Snap Grid

Ñ US Geology, currently a vector dataset − Convert to Raster and limit extent using the snap grid

Ñ STATSGO soils, currently a vector − SSURGO is better resolution but gaps can exist when

using it for a large area (such as a state) − Convert to raster and limit the extent using the snap grid

Using ArcGIS to Create Environmental Layers Elevation and Slope


Elevation and Slope

Ñ Extract Elevation from the National Elevation Dataset or other gridded dataset to Snap Grid

Ñ Percent Slope is calculated from the Elevation Dataset using the standard surface toolbox within the Spatial Analyst toolset. Specify Snap Grid in Environment

Using ArcGIS to Create Environmental Layers Aspect


Aspect

Ñ Aspect is calculated from the Elevation Dataset using the standard surface toolbox within the Spatial Analyst toolset. Specify Snap Grid in Environment Settings

Ñ Further steps are required to extract North/South Aspect and East/West Aspect


Northness and Eastness Variables vs. Aspect in Degrees

-1

-0.8

-0.6

-0.4

-0.2

0

0.2

0.4

0.6

0.8

1

0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360

Dire

ctio

nalit

y Sc

ore

Aspect (Degrees)

Northness

Eastness

Zar, J. H. 1999. Biostatistical Analysis. Prentice Hall, New Jersey. 663 pp. Eastness = sin ((aspect in degrees * PI)/180) Northness = cos ((aspect in degrees * PI)/180)

N E

S W


Toolbox to generate the two Aspect Layers

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Using ArcGIS to Create Environmental Layers Terrain Ruggedness


Terrain Ruggedness Calculated from Elevation

Ñ Python tool for calculating ruggedness based on paper by Sappington et al. 2007

Ñ Sappington, J.M., K.M. Longshore, and D.B. Thomson. 2007. Quantifiying Landscape Ruggedness for Animal Habitat Anaysis: A case Study Using Bighorn Sheep in the Mojave Desert. Journal of Wildlife Management. 71(5): 1419 -1426


Terrain Ruggedness calculated from Elevation

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Using ArcGIS to Create Environmental Layers Climate


Climate Datasets

Ñ PRISM (Oregon State University) Ñ Maximum Temperature Ñ Minimum Temperature Ñ Annual Precipitation Ñ 1981-2010 Normals 800m cell size Ñ Monthly 4km data Ñ Can also use a specific month or bins of months for

maximum and minimum temperature Ñ Other climate datasets available based on region such as

Climate Impacts Group (CIG), National Centers for Environmental Prediction (NCEP), etc.


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Using ArcGIS to Create Environmental Layers Distance to Water


Distance to Water

Ñ Perennial Waters (Water Bodies and Streams) converted to rasters and mosaiced to create a single layer

Ñ Euclidean Distance is used to measure distance from perennial water throughout the raster

Ñ Data Sources: State Datasets, National Hydrographic Dataset, etc.


Distance to Water Model

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Distance to Water

Using ArcGIS to Create Environmental Layers Solar Radiation


Solar Radiation Index

Ñ The Solar Radiation Index (SRI) was calculated for the Equinox, Winter Solstice and Summer Solstice following the method described by Keating et al in their paper “A Simple Solar Radiation Index for Wildlife Habitat Studies”. Journal of Wildlife Management 71 (4); 1344–1348; 2007

Ñ SRI = (mean sun-earth distance / daily sun-earth distance)2* {[sin(latitude)cos(slope) – cos(latitude)sin(slope)cos(aspect)]sin(declination) + [cos(latitude)cos(slope) + sin(latitude)sin(slope)cos(aspect)]cos(declination)cos(hour angle) + cos(declination)sin(slope)sin(aspect)sin(hour angle)}


Solar Radiation Index

Ñ Mean Sun-Earth Distance = 1 astronomical unit (au) Ñ Daily Sun-Earth Distance: Equinox = 1 au, Winter Solstice =

0.983747 au, Summer Solstice = 1.017204 au Ñ Hour Angle: All calculations are for the hour surrounding Solar

Noon. The Hour Angle during this time = 0. Ñ Latitude: “$$Ymap” command used in Raster Calculator to create a

raster with the latitude of each cell center as the cell value. Converted to radians.

Ñ Slope: Slope raster in degrees converted to radians. Ñ Aspect: 180 – Aspect raster (converts the 0-360 degree data set to a

-180-180 degree data set), converted to radians. Ñ Declination: Equinox = 0, Winter Solstice = -23.45 degrees,

Summer Solstice = 23.45 degrees, converted to radians.


Solar Radiation Index Ñ Equinox: SRI = cos(latitude)cos(slope) +

sin(latitude)sin(slope)cos(aspect)

Ñ Winter Solstice: SRI = (1/0.983747)2* {[sin(latitude)cos(slope) – cos(latitude)sin(slope)cos(aspect)] * (-0.39794863130761038954479576746719) + [cos(latitude)cos(slope) + sin(latitude)sin(slope)cos(aspect)] * (0.91740769935748826377361893702175)

Ñ Summer Solstice: SRI = (1/1.017204)2* {[sin(latitude)cos(slope) – cos(latitude)sin(slope)cos(aspect)] * (0.39794863130761038954479576746719) + [cos(latitude)cos(slope) + sin(latitude)sin(slope)cos(aspect)] * (0.91740769935748826377361893702175)

Using ArcGIS to Create Environmental Layers Conversion to ASCII Raster


Conversion to Raster

Ñ All Environmental Rasters need to be in ASCII raster format for use in the model.

Ñ All ASCII rasters need to have the same: − Extent − Cell size − Projection

Ñ Conversion to ASCII can be done from ArcToolbox Conversion toolbox

Ñ Helpful to specify the snap grid using extent, cells size, snap raster, etc in the Environment settings just to be safe

Using ArcGIS to Create Environmental Layers Extract Occurrence Data


Occurrence Data

Ñ Accuracy − Timeliness (old data, spatial recording method) − Precision (GPS, trapping records, etc.)

Ñ Relevance − road kill data or observations taken from a road (don’t

necessarily want to have roads modeled as suitable habitat


Extract Occurrence Data to CSV

Ñ Extract occurrence data in the same projection and extent as the raster environmental layers.

Ñ Needs to be in a specific structure − Name (of what is being modeled) − X (Easting) − Y (Northing) − Additional Columns with can be added for ‘Samples

with Data’


Samples with Data Ñ Used when the analysis cell size being used within Maxent is

greater than the native data. − Using 90m cell resolution when your elevation or vegetation

datasets originally were in 30m resolution Ñ The original value is extracted from the native dataset and

stored with the occurrence data in a column with the CSV file. Ñ This allows for more accuracy and prevents Maxent from

extracting the value from a more coarse dataset when the model is run

Ñ Samples with data are stored in the CSV file − Column name should match the environmental raster layer name − Must be in the same order that the environmental layers are

stacked within the Maxent model


Samples with Data

Ñ Tools such as Hawth’s Tool’s ‘Point Intersect Tool’ or Geospatial Modeling Environment’s ‘isectpntrst’ function − Allows for the processing many rasters at once.

Ñ http://www.spatialecology.com/htools/isect.php

Ñ http://www.spatialecology.com/gme/isectpntrst.htm

http://www.spatialecology.com/htools/isect.php

http://www.spatialecology.com/gme/isectpntrst.htm

Using ArcGIS to Create Environmental Layers Running Maxent


Maxent Modeled Output

Ñ The results of a Maxent model run contain values that range from 0 to 1.

Ñ Values closer to 0 have less potential suitable habitat while values closer to 1 have higher potential suitability.

Ñ A threshold is defined that determines what value between 0 to 1 is the cutoff for what is potentially suitable habitat and what is not.

Using ArcGIS to Create Environmental Layers Pitfalls


Suggestions for Minimizing Headaches

Ñ Start first by making a snap raster and use it in the environment settings.

Ñ Make sure all the rasters have the same extent, projection, alignment Ñ Error messages will occur if occurrence data doesn’t overlap study

area. Maxent will still run but will pop up an error message for each one.

Ñ Use the ArcToolbox Conversion Tool to convert ASCII grid to Raster. Make sure to choose ‘Float’ instead of the default ‘Integer’

Ñ Careful of Pyramids. Maxent data can be very pixelated so pyramiding data may give a map a different view point.

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Maxent Topics Not Able to Cover

Ñ Due to time constraints and being a GIS conference I focused on the role of ArcGIS within running Maxent modeling. I purposely glossed over the actual running of the model, validation results, replicates, defining thresholds, etc.


Acknowledgments

Ñ Scott Story: Montana Fish Wildlife and Parks Ñ Anthony Titolo: BLM Wildlife Habitat Spatial Analysis Lab Ñ Lara Juluisson: BLM Wildlife Habitat Spatial Analysis Lab

arcgis role in maxent modeling - recent proceedings · 2014-07-09 · raster, etc in the...

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