Evaluating Terrestrial Invasive Plant Species in Eau Claire County, WI

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Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin

David Hon

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Outline

• Introduction to Python• Applications of Python to GIS• Primer to the project• Research questions• Data• Descriptive analysis• Predictive analysis with Python• Conclusions

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Introduction to Python

What is Python?

“Python is designed to be an easy-to-use, easy-to-learn dynamic scripting language” (Butler, 2005)

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Applications of Python to GIS

Why Python?

• Increase efficiency• Reduce error• Customize processes• Create script tools• Formalize a process

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Introduction to Python

How to use Python in GIS (or at least how I did!):

• Learn Python basics• Learn Python the Hard Way, by Zed

Shaw• Plan• Psuedocode• Get help, or Help• Import modules (gp. and arcpy. important)• Define variables• Execute tools• Go crazy with comments• Make it work• Make it better• Make your tool and use it!

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Project Primer

• Document impacts of terrestrial invasive plants (aka TIPS)• Forest productivity• Biodiversity• Endangered species

• Create a scientific collection process (yes, we made it up!)

• Gather rich baseline data• Engage citizen scientists• Describe human and environmental

characteristics of TIPS• Create a basic predictive habitat

suitability model to prioritize areas for future monitoring

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Literature Review

• Terrestrial invasive plant species = TIPS• Defining TIPS• Long natural history (Maron et al, 2004)

• Many negative effects (Pimental, 2000; Chornesky et al, 2003; Hedja et al, 2009; Lodge et al, 2006; Mascaro et al, 2007; Wisconsin Department of Natural Resources, 2010)

• Humans facilitate invasions (Robbins 2004)

Lodge et al, 2007

• Invasions exist through a process (Lodge et al, 2007; Wisconsin Department of Natural Resources, 2010; Theoharides et al, 2007; Blumenthal, 2005)

• TIPS difficult to control (Anderson et al, 2003; DiTomasao et al, 2006; Kirby et al, 2000; Wisconsin Department of Natural Resources, 2010)

• Policy change best for controlling TIPS (Hauser et al, 2009; Wisconsin Department of Natural Resources, 2009; Shine and Doody, 2011)

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Research Questions


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Matt MorisOther thanks to:Aaron McEachernJudy SchwarzmeierJosh RuttschowAnna MaresJeanette KellyPaula Kleinjes-NeffSean Hartnett

(Hon, 2011)


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Region of Interest

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Species Used In Analysis

Leafy Spurge

Reed Canary Grass

Orange/Yellow Hawkweed

Common St. John’s Wort

Spotted Knapweed Bush Honeysuckles

(Hon, 2011)

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Data

Understanding the Field Data (Summer 2011)

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Data: Base Layers

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Data: Invasive Species in GIS

Orange/Yellow Hawkweed

Spotted Knapweed Leafy Spurge

Common St. John’s Wort

Reed Canary Grass Bush Honeysuckles

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Data: ControlsHuman Factors

Environmental

Factors

Mixed Factors

Based on field

observations!

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Methods: GIS Data Flow for Descriptive Model

Lines to points

Merge with points

Join point data with factor layers

Generate factor layers Split

species by infestation intensity

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Results

Species

Total Number Used in Analysis (n)

% Infestations Classified as Rare

% Infestations Classified as Infrequent/Occasional

% Infestations Classified as Locally Abundant

% Infestations Classified as Dominant

Orange and Yellow Hawkweed 729.00 13.44 52.81 33.33 0.41

Leafy Spurge 114.00 1.75 29.82 59.65 8.77

Common St. John's Wort 46.00 36.96 34.78 28.26 0.00

Bush Honeysuckles 137.00 43.80 25.55 30.66 0.00

Spotted Knapweed 412.00 20.63 30.58 41.50 7.28

Reed Canary Grass 123.00 13.01 53.66 31.71 1.63

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Results

SpeciesMean Soil Drainage

Mean Slope

Mean Distance from Cities (m)

Mean Distance from Roads (m)

Mean Road Density (m/m^2)

Mean Distance from Rivers (m) Mode Land Cover

Orange and Yellow Hawkweed 27.8 1.20 9401.4 452.3 0.001042 248.0 Coniferous Forest

Leafy Spurge 20.8 1.15 9431.3 99.0 0.001256 277.8 Coniferous Forest

Common St. John's Wort 43.0 1.85 11219.1 632.8 0.000655 230.7 Deciduous Forest

Bush Honeysuckles 40.3 1.36 5896.4 278.3 0.003204 113.1 Deciduous Forest

Spotted Knapweed 25.3 1.31 9054.5 361.0 0.001152 221.0Forest Edge or

Forest Transition

Reed Canary Grass 48.2 1.29 10216.4 536.7 0.000959 277.8 Deciduous Forest

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Orange

and Ye

llow Haw

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Leafy

Spurge

Common St. Jo

hn's Wort

Bush Honey

suckl

es

Spotted

Knapwee

d

Reed Can

ary Gras

s0.00

100.00

200.00

300.00

400.00

500.00

600.00

Distance from Rivers

RareInfrequent/OccasionalLocally AbundantDominant

Terrestrial Invasive Species

Dist

ance

(m)


Results

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Results

SpeciesSummary of Controls on Infestation

Intensity

Orange/Yellow Hawkweed Slope, distance from rivers, road density

Leafy SpurgeSoil drainage, distance from rivers, distance from roads, land cover

Spotted KnapweedSoil drainage, slope, distance from rivers, distance from roads, distance from cities, road density, land cover

Common St. John's Wort Soil drainage, distance from cities, road density, land cover

Bush HoneysucklesSoil drainage, slope, distance from rivers, distance from cities, road density, land cover

Reed Canary GrassSoil drainage, slope, distance from rivers, distance from cities, road density, land cover


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Timeline: Predictive Habitat Suitability Model

The “Hon Method”

• Learn Python basics (Sept. to Nov.)• Learn Python the Hard Way, by Zed

Shaw• Plan (Week 1 Nov.)• Psuedocode (Week 1 Nov.)• Create a simple mimic-tool (Week 2 Nov)• Get help, or Help (Week 2 Nov.)• Import modules (gp. and arcpy. important)

(Week 2 Nov – Dec)• Define variables (Week 2 Nov – Dec)• Execute tools (Week 2 Nov – Dec)• Go crazy with comments (Week 2 Nov –

Dec)• Make it work (Week 1 Dec.)• Make it better (Weeks 1-2) Dec.)• Make your tool and use it! (Week 3 Dec.)


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Predictive Habitat Suitability Model

The Plan

• Use known locations of invasive speciesData issues:• Points represent areas• Environmental and human influences

all assumed to be equal• Samples not even across landscape• Samples not stratified

• Python because of replicability• Use loops for point data• Find unique values of all factor data• Binary model (Yes/No)• Reclass by table• Add binary layers to create surface

Result – deterministic index (0-7) model of invasive species habitat


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Mimic tool: multiclip 10.5.11

# Import arcpy moduleimport arcpyimport os

# Declared variables:inFCs = arcpy.GetParameterAsText(0) #input feature classesclip_FC = arcpy.GetParameterAsText(1) #clip featureoutput_WS = arcpy.GetParameterAsText(2) #output workspace

inFCs = inFCs.split(";") #splits features into multiple features

for inFC in inFCs: (filePath, fileName) = os.path.split(inFC) dotInd = fileName.find(".") #finds the extension name e.g. .shp if dotInd <> -1: #looks at what is before the extension name newFC = fileName[0:dotInd] #declares the filename that is before the extension filename outFC = newFC + "_clip" #adds "_clip" to the new features else: outFC = fileName + "_clip"

# execute clip toolarcpy.Clip_analysis(inFC, clip_FC, output_WS + “//" + outFC)


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Pseudocode sample

If: IP exists on LULC 1, 3, 5Then: LULC layer 1, 3, 5 = 1 LULC layer 2, 4, 6, 7, 8 = 0


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Get Help!


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Import modules

import arcpyfrom arcpy import envfrom arcpy.sa import *import sys, osimport arcgisscriptinggp = arcgisscripting.create(9.3)


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Define variables invasives = arcpy.GetParameterAsText (0) #invasive species fcs;multivalue#variable#definition#commentdfc = arcpy.GetParameterAsText (1)dff = arcpy.GetParameterAsText (2)dfr = arcpy.GetParameterAsText (3)DI = arcpy.GetParameterAsText (4)slp = arcpy.GetParameterAsText (5)rdn = arcpy.GetParameterAsText (6)rlu = arcpy.GetParameterAsText (7)#inraster1-7 are the factors used for reclassingout_ws = arcpy.GetParameterAsText (8) #output workspace


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Execute tools

for invasive in invasives:(filePath, fileName) = os.path.split(invasive)dotInd = fileName.find(".") #finds the extension name

e.g. .shpif dotInd <> -1: #looks at what is before the

extension namenewFC = fileName[0:dotInd] #declares the

filename that is before the extension filenameout_inv = newFC + "_" #adds "_" to the new

features' filenameelse:

out_inv = fileName + "_"

#loops through all of the invasive speciesgp.addmessage("finding unique values for reclass

tables...")freq_dfc = arcpy.Frequency_analysis(invasive, out_ws

+ “//" + out_inv + "dfc", "dfrmcities2_slice"...


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Results: Predictive Habitat Suitability Model

Altoona

Fall Creek

Augusta

Fairchild

Eau Claire

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Conclusions

• Disconnect between citizens, scientists, policymakers, and foresters

• Leafy spurge• Improvements for next time• Python and predictive modeling for other projects

• Location analysis• Hazard mapping• Population growth• Urbanization• What else?

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Any questions?

(Hon, 2011)

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ReferencesAnderson, G. L., E. S. Delfosse, N. R. Spencer, C. W. Prosser, and R. D. Richard. 2003. Lessons in Developing Successful Invasive Weed Control Programs. Journal of Range Management 56 (1):2-12.Blumenthal, Dana. 2005. Interrelated Causes of Plant Invasion. Science 310 (5746):243-244.Bonnet, Alastair. 2008. What is Geography? 2455 Teller Road, Thousand Oaks, California: Sage Publications Inc.Butler, Howard. 2005. A guide to the Python universe for ESRI users. ArcUser Apr-May 2005.CareerOneStop, “Geospatial Technology Competency Model,” CareerOneStop,

http://www.careeronestop.org/CompetencyModel/blockModel.aspx?tier_id=2&block_id=696&GEO=Y (accessed 9/28/11).Chornesky, Elizabeth A., and John M. Randall. 2003. The Threat of Invasive Alien Species to Biological Diversity: Setting a Future Course. Annals of the Missouri Botanical Garden 90 (1):67-76.Ditomaso, Joseph M., Matthew L. Brooks, Edith B. Allen, Ralph Minnich, Peter M. Rice, and Guy B. Kyser. 2006. Control of Invasive Weeds with Prescribed Burning. Weed Technology 20 (2):535-548.Hauser, Cindy E., and Michael A. McCarthy. 2009. Streamlining ‘search and destroy’: cost-effective surveillance for invasive species management: Wiley-Blackwell.Hawaii Geographic Alliance, “Geography for Life National Geography Standards 1994,” Hawaii Geographic Alliance, http://www.hawaii.edu/hga/Standard/Standard.html (accessed 9/28/11).Hejda, Martin, Petr Pyšek, and Vojtěch Jarošík. 2009. Impact of invasive plants on the species richness, diversity and composition of invaded communities. Journal of Ecology 97 (3):393-403.Henery, Martin L., Gillianne Bowman, Patrik Mráz, Urs A. Treier, Emilie Gex-Fabry, Urs Schaffner, and Heinz Müller-Schärer. 2010. Evidence for a combination of pre-adapted traits and rapid adaptive change in the invasive plant Centaurea stoebe. Journal of Ecology 98 (4):800-813.Jackson, Peter. 2006. Thinking Geographically. Geography 91(3): 199-204. Kirby, Donald R., Robert B. Carlson, Kelly D. Krabbenhoft, Donald Mundal, and Matt M. Kirby. 2000. Biological Control of Leafy Spurge with Introduced Flea Beetles (Aphthona spp.). Journal of Range Management 53 (3):305-308.Lewis, Peirce. December 1985. Beyond Description. Annals of the Association of American Geographers 75(4): 465-478.

http://www.careeronestop.org/CompetencyModel/blockModel.aspx?tier_id=2&block_id=696&GEO=Y

http://www.careeronestop.org/CompetencyModel/blockModel.aspx?tier_id=2&block_id=696&GEO=Y

http://www.hawaii.edu/hga/Standard/Standard.html

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References

Lodge, David M., Susan Williams, Hugh J. MacIsaac, Keith R. Hayes, Brian Leung, Sarah Reichard, Richard N. Mack, Peter B. Moyle, Maggie Smith, David A. Andow, James T. Carlton, and Anthony McMichael. 2006. Biological Invasions: Recommendations for U.S. Policy and Management. Ecological Applications 16 (6):2035-2054.Maron, John L., Montserrat Vilà, Riccardo Bommarco, Sarah Elmendorf, and Paul Beardsley. 2004. Rapid Evolution of an Invasive Plant. Ecological Monographs 74 (2):261-280.Mascaro, Joseph, and Stefan A. Schnitzer. 2007. Rhamnus cathartica L. (Common Buckthorn) as an Ecosystem Dominant in Southern Wisconsin Forests. Northeastern Naturalist 14 (3):387-402.Pattison, William D. Late Summer 1990. The Four Traditions of Geography. Journal of Geography . September/October 1990: 202-206.Pimentel, David, Lori Lach, Rodolfo Zuniga, and Doug Morrison. 2000. Environmental and Economic Costs of Nonindigenous Species in the United States. BioScience 50 (1):53.Robbins, Paul. 2004. Comparing Invasive Networks: Cultural and Political Biographies of Invasive Species. Geographical Review 94 (2):139-156.Shine, Richard and Doody, J Sean. 2011. Invasive species control: understanding conflicts between researchers and the general community. Frontiers in ecology and the environment 9 (7):400-406.Solem, M., Chueng, I., and Schlemper, B.M. 2008. Skills in Professional Geography: An Assessment

of Workforce Needs and Expectations. The Professional Geographer 60(3): 356-373.Theoharides, Kathleen A., and Jeffrey S. Dukes. 2007. Plant invasion across space and time: factors affecting nonindigenous (accessed October 11th 2011).Wisconsin Department of Natural Resources.. 2011. Invasive Species. 2010. Available from http://dnspecies success during four stages of invasion. New Phytologist 176 (2):256-273.Wisconsin Department of Natural Resources. 2009. Wisconsin's Forestry Best Management Practices for Invasive Species. http://dnr.wi.gov/invasives/species.asp?filterBy=Terrestrial&filterVal=Y r.wi.gov/invasives/species.asp?filterBy=Terrestrial&filterVal=Y (accessed October 11th 2011).Zelinsky, Wilber. 2001. The Geographer as Voyeur. Geographical Review 91(1/2): 1-8.

http://dnr.wi.gov/invasives/species.asp?filterBy=Terrestrial&filterVal=Y







