Terrestrial invasive plant species, or non-native plant species that are successful outside their natural range, cause a multitude of problems: they have been estimated to cause $137 billion of damage each year, decrease biodiversity, deteriorate ecosystem services, decrease agricultural productivity, and can even change geomorphic processes like sedimentation and runoff. Understanding where and why terrestrial invasive plant species thrive, thus, is an important step towards controlling the economic and environmental damage that they cause. By collecting terrestrial invasive species field data with a unique method, creating a descriptive model in ArcGIS which depicts which environmental and human factors cause a high intensity infestation for six indicator species, and writing a predictive model using Python to create a surface that prioritizes areas for control, this project creates a number of outputs which can cut monitoring costs and elicit policy changes in Eau Claire County, WI.

1. Evaluating Terrestrial Invasive
Plants in Eau Claire County,
Wisconsin
David Hon
1

2. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Outline
• Introduction to Python
• Applications of Python to GIS
• Primer to the project
• Research questions
• Data
• Descriptive analysis
• Predictive analysis with Python
• Conclusions
2

3. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Introduction to Python
What is Python?
“Python is designed to be an easy-to-use,
easy-to-learn dynamic scripting language”
(Butler, 2005)
3

4. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Applications of Python to GIS
Why Python?
• Increase efficiency
• Reduce error
• Customize processes
• Create script tools
• Formalize a process
4

5. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
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!
5

6. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
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
6

7. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
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)
• 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)
7
Lodge et al, 2007

8. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Research Questions
8

9. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Other thanks to:
Matt Moris Aaron McEachern
Judy Schwarzmeier
Josh Ruttschow
Anna Mares
Jeanette Kelly
Paula Kleinjes-Neff
Sean Hartnett
9
(Hon, 2011)

10. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Region of Interest
10

11. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Reed Canary Species Used
Grass
In Analysis
Orange/Yellow Hawkweed
Leafy Spurge
Common St.
John’s Wort
Spotted Knapweed Bush
Honeysuckles
11
(Hon, 2011)

12. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Data
Understanding the Field Data (Summer 2011)
12

13. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Data: Base Layers
13

14. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Data: Invasive Species in GIS
Orange/Yellow Hawkweed Spotted Knapweed Leafy Spurge
Common St. John’s Wort Reed Canary Grass Bush Honeysuckles
14

15. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Human Environmental
Data: Controls
Factors Factors
Mixed Factors
Based on field
observations!
15

16. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Methods: GIS Data Flow for Descriptive Model
Generate
factor layers
Split species
by
infestation
Merge with intensity
points
Lines to
points
Join point
data with
factor layers
16

17. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Results
Total Number % Infestations % Infestations % Infestations
Used in % Infestations Classified as Classified as Classified as
Species Analysis (n) Classified as Rare Infrequent/Occasional Locally Abundant 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 17

18. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Results
Mean Mean Mean Mean
Distance Distance Road Distance
Mean Soil Mean from from Density from
Species Drainage Slope Cities (m) Roads (m) (m/m^2) 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
Forest Edge or
Spotted Knapweed 25.3 1.31 9054.5 361.0 0.001152 221.0 Forest Transition
Reed Canary Grass 48.2 1.29 10216.4 536.7 0.000959 277.8 Deciduous Forest
18

19. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Results
Distance from Rivers
600.00
500.00
400.00
Distance (m)
300.00
200.00 Rare
Infrequent/Occasional
100.00
Locally Abundant
Dominant
0.00
Terrestrial Invasive Species
19

20. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Results
Summary of Controls on Infestation
Species Intensity
Orange/Yellow Hawkweed Slope, distance from rivers, road density
Soil drainage, distance from rivers, distance from
Leafy Spurge roads, land cover
Soil drainage, slope, distance from rivers, distance from
Spotted Knapweed roads, distance from cities, road density, land cover
Common St. John's Wort Soil drainage, distance from cities, road density, land cover
Soil drainage, slope, distance from rivers, distance from
Bush Honeysuckles cities, road density, land cover
Soil drainage, slope, distance from rivers, distance from
Reed Canary Grass cities, road density, land cover 20

21. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
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.)
21

22. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Predictive Habitat Suitability Model
The Plan
• Use known locations of invasive species
Data 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 22

23. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Predictive Habitat Suitability Model
Mimic tool: multiclip 10.5.11
# Import arcpy module
import arcpy
import os
# Declared variables:
inFCs = arcpy.GetParameterAsText(0) #input feature classes
clip_FC = arcpy.GetParameterAsText(1) #clip feature
output_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 tool
arcpy.Clip_analysis(inFC, clip_FC, output_WS + “//" + outFC)
23

24. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Predictive Habitat Suitability Model
Pseudocode sample
If:
IP exists on LULC 1, 3, 5
Then:
LULC layer 1, 3, 5 = 1
LULC layer 2, 4, 6, 7, 8 = 0
24

25. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Predictive Habitat Suitability Model
Get Help!
25

26. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Predictive Habitat Suitability Model
Import modules
import arcpy
from arcpy import env
from arcpy.sa import *
import sys, os
import arcgisscripting
gp = arcgisscripting.create(9.3)
26

27. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Predictive Habitat Suitability Model
Define variables
invasives = arcpy.GetParameterAsText (0)
#invasive species fcs;multivalue
#variable
#definition
#comment
dfc = 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
reclassing
out_ws = arcpy.GetParameterAsText (8)
#output workspace 27

28. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Predictive Habitat Suitability Model
Execute tools
for invasive in invasives:
(filePath, fileName) = os.path.split(invasive)
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
out_inv = newFC + "_" #adds "_" to the new
features' filename
else:
out_inv = fileName + "_"
#loops through all of the invasive species
gp.addmessage("finding unique values for reclass
tables...")
freq_dfc = arcpy.Frequency_analysis(invasive, out_ws +
“//" + out_inv + "dfc", "dfrmcities2_slice"
...
28

29. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Results: Predictive Habitat Suitability Model
Eau Claire
Altoona
Fall Creek
Augusta
Fairchild
29

30. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
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?
30

31. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
Any questions?
31
(Hon, 2011)

32. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
References
Anderson, 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.
32

33. Evaluating Terrestrial Invasive Plants in Eau Claire County, Wisconsin
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.
33