Published on March 6, 2014
Exercise 8 Assessing citizen science portals and analyzing citizen science data in invasive species In this exercise, you will have the opportunity to assess the utility of different citizen science portals and then to analyze data from citizens and government agencies on invasive species using GIS. As part of this exercise, you will use public domain spatial data from the National Atlas of the United States. Map of zebra mussel distribution and hydrology you will produce in this exercise. Exercises for The GIS Guide to Public Domain Data
Context Problem During the last forty years, invasive species have become a global concern with an increased awareness of the importance of biodiversity and how easy it is for biodiversity to become disturbed. You have been hired by the US Environmental Protection Agency (EPA) to analyze zebra mussels, Africanized honey bees, Chinese privet, tallowtree, leafy spurge, common gorse, and purple loosestrife. How and where biodiversity is affected by any phenomenon that varies in space and time—people, climate, and the invasive species themselves—lends itself to GIS-based analysis. In this exercise, you will have the opportunity to assess the source, method of movement, and dispersal of several invasive species through a framework of spatial analysis using ArcGIS for Desktop. The EPA needs you to assess specifics about the invasive species as follows: Where is the source of each of the invasive species? How do each of the invasive species move? You will also assess the quality, breadth, and depth of data on a series of different citizen science portals, as well as assess their ability to accept your own data and your ability to obtain spatial data from the portal. Where have the invasive species spread, and what is the predicted range of the invasive species in ten years? What might be the most effective strategy to deal with each of the invasive species spatially?
Skills Required Resources Downloading and formatting vector and raster spatial data from an online spatial data portal TIME This exercise contains eighty questions and will require two to four hours to complete. Understanding spatial data based on information from associated metadata files Working with a geodatabase Projecting spatial data Performing tabular and spatial sorting and querying Analyzing spatial statistics (mean center and standard deviational ellipse) Creating map layouts Solving a problem based on spatial analysis SOFTWARE ArcGIS 10.0 or later, from Esri.
Work package 1: Mapping zebra mussels with web GIS 1) Preparation Steps 1 - 4 Create a folder into which you will download, unzip, and work with your data. For this exercise, it might be helpful to establish a series of subfolders underneath your project folder, with the following names: county_boundaries_2000, federal_lands, invasives, state_boundaries, streams_waterbodies, and wilderness_preservation_areas. 2) Access the National Atlas Access the National Atlas of the United States at http://nationalatlas.gov. Select the About link. 2.1) What is the purpose of the National Atlas of the United States? 2.2) What is the history behind this particular web GIS version of the National Atlas? 2.3) Review the information on the Partners web page. How many agencies cooperate on generating and maintaining content for the National Atlas? 2.4) Which agency is responsible for serving and administering the National Atlas site? 3) Examine map layers Examine the map layers available from the National Atlas. Click the Map Layers button. 3.1) Name some of the major categories of data on this site. 3.2) In which raster and vector formats are the datasets distributed in from this site?
Work package 1: Mapping zebra mussels with web GIS 3) Examine map layers (contd.) Steps 1 - 4 3.3) Under which data categories do you find data on invasive species? 3.4) What organization created the data for the invasive species that you will examine in this activity? 4) Access the National Atlas Examine the zebra mussels map layer online. Under Biology, select the Invasive Species—Zebra Mussel distribution. Click View sample layer in Map Maker. After the map draws, scroll down on the right side and find the layer Streams and Waterbodies. Check it to make it visible. From the list Zoom to states, select Lower 48 States. Select the tab Map Key. Your map should look similar to the following: National Atlas web GIS map of zebra mussel distribution and hydrology.
Work package 1: Mapping zebra mussels with web GIS 4) Access the National Atlas (contd.) Steps 1 - 4 4.1) Describe the spatial pattern of the zebra mussel distribution in the United States. 4.2) How do you think the zebra mussel migrates? What about its spatial pattern made you think that? 4.3) How easy was it for you on the National Atlas site to create the map of zebra mussels and streams and water bodies? 4.4) What are two advantages and two disadvantages of looking at the online map versus examining the data inside a desktop GIS environment? End of work package
Work package 2: Downloading data and analysis in desktop GIS Steps 5 - 9 5) Download data With the map maker page still active in your web browser, click the Map Layers button. Then select biology, and then the blue hyperlinked text, Invasive specieszebra mussel distribution. In the new browser window that appears, (http://www.nationalatlas.gov/mld/zmusslx.html), under Raw Data Download, select the Invasive Species: Zebra Mussel Distribution link. You will be redirected to a download screen. On the download screen, locate the Zebra Mussel Distribution entry (it should be near the top of this long list of data links) and select the link zmusslsx020.tar.gz under Shapefile. The .gz portion of the extension indicates a gnu-zipped file, a special type of zipped, or archived, compressed, file. The .tar portion of the extension indicates that the file resulted from a Unix utility that combines a series of files into one tape address register file. These files can be extracted and used just like any other compressed file; they just require a few extra steps to do so. The tar file is a compressed and zipped data format. Select Save File to download the data into your zebra mussel folder underneath your project folder. Downloading Zebra Mussel data from the National Atlas website.
Work package 2: Downloading data and analysis in desktop GIS Steps 5 - 9 5) Download mussels data (contd.) Decompress (unzip) the .tar.gz file to extract your data. Examine the data in ArcCatalog. 5.1) In which spatial data format is your zebra mussels data? 5.2) Is your zebra mussels data a vector or a raster dataset? 6) Download hydrology data Download and format your streams and waterbodies data into the folder you established for this project. On the webpage showing the data layers (http://www.nationalatlas.gov/atlasftp.html#zmusslx), scroll up to the top of the page until you see the Raw Data Download by Chapter heading. Select Water, and then, on the resulting water-related data screen, scroll until you find the shapefile hydrogm020.tar.gz. Download this file. Recall our discussion in the book on the other format of streams and waterbodies offered, the Spatial Data Transfer Standard (SDTS) version. 6.1) What is SDTS? 6.2) Why might the SDTS format be more difficult to work with than the shapefile format?
Work package 2: Downloading data and analysis in desktop GIS Steps 5 - 9 7) Download other data Download the other data you will need for this project: Under Boundaries, download: Federal Lands State Boundaries County Boundaries, 2000 Wilderness Preservation System Areas Under Biology, download: 8) Create new file geodatabase Africanized honey bees Chinese Privet Common Gorse Leafy Spurge Purple Loosestrife Tallowtree Forest Cover Types Land Cover, 1 km resolution Land Cover Diversity Open ArcCatalog; navigate to the location where you will store and work with your data. Right-click the folder, select New, and create a new File Geodatabase and name it invasive_species.gdb.
Work package 2: Downloading data and analysis in desktop GIS Steps 5 - 9 9) Set up workspaces Open ArcMap. Establish your workspaces by going to the Geoprocessing menu and then select Environments > Workspace. Set the current workspace and the scratch workspace to the geodatabase that you created for this exercise, as shown next. Establishing the workspaces for the exercise. End of work package
Work package 3: Projecting and loading data 10) Check mussels layer Steps 10 - 16 In Catalog, right-click the zebra mussels layer and check > Properties > XY Coordinate System. 10.1) Does this layer have a coordinate system established? What is its coordinate system? 11) Check water feature line layer In Catalog, right-click the streams and waterbodies line layer and check > Properties > XY Coordinate System. 11.1) Does this layer have a coordinate system established? 12) Check water feature polygon layer In Catalog, right-click the streams and waterbodies polygon layer and check > Properties > XY Coordinate System. 12.1) Does this layer have a coordinate system established? Note that the situation that you encountered above, with different data layers having different projections, or no projection at all, is common with spatial data portals. Often, the GIS analyst or administrator uploading data to the portal lacks the time to fully document or project each layer. So, although there are many useful data themes available, that also means more work for you, the end user. You need to pay close attention to each data layer and any metadata available so that you can understand the nature of the data you are working with—a key skill that will serve you well in the future.
Work package 3: Projecting and loading data Steps 10 - 16 Even though the zebra mussels layer is projected, it is not in a projection that will be accurate for your analysis. Therefore, you will project all of your data into USA Contiguous Albers (since you will be largely working in the contiguous USA for your invasive species study), which is an equal area projection. The layers that are unprojected will need to have the coordinate system defined before they can be reprojected. There are two main ways to project data in ArcGIS. One is inside the System Toolbox, using the Projections and Transformations tools, and using Define Projection and Project. Note that Define Projection and Project are two very different things. If a dataset has no projection defined, Define Projection must be used. Define Projection cannot change a projection from Projection A to Projection B. That is what Project (Data) are for. If you attempt to use Define Projection to change the projection of a dataset, you will receive an error message. All datasets used in your GIS projects should have a projection defined. If a dataset has no projection, you should define one, based on the metadata or some other documentation that you may have. If you cannot determine which projection should be used, then use the Georegistration function to register your data against data in a known projection.
Work package 3: Projecting and loading data Steps 10 - 16 The other way to project data, outside the System Toolbox, is to set the Data Frame projection/coordinate system properties in ArcMap. This does not change the projection of the data, but rather, it just changes how the data appear in the Data Frame. If your data have a projection defined, they will be recast into the projection currently set for the data frame. This is known as projecting on the fly because it recasts spatial data simply by changing the data frame properties. This is a temporary re-projection because it only applies to the appearance of the data in the map document. In the steps below, you will use this method, but you will then use the Data Frame properties as the properties for setting the projection in the data themselves. This is a permanent re-projection and you will do this by exporting the data. When you export spatial data, you have the option of using the Data Frame properties projection as the new projection for your data. For additional discussion on projections and coordinate systems, see the following: A large volume of helpful information can be found in ArcGIS Help under projections, complete with graphics and videos. Another resource is the new helpful book by Maher (Esri Press) titled Lining Up Data, available from http://www.esri.com/books.
Work package 3: Projecting and loading data 13) Project mussels data Steps 10 - 16 First, in ArcMap, add your zebra mussels data. Then project the data by setting the Data Frame properties to USA Contiguous Albers Equal Area Conic (under Projected > Continental > North America). Next, right-click your zebra mussels layer and export it into your file geodatabase. Choose the Data Frame for the coordinate system, as shown next in the Export Data dialog box, because you want your final data layers to be in Albers Equal Area Conic, and not GCS North American 1983. Exporting the raw zebra mussels data to file geodatabase.
Work package 3: Projecting and loading data 14) Investigate hydrology layers metadata Steps 10 - 16 To define your undefined hydrology layers, you must determine which coordinate system is embedded in the data. In Windows Explorer, access the text file (.txt) that is associated with the hydrology lines and hydrology polygons (hydrogm020.txt) . 14.1) What does the text file say about the horizontal coordinate system? 15) Define coordinate systems Based on the information in the text file, you can now define the undefined layers beginning with hydrology lines. Define the hydrology lines layer as World, Geographic WGS 84, by right-clicking the hydrology lines in Catalog and selecting Properties > XY Coordinate System, and then Select > Geographic> World> WGS 84. Repeat the above process for the hydrology polygons, define them as WGS 84, and then add the hydrography lines and polygon layers to your data frame in ArcMap. Next, right-click the hydrography lines layer and export it into your file geodatabase by choosing the Data Frame for the coordinate system, so that your final data layers will be in Albers Equal Area Conic. Name your resulting layer hydro_lines and store it in your file geodatabase. Repeat this for your hydrography polygons name your resulting layer hydro_polys, and store it in your file geodatabase. 15.1) Do any of the following data layers have a coordinate system defined: County boundaries, federal lands, state boundaries, wilderness preservation areas, or Africanized honey bees?
Work package 3: Projecting and loading data 15) Define coordinate systems (contd.) Steps 10 - 16 Repeat the above process for these other layers: Use Catalog and define the projection for each as Geographic, World, WGS 84. Add the other layers to your ArcMap session and export them to the file geodatabase in the Albers projection of the data frame. 15.2) Do any of the following raster data layers have a coordinate system defined: forest cover types, land cover, or land cover diversity? If yes, can you add them to your ArcMap session? 16) Export raster layers Export each of your raster layers to the file geodatabase, make sure that the spatial reference is set to the Data Frame, and save the result as a raster dataset inside your file geodatabase with the names forest_types, land_cover, and land_cover_diversity, as shown next. Alternatively, you can access Catalog, navigate to the geodatabase, and import the raster layers. Name your resulting layer hydro_lines and store it in your file geodatabase. Repeat this for your hydrography polygons name your resulting layer hydro_polys, and store it in your file geodatabase.
Work package 3: Projecting and loading data Steps 10 - 16 16) Export raster layers (contd.) Exporting raster data to file geodatabase. 16.1) What are a few advantages of exporting your layers to a geodatabase? End of work package
Work package 4: Analyzing zebra mussel distribution 17) Analyze zebra mussels data Steps 17 - 28 Analyze your zebra mussels data through classification and visual assessment. Symbolize the zebra mussels as unique value by year. 17.1) Based on the data, in what lake did the zebra mussel first appear? 17.2) How would you characterize the spread of the zebra mussel? Which three lakes and which three rivers would you say were the primary means by which they spread? 18) Summarize zebra mussels data Summarize the zebra mussel data by year and create a graph for the data. 18.1) Which are the top three years when more sightings occurred than any other? 18.2) Observe the zebra mussel sighting in Colorado. In what reservoir did this sighting take place? file geodatabase. Exporting raster data to 18.3) Through which river might the zebra mussel in this reservoir have migrated? Do you think they migrated upstream or downstream? Why? 18.4) Where do you think the zebra mussel will migrate to next? Why?
Work package 4: Analyzing zebra mussel distribution 19) Research zebra mussels Steps 17 - 28 Read about zebra mussels on the following web page from the US Fish and Wildlife Service: http://www.fws.gov/midwest/endangered/clams/zebra.html. 19.1) What are the major problems that zebra mussels bring? 19.2) Does the article validate your own spatial analysis of the origin and spread of the zebra mussel? 19.3) What other means can the zebra mussel use to migrate besides the one that you identified earlier, i.e. along waterways? 20) Using mean center Analyze your zebra mussels data through an analysis of the mean center. Search for the tool called Mean Center. 20.1) What is a mean center? 21) Identify mussels in 1995 Analyze your zebra mussels data through an analysis of the mean center. Search for the tool called Mean Center. 21.1) In what state and county was the mean center for the zebra mussels in 1995? 22) Identify mussels in 2000 and 2005 Repeat the above procedures to calculate the mean center for zebra mussels in 2000, and in 2005. 22.1) How did the mean center for zebra mussels change from 1995 to 2000 to 2005? Why did it change the way it did?
Work package 4: Analyzing zebra mussel distribution 23) Using directional distribution Steps 17 - 28 Analyze your zebra mussels data through an analysis of the directional distribution (standard deviational ellipse). Search for the tool, Directional Distribution. 23.1) What is a directional distribution? 24) Calculate distribution for 1995 Use Select By Attribute to select the zebra mussels that appeared in 1995. Calculate the directional distribution for the zebra mussels in 1995. 25) Calculate distribution for 2000 and 2005 Repeat the above procedures to calculate the directional distribution for zebra mussels in 2000 and in 2005. 24.1) Describe the shape, length, and width of the directional distribution for the zebra mussels in 1995. 25.1) How did the directional distribution for zebra mussels change from 1995 to 2000 to 2005? Why did it do so? 25.2) Examine the attribute data. What would have been the problem with comparing 1988 and 2008 data to 2000 data in your mean center and directional distribution analysis? Why do you think it was better to use 1995 and 2005 as your start and end years?
Work package 4: Analyzing zebra mussel distribution 26) Analyze states Steps 17 - 28 Analyze your zebra mussels data through an analysis of the states where the invasive species was found. Right-click the zebra mussels layer. Perform a spatial join by state, as follows, storing the output in your geodatabase or in a shapefile named zebra_mussels_by_state, as shown next. Performing a spatial join between two layers—states and zebra mussels
Work package 4: Analyzing zebra mussel distribution 27) Summarize results Steps 17 - 28 When done, open the attribute table for your new layer. Right-click the state names and Summarize. Store your results in a dbf file named zebra_mussels_by_state_sum.dbf in your working folder. Next, open your summary table and sort your count by state field. 27.1) Which state contained more zebra mussel sightings than any other? In which state would you say that the density of sightings was highest? 27.2) Notice the third most common sighting occurred in areas with no state identified. Where are these sightings? 27.3) Knowing that there are fifty-one unique states and state equivalents (including Washington DC), how many states contained no zebra mussels sightings? 28) Analyze results Analyze your zebra mussels data by examining the counties where the invasive species occurred. Repeat the above process by county: Join the zebra mussels to the county layer and summarize on county name. 28.1) In which three counties (and their associated states) were the most zebra mussels found? End of work package
Work package 5: Investigate forest type and land cover 29) Investigate forest types Steps 29 - 31 Expand the legend for the forest types. 29.1) Can you determine the names of the forest types based on the legend? Fortunately, you do have a file containing forest types that you downloaded from the National Atlas site. 29.2) Which metadata file did you download that provides the value for each forest type? 29.3) Visually examining the map and the above metadata file. Name three forest types in which the zebra mussel seems predominant. 29.4) Which GIS procedures would you need to run through to quantitatively assess which forest types contain the most zebra mussel sightings? 30) Investigate land cover Expand the legend for the land cover. 30.1) Can you determine the names of the land cover classes based on the legend? If not, check the file containing land cover classes you downloaded from the National Atlas site. 30.2) Which metadata file provides the value for each of the land cover classes? 30.3) Visually examining the map and the above metadata file. Name three land cover classes in which the zebra mussel seems predominant. 30.4) Which GIS procedures would you need to run through to quantitatively assess which land cover classes contain the most zebra mussel sightings?
Work package 5: Investigate forest type and land cover 31) Investigate land cover density Steps 29 - 31 Analyze the relationship of zebra mussels to land cover diversity. 31.1) Knowing that the land cover diversity is high at 255 and low at the value of 09, can you detect any relationship between zebra mussel distribution and land cover diversity? 31.2) Knowing what you know about the impact of zebra mussels on diversity, what types of data might you need, and at what scale, to detect any impact of zebra mussels on species richness and diversity? 31.3) Do you think you would be able to obtain this type of data on the National Atlas website? Why or why not? End of work package
Work package 6: Volunteered geographic information (VGI) 32) Investigate VGI Step 32 Assess the zebra mussel with regards to volunteered geographic information. 32.1) Do you think zebra mussels easily lend themselves to volunteered geographic information, with citizens posting the information to an online data portal? What would be the challenges and benefits of doing so? 32.2) Do you think the National Atlas is set up in such a way where citizens could add their own data to the site? 32.3) Based on what you know about VGI portals, name three things that would need to happen for citizens to be able to post their data about zebra mussels to an online portal. End of work package
Work package 7: Assessing other invasive species data 33) Examine honey bee layer Steps 33 - 35 Examine your Africanized honey bees layer. 33.1) How is this data differently organized and formatted compared to the zebra mussels data? 33.2) Make three observations about the distribution of Africanized honey bees in the USA. 33.3) Make three observations about the spread of Africanized honey bees in the USA. 34) Research honey bees 35) Examine other datasets Do some research on Africanized honey bees. 34.1) What are some problems or issues of concern with these bees? Examine your data for common gorse, leafy spurge, purple loosestrife, and tallowtree. 35.1) How are the datasets for these species organized and formatted differently compared to the zebra mussels and Africanized honey bee data? 35.2) What would you need to do in order to spatially analyze these datasets? End of work package
Work package 8: Assessing other citizen science portals 36) Assess other portals Step 36 Assess other citizen science portals. 36.1) Compare Landscope (www.landscope.org), FieldScope (www.fieldscope.org), GLOBE (www.globe.gov), What’s Invasive! (www.whatsinvasive.com), and OpenStreetmap (www.openstreetmap.org) in terms of their goals and data themes. 36.2) Again, considering these citizen science portals, compare the ease of obtaining data from the sites. 36.3) Compare the ease of contributing data to these citizen science portals. 36.4) What impact do you think the ease of use has on the amount of data contained on the site? 36.5) What are the main reasons that cause citizen science portals either to thrive—or to wither—in your judgment? End of work package
Work package 9: Presenting results of your analysis 37) Create layout Steps 37 - 39 Create a final map showing your data for your US EPA report. All of the information you wish to include in the final plot will be in a layout view. Access the layout view by selecting the button on the lower left of the data frame. Alternatively, you could also use the View menu and select Layout View. You may also wish to use Customize > Toolbars> Layout to display the layout tools. Using the Insert menu, add: 38) Save a scale bar in kilometers a title your name the date a text box explaining some details of your analysis a text box explaining your data sources used a photograph of a zebra mussel any other information that you think is pertinent Create a digital copy of your layout and save your map document.
Work package 9: Presenting results of your analysis 38) Assessing results Steps 37 - 39 Assess the results of your analysis. 38.1) Assess the ease of use of working with the National Atlas data in terms of accessing, downloading, and using the data within a GIS environment. 38.2) Assess the quality of the National Atlas data in terms of scale, spatial accuracy, attribute completeness, and metadata. 38.3) Would you use National Atlas data again in the future? Why or why not? 38.4) What other data layers on the National Atlas website might you have wanted to use to deepen your analysis of invasive species? 38.5) What other data layers that were not on the National Atlas website might you have wanted to use to deepen your analysis of invasive species? 38.6) What organizations might produce the data that you need? 38.7) What factors have you considered that would also be important in other regions of the world? 38.8) Are there any factors that would not be important considerations elsewhere in the world but are important in the United States? 38.9) Summarize in a few sentences what you have learned about the spatial pattern of zebra mussels in this exercise.
Work package 9: Presenting results of your analysis 38) Assessing results (contd.) Steps 37 - 39 38.10) Summarize in a few sentences what you have learned about the spatial pattern of Africanized honey bees in this exercise. 38.11) How did GIS help you in your analysis of zebra mussels, Africanized honey bees, and the cultural and physical geography of the United States? 39) Create presentation Create a ten-minute presentation for the US EPA that summarizes your results and, based on your reading, your recommendations as to what might be done to combat zebra mussels and Africanized honey bees in the United States. Note that you also downloaded wilderness preservation areas and federal lands. Include an assessment of whether the wilderness preservation areas and federal lands have been impacted and, if so, which ones, and whether it would be fruitful to concentrate your efforts on keeping the wilderness areas and federal lands free of the zebra mussel in your presentation. End of work package
Chapter 8 quiz 1) Name three implications that the phrase “data user as data provider” has on GIS and public domain data. 2) Name and describe three major citizen science data collection initiatives. 3) Name three ways in which citizen science activities have impacted government operations or policies. 4) Describe the impact of citizen science activities on issues of data quality. 5) What does the phrase “citizens as sensors” mean? How do you think this will change GIS and public domain data by the end of the current decade? 6) From what resource did you use data for your study of invasive species in the United States? What is your assessment of the quality and variety of data from this resource? 7) What steps did you perform on the data for the invasive species and the base layers before you were able to use them? Compare the number of steps involved with the process you went through versus other problems and with other organizations’ data. Were the number of steps involved in processing this exercise acceptable to you as a GIS data user? Why or why not?
Chapter 8 quiz (contd.) 8) A variety of geoprocessing (overlay, buffer, sort, query, etc.) and statistical tools (classification, summarizing, mean center, etc.) exist. Name two geoprocessing or statistical tools that you used in your analysis on invasive species. Why was each of them used? 9) Did the scale at which the data were collected affect your invasive species study? Why or why not? 10) Name one thing about the invasive species study that frustrated or confused you, one thing that surprised you, and one thing that you were pleased with in the course of your analysis. For each, provide the reason why and explain what you might do about that issue in the future.
1. Exercise 8 Assessing citizen science portals and analyzing citizen science data in invasive species In this exercise, you will have ...
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