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We will again be using ArcView for this
exercise. Hopefully, by this time you are relatively familiar with ArcView,
however, you can refer back to the notes from Lab 2 for general instructions
on how to use it. This lab will also help you gain
more familiarity with ArcView's capabilities.
This lab is intended to show you a different approach of combining habitat mapping with species presence/absence data to delineate the distribution of a species. |
Use the Windows File Manager or other methods to copy all files and subdirectories from s:\courses\wlf448\arcmaps2 to your personal directory on a network drive. If you don't know how to do this, ask and I will show you. If you do not have enough room on your network drive, then copy the maps to a portable hard drive or other removable device.
I strongly encourage you to create a separate working directory for this week's in-class exercise and problem set. It will alleviate problems with ArcView trying to overwrite other needed files during save operations (see Help/Hints for more information).
Log on to the UI network
Click on Start - All Programs - Analytical - ArcView GIS 3.3 - ArcView GIS 3.3 to open the program. This may take awhile, depending on the server's workload.
Click OK when asked if you want to "Create a new project".
Click No when asked if you want to "Add data to the view".
You now need to add the Spatial Analyst extension. To do that, click on File - Extensions from the pull-down menus. A list of available extensions will appear. Use your mouse to go down the list and check the box next to "Spatial Analyst". Click OK. A few more pull-down menus will appear across the top of your ArcView window.
Click on the "Add Theme" button.
In the next window, click on "Drives" in the lower part of the window and navigate to your network drive.
Double-click on "arcmaps2" (or whatever directory to which you copied the data files).
Change the "Data Source Type" to "Grid Data Source". When you do this, you will see a theme appear in the left side of the Add Theme window.
Double-click on "idveg_resamp" The theme name will appear in the View window.
Click on the check box next to "idveg_resamp" and the map theme should appear. This is a grid theme, which means it is raster data. This is the Idaho Gap Analysis Project vegetation map, which has been resampled from a 30 meter grid cell size to 90 meter cell size. This was done for our lab because the resampled map is smaller in size and easier to work with.
Start the Legend Editor for this theme. Double-click on the symbol under "idveg_resamp" and the Legend Editor window appears.
In the Legend Editor, click on the "load" button at the top right of the Legend Editor window. A new window should appear. Select the file named 'idveg.avl' and then click 'OK'. Another window will appear you want to make sure the field that is selected is 'Value' and that there is a check by 'All'. Click 'OK'. You will now see the new legend loaded in your Legend Editor window.
Once your legend is loaded in the Legend Editor, click "Apply" to apply your changes to the current view. Then close the Legend Editor window by clicking on the upper right corner (the "X" sign).
It is a good idea to save your work as a project. It is not uncommon to run into segmentation errors or other errors that kick you out of the program. Consequently, save early and save often!
Go to the main window (project window or "untitled1" window) and select File - Save Project As from the pull-down menu. Give your project a name (keep the "apr" extension). Make sure it is saving the file to your working directory on your network drive.
V. Choosing habitat types based on species information:
The map you have displayed includes all the vegetation types that occur in Idaho. Using MS-Word, open the "idveg" Word file in the arcmaps2 directory. This document provides details about grass, shrub, and tree species occurring within each of the idveg_resamp vegetation types. Explore this document by selecting a vegetation type from your map and reading about the species included. For example, what species are included in the vegetation type "Curlleaf Mountain Mahogany"?
Next,open the MS-Word file "species_info" in arcmaps2. This file provides species profile information regarding preferred habitat types of 3 Idaho species (mountain lion, tailed frog, and black-chinned hummingbird). For the in-class exercise we will be using the tailed frog and in your problem set, you will be using either the mountain lion or black-chinned hummingbird.
Read over the habitat description for the tailed frog in the 'species_info' file. Use this information to select the appropriate habitat types for this species from the vegetation type list (i.e., idveg).
What vegetation types would you choose for the tailed frog? Does "61XX, Forested Riparian" sound right?
Once you have decided upon the vegetation types that are used by the tailed frog, select them from the "idveg_resamp" theme. Do this by opening the attribute table for the theme. You will see 2 fields in the table, "Value" and "Count". You want to match up the numerical code from the 'idveg' word file with the number in the 'Value' column. Select all the 'Value' records that correspond with your vegetation types (e.g., 6101, 6102, 6103, and 6104). Remember to use the shift key to select multiple records.
Your map should now show the all the vegetation types that tailed frogs use in Idaho. We want to save this map and overlay the presence/absence data based on hexagons for tailed frogs. On the main menu bar, click 'Theme' and the choose 'convert to grid'. This will save just the vegetation types you have selected. You will need to provide a name for the new file and be sure to save it to your working directory. Click OK. You will be asked if you want to add the new grid theme to your view. Click Yes. Add the legend file for 'idveg_resamp' to this theme (see instructions in section III, steps 8-10).
To see your new map, click on the box next to 'idveg_resamp' to turn it off and then click on the box next to your new theme to turn it on. You have created a tailed frog distribution map based on habitat. You can also close the attribute table for 'idveg_resamp'.
VI. Incorporating presence/absence data:
Let's add the hexagon theme to our habitat map. Click the "Add Theme" button and then navigate to the 'cov' folder. Open the folder and find the theme called 'Hexagon'. Be sure your 'Data Source Type' is set to 'Feature Data Source'.
Click on the check box in the View window to display the hexagon map for Idaho.
To see the hexagons in which there is presence data for the tailed frog, we need to open a new table. Click on the Project window and then click on 'Tables'. Click on the 'Add' button. Navigate to /arcmaps2/spreadsheet/herphex.dbf. Select that file and then click OK. NOTE: You will import a *.txt file, instead of a *.dbf file for the problem set. After opening the *.txt table, all subsequent commands are identical. See Help/Hints for more information.
Open the attribute table for the 'Hexagon' map.
In both of these tables (i.e., herphex.dbf and Attributes of Hexagon), you will see a field called 'hexagon-id'. We need to link these 2 tables by 'hexagon-id'. To do this successfully, the tables and fields have to be selected in a specific order.
First, select the Attributes of Hexagon table (the top bar will be darker when the table is selected) and then highlight the 'hexagon-id' field by clicking on the field name (it should turn a darker gray with white text when it is highlighted). Second, select the herphex.dbf table and highlight the 'hexagon-id' field.
Third, go up to the main menu under 'Table' and click on 'Link'. You will not notice anything change, but if you select any record in the herphex.dbf table, a record with the same 'hexagon-id' value also will be selected in Attributes of Hexagon. This is how you will know you linked the tables successfully.
There are no species names in the 'herphex.dbf' file, but instead there are element codes (Elcode is the field name), which identify each species. Look back at your 'species_info' file to determine the element code for tailed frog (AAABA01010).
Select the 'herphex.dbf' table and then do a query on it using the element code for tailed frog. To do a query, choose the hammer button on the toolbar and then select ([Elcode] = "AAABA01010"). Be sure to use capital letters because the query is case sensitive. Also, the Elcode value must be in double-quotes because it contains letters.
If done successfully you should have 283 of 8398 records selected in herphex.dbf and you should also have 164 of 404 records selected in the Attributes of Hexagon table and on the hexagon map.
Close both tables and the query builder. Make sure the 'hexagon' map is highlighted in the View window (it will appear raised).
Now we want to save the tailed frog hexagon map. On the main menu bar, click 'Theme' and the choose 'Convert to shapefile'. This will save just the hexagons that are selected. You will need to provide a name for the new file and be sure to save it to your working directory where you have saved everything else. Click OK. You will be asked if you want to add the new shapefile to your view. Click Yes. The 'hexagon' map can now be unchecked or deleted from the display.
VII. Making the final distribution map:
Now you have a habitat map and a presence/absence map for the tailed frog. We want to combine these to make a distribution map for the tailed frog in Idaho.
Open the attribute table for the tailed frog hexagon map. Under 'Table' on the main menu select 'Start editing'. Then under 'Edit' on the main menu select 'Add Field'. A 'Field Definition' window will pop up. Name the new field TailedFrog and choose 'Number' for 'Type' and 4 and 0 for 'Width' and 'Decimal places', respectively. Click OK.
Make sure your new 'TailedFrog' field is highlighted and click on the calculate button (it looks like a calculator on the toolbar). A field calculator window should appear. It should already say [tailed frog] =. Just type 1 in the text box and click OK. All the records in the field 'tailed frog' should now equal 1.
Under 'Table' on the main menu select 'Stop editing' and say 'yes' to 'Save edits?'.
Select your View window and be sure that your tailed frog hexagon theme is highlighted (it will appear raised). Go under 'Theme' and select 'convert to grid'.
Select a new file name and make sure it is being saved to your working directory. Click OK.
A 'Conversion Extent' window will appear. Choose 'idveg_resamp' for both the 'Output grid extent' and the 'Output grid cell size'. The cell size should change to 90. Click OK.
Another window will appear. Pick 'TailedFrog' as the field for cell values. Click OK.
Click Yes to "Join feature attributes to grid?" and click Yes to "Add grid as theme to View?".
Turn on your new theme.
The last steps involve clipping your vegetation map to the extent of your hexagon map.
Under 'Analysis' on the main menu choose 'Map Calculator'. A new window will appear.
Double click on your distribution map for the tailed frog (it should be the file name with no extensions), then click on the multiply button (*) and double click on your vegetation map for the tailed frog. Then click Evaluate.
A new grid will be created. When the analysis is complete, close the Map Calculator window (click in upper right corner on X).
Your new distribution map will be categorized by vegetation. You can load the vegetation legend from 'idveg_resamp' (see instructions in section III, steps 8-10).
Remember to save your project before closing ArcView. You can use the instructions from Lab 2 (section IX) to print out a map of your tailed frog distribution (not required for the in-class exercise).
Revised: 02 September 2011