ESRI ArcGIS for the Amphibian RLA
The chapters below explain the steps required to set up your copy of ESRI ArcMap and guide you through the basic
tasks used to create the spatial data for species on The IUCN Red List of Threatened SpeciesTM.
This is a working document, so you are welcome to make notes for your own reference. Please note that there are
usually multiple ways to do a particular task in ArcGIS. In this document you will find one suggestion, but you may
find an alternative route that you prefer and may want to record here or elsewhere.
Finally, if you have any suggestions on how to improve this document, please get in touch with someone in the
Amphibian RLA central coordinating team.
Contents
System requirements ........................................................................................................................................................ 2
Software download and licencing ..................................................................................................................................... 2
Installation and authorization of ArcGIS ........................................................................................................................... 2
Storing and organising ArcGIS files ................................................................................................................................... 2
Mapping tools, layers and the master amphibian shapefile ............................................................................................ 2
Basic introduction to the ArcGIS Desktop 10.1 ................................................................................................................. 3
Basic GIS introduction course ........................................................................................................................................... 3
Create your Amphibian assessment basemap .................................................................................................................. 3
Querying the master amphibian shapefile to make changes to a shapefile .................................................................... 4
Creating new shapefiles .................................................................................................................................................... 5
Modifying shapefiles ......................................................................................................................................................... 6
Clipping a shapefile to the coastline ................................................................................................................................. 6
Maintaining the information in shapefile attribute tables ............................................................................................... 7
Calculating polygon area ................................................................................................................................................... 7
Smoothing a polygon ........................................................................................................................................................ 8
Creating a circle of 10km2 ................................................................................................................................................. 9
System requirements
ArcGIS for Desktop has been certified for Windows operating systems and requires Microsoft .NET Framework to be
installed. For further details, please see http://www.esri.com/software/arcgis/arcgis-for-desktop/systemrequirements.
Unfortunately, ArcGIS for Desktop is not certified or supported on the Mac operating system. If you have an Apple
computer running Windows, you can install ArcGIS for Desktop using VMWare, BootCamp, or Parallels. For more
information see http://edcommunity.esri.com/software-and-data/mac-os-support.
Another option is for you to use Google Earth or QGIS to make your range map. However, these do present some
drawbacks and might delay the completion of your assessments. Please see the instructions on our website (under
mapping tools) dedicated to these alternatives and liaise with the Amphibian RLA Central Coordination Team with
any questions you might have.
Software download and licencing
To access the latest version of ESRI’s ArcMap software, contained in the ArcGIS for Desktop download, please go to
http://www.esri.com/software/arcgis/arcgis-for-desktop to begin a 60-day free trial. Complete the download with
service packs applied. You will need to create an account on the ESRI site prior to this download.
Before installing the latest version of ArcGIS for Desktop, please make sure to uninstall any previous versions of
ArcGIS and any corresponding extensions (ETGeowizards, Xtools Pro, etc.) first. Once you have removed any
conflicting versions/extensions, please follow the installation instructions below.
Once your free trial has or is about to expire, we are happy to provide a longer-term licence for you (typically a
maximum of 1 year). We will grant you a licence for ArcGIS for Desktop Basic (formerly ArcView) Single Use license.
Please note that these licenses are to be used for assessment purposes. You are welcome to use them in your
conservation research, but the primary purpose of these licenses is for assessment-related mapping and should
under no circumstances be used commercially.
Installation and authorization of ArcGIS
Please follow the instructions on the download page. If you have any questions or issues please get in touch with the
Amphibian RLA central coordination team.
Storing and organising ArcGIS files
We advise you to store all GIS-related files in a single folder on your computer. Create a GIS folder in My Documents
or use the default GIS folder. This will make finding and opening files through ArcMap much easier.
If you need to move an ArcGIS file, please consider using the ArcCatalog application included in the software
download (also accessible when ArcMap is open). This method helps keep all related files together, e.g. a single
shapefile in ArcMap is actually 6-7 files on your computer and all must be in the same folder and have the same base
name in order to be read by ArcMap. Renaming these files should also be done through ArcCatalog to ensure that all
related files are named the same way and extensions are not lost.
Mapping tools, layers and the master amphibian shapefile
Once you’ve downloaded and installed your software, you are ready to download the layers and tools you’ll need for
mapping. We recommend saving all these in your GIS folder.
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1. Download the current Master amphibian shapefile from the Amphibian RLA website:
http://www.amphibians.org/redlist/map-resources. This contains all the shapefiles for all the amphibian
species currently on The IUCN Red List.
2. Download the Layers and tools folder at http://www.amphibians.org/redlist/map-resources which contains
the following:
 Amphibian smoothing tool – see instructions below on how to add it and use it
 Country1mVMAP – a layer of country outlines for the entire globe
 EOO Calculator v1.0 – see instructions below on how to add it and use it
 RedListToolBox – see instructions below on how to add it and use it
Basic introduction to the ArcGIS Desktop 10.1
ArcGIS Desktop is comprised of multiple integrated applications, some of which are found in Start menu>All
Programs>ArcGIS. Below is a description of the ones you will use for mapping species.



ArcMap is the actual mapping application, which you will use to create and edit species shapefiles.
ArcCatalog organizes the GIS files contained on your computer. It
can be accessed through ArcMap or in the ArcGIS folder in your
programme folder. It is analogous to Windows Explorer, except
that it is designed to handle shapefiles and associated data. A
single shapefile is comprised of multiple files, all of which are
necessary, so it’s important to keep them together in the same
folder. You can also search, preview and add data to ArcMap
using this application. ArcCatalog is the most failsafe way to
manage and name/rename your GIS files.
ArcToolbox is not accessible through your Start menu, but is found within ArcMap and ArcCatalog. As its
name implies, ArcToolbox contains a variety of tools you will need to manage your spatial data. You will also
add a few tools the IUCN Red List Unit has custom-built for mapping for species assessments.
Basic GIS introduction course
If this is your first time using GIS, you may appreciate taking a free online course on the ESRI website (requires you to
log in on the site). The “Getting Started with GIS” course and related information can be found at
http://training.esri.com/gateway/index.cfm?fa=catalog.webcoursedetail&courseid=2500. The course is 4 hours long
and should be helpful in introducing the concepts of GIS and basic navigation around the ArcMap software.
Create your Amphibian assessment basemap
Now that you have downloaded and installed your software, and downloaded our layers and tools, you’re ready to
set up ArcMap to begin mapping. This step creates the basemap template that you will use for all amphibian
assessments. You will open it every time you launch ArcMap, so name it something memorable (e.g. Red List
amphibian mapping) and save it in your main GIS folder.
1. Open ArcMap and in the left pane select “New Maps”. Then under “My Templates” in the main window
select “Blank map”. (You can skip this step by clicking on “Cancel”. However, we recommend creating a map
as it serves as a shortcut to your most-used data.) Save your map to the GIS folder in which you will be
keeping your ArcGIS data, otherwise ArcMap will makes a default geodatabase for you under your My
Documents folder.
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2. Add data – there are two ways to add data. Note that some layers, like shapefiles, are comprised of several
files, but when viewed in ArcCatalog or ArcMap they are shown as a single file.
a. The first option is to open ArcCatalog by clicking
. Then navigate to the folders containing the
files you wish to open. You can drag the file to the Table of Contents to add it. If your GIS folder isn’t
listed as an option in the “Add Data” window, you may need to click on
connection between ArcMap and that folder.
b. The other option is by clicking the “Add Data” button
in your computer’s folders.
c. Add the following layers:
to establish a folder
in the toolbar and navigating to the data
i. Basemap: click
and select “Basemap” from the drop-down menu. Once in the
Basemaps window select the Topographic map – this is the base layer we find most helpful
as it contains a lot of information, including contour lines. Please note that this basemap is
not a good source of information on protected areas; you should reference
www.protectedplanet.net for more complete information. Also, note that more detail is
revealed when you zoom in, e.g. more river tributaries are revealed the closer in you are.
ii. Country1mVMAP, which is a layer of country boundaries – this is a helpful layer if your
computer has a hard time loading the Topographic Basemap and will be used for clipping
shapefile to geographic features like coastlines.
iii. Master amphibian shapefile.
d. Add the Red List custom-made tools to the ArcMap Toolbox by first opening it
and then rightclicking on the ArcToolbox title and selecting Add Toolbox… (see image at right). Navigate to the
folder where you have saved your layers and tools and add
the following:
i. Amphibian smoothing tool
ii. EOO Calculator v1.0
iii. RedListToolBox
Querying the master amphibian shapefile to make changes to a shapefile
Most often, you will need to modify one or more existing polygons for a species already contained in the master
amphibian shapefile or add a new polygon to its shapefile. The first step here will be to extract all polygons relevant
to that species, save them as a new shapefile and add them as a new layer to your ArcMap Table of Contents before
making any changes to that species’ shapefile. This shapefile must accompany the final submission to the Red List
Unit.
1. Open the Attribute Table of the master amphibian shapefile by right-clicking on its name in the Table of
Contents.
2. Click the options button
and open the Select by Attributes… option.
3. Double click “BINOMIAL” and using the buttons available, create a string in the text box like this one:
"BINOMIAL" = 'Arthroleptis bioko', noting that there is one space on either side of the = sign and that the
species scientific name only requires a single quotation mark on either side. Click Apply and if you do not see
your species in the Attribute Table, click the Show Selected Records button
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at the bottom of the
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attribute table window in order to display the records selected by your query. (If you still don’t see it, the
species may not be in the master amphibian shapefile (i.e. it’s newly described), or check your spelling or if
there have been any taxonomic changes to the species name)

You can zoom to the polygons you selected by clicking the Zoom to Selected button
in the
Attribute Table or close the Attribute Table and right-click the Master Amphibian shapefile name,
selecting Zoom to Layer in the dropdown list.
4. Export the selected polygon(s) to a new shapefile
a) Once you have selected the polygons for a species in the Attribute Table, export them into a new
shapefile which you will then edit: close the Attribute Table and right-click the master amphibian
shapefile and select “Data>Export Data…”.
b) Using the default settings, select the folder into which you want to save this shapefile. We would
recommend creating a subfolder in your GIS folder specifically for all species shapefiles. You may
also want to create a folder where you move finalised shapefiles ready for submission.
c) There is an important naming convention for IUCN Red List shapefiles: be sure the species binomial
is separated by an underscore: Genus_species. This need only apply to the file name – the species
name in the Attribute Table does not contain an underscore.
d) Before clicking save, make sure that that the selected file type you are saving is “Shapefile”.
Creating new shapefiles
If your species is new and doesn’t yet have a map on the Red List, you will need to create a new shapefile for that
species.
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Open the IUCN Species Mapping Tools Toolbox, double-click 1. Create Empty Species Shapefile
o Input the binomial species name separated by an underscore and save it in the appropriate folder
(i.e. Arthroleptis_bioko).
Start an editing session in the Editor Toolbar (see image at right).
o If the Editor Toolbar is not visible, click Customize at the top of the ArcMap
window and select Toolbars…>Editor (to be visible, Editor should have a
tick next to it). Here’s what it looks like when an editing session is not open:
Open the Create Features window by clicking this button:
.
Select from the list in the popup window the shapefile you want to edit.
Select from the Construction Tools the type of shape you want to make (sometimes you need to click on the
shapefile name in the Create Features window to make the Construction Tools visible in that same window).
Draw your shapefile using one of the drawing options and double click on the last point to complete it.
Consider using the Polygon or Freehand tools for drawing as these are the easiest to customize and follow
contour lines/habitat types.
Save your edits and stop the editing session.
In the Species Toolbar, click 2. Add Attribute Fields and select your new shapefile as the input.
o Open the attribute table by right-clicking on the shapefile name.
o Start an editing session and complete the attribute table according to the instructions below titled
“Maintaining shapefile attribute tables”.
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Modifying shapefiles
This task applies both to new shapefiles which you have just created or existing shapefiles which require editing. In
some cases, you can just edit the existing polygons, but in others you may want to redraw or even delete a polygon.
To edit the contours (or vertices) of a polygon
a. In your Editor Toolbar, click the dropdown list
and select “Start Editing”. You will want to
select your new shapefile in the first window which appears and click “Continue” in the second window.
b. Using the Editor Arrow
blue.
, select the polygon you wish to edit, its contour should become highlighted in
c. To edit a vertex or vertices, in the Editor Toolbar select the Edit Vertices button
along the contour of the selected polygons to change its extent.
and use the points
d. The Reshape Feature Tool
is another way to edit the contours of a polygon. By clicking a first point
on the contour and double clicking on another, you will draw a line which will become the new contour
of that polygon.
e. There are other tools you can use, but those outlined above are the ones you are likely to use most
often. Don’t forget to save your edits in the dropdown list and then “Stop editing” when you are
finished.
To create a new polygon
f.
In your Editor Toolbar, click the dropdown list
and select
“Start Editing”. You will want to select your new shapefile in the first
window which appears and click “Continue” in the second window.
g. In the “Create Features” window (can be opened by clicking
in the
Editor Toolbar), select the shapefile you want to modify and then the
Construction Tool you want (polygon etc.)
h. Polygon: Every click you make on the map will create the beginning or
end of a vertex, double click to complete your polygon and, in the
Editor dropdown list, select “Save Edits” to keep your work.
To delete a polygon
a. In your Editor Toolbar, click the dropdown list
and select “Start Editing”. You will want to
select your new shapefile in the first window which appears and click “Continue” in the second window.
b. Using the Editor Arrow, select the polygon you wish to delete and type the delete button on your
keyboard. Alternatively, in an editing session, you can open the Attribute Table for the shapefile and
select the line you want to delete (it will highlight in blue).
c. Save your edits and stop editing.
Clipping a shapefile to the coastline
When clipping to a coastline, it is easiest to extend your polygon beyond the coastline, so that the software can
recognize that this is what you want to clip.

Navigate to ArcToolbox>Analysis tools>Extract>Clip
o Input Features: the shapefile you are trying to clip
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o
o
Clip Features: Country1mVMAP_un2008
Output Feature Class: either the default or whatever you want it called (i.e.
Arthroleptis_bioko_clipped)
Maintaining the information in shapefile attribute tables
Once you have created a new shapefile or if you have edited an existing shapefile, you will need to ensure the fields
in the Attribute Table are properly completed. If no changes have been made to a species’ map, you only need to
update the date to the current year (e.g. 2014) and ensure the citation field is suitably completed.
a. The Amphibian RLA usually only completes the required fields of the Attribute Table. Some fields are
filled out automatically by ArcMap and some are optional. The table below is your guide to the notations
used by the Amphibian RLA, which you should ensure are completed for each polygon of each species.
b. Use the information in the spreadsheet titled Spatial attributes and codes Annex1 to do this. The sheets
titled 1. Polygon Data and mapping codes will be your main references for the relevant codes.
Field Name
Action
FID
Shape
Binomial
Presence
Origin
Filled out automatically
Filled out automatically
Species scientific name: Genus species (no underscore)
See Spatial Attributes and codes Annex1 for appropriate code
See Spatial Attributes and codes Annex1 sheet for appropriate code
See Spatial Attributes and codes Annex1 sheet for appropriate code; N.B. this
field might be found in the far right column of the Attribute Table
Your name and surname if you made a change to this polygon or created it
Year in which the polygon was mapped or compiled, or modified (even if no
change was made, this needs to be updated)
IUCN (International Union for Conservation of Nature), Conservation
International for Old World species; for New World species it is IUCN
(International Union for Conservation of Nature), Conservation International
& NatureServe. N.B. if you are assessing species with an institution under a
formal, signed agreement with the Amphibian RLA, then the name of your
institution should be included here (e.g. CONABIO).
See sheet for codes used if your species’ spatial data should be concealed
from publication on the Red List
Area of each polygon in Km2; completed automatically if Attribute Table was
created using IUCN Species Mapping Tools; otherwise see below for
instructions
Seasonal
Compiler
Year
Citation
Data_sens
AreaKm2
Calculating polygon area
Historically, the approach used by the Global Amphibian Assessment (GAA) in the calculation of EOO values was to
use the range polygons as a proxy for EOO (and AOO when appropriate). For the sake of continuity and pending an
official decision on how to calculate EOO for all taxonomic groups, this methodology continued to be the practice of
the Amphibian RLA until May 2014. This step is no longer required to calculate extent of occurrence (EOO).
Since the adoption of new guidelines (sections 4.9 and 4.10.7 in Guidelines for Using the IUCN Red List Categories
and Criteria version 11, February 2014), a GIS tool has been made available to accomplish this task, which calculates
EOO using a minimum convex polygon. See instructions below for calculating EOO.
See instructions below specific to calculating AOO.
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Calculating extent of occurrence (EOO)
Based on version 11 of the Guidelines, it is now strongly encouraged that EOOs should be calculated using a
minimum convex polygon without excluding large areas of unsuitable habitat. To facilitate implementation of the
new guidelines, a tool has been developed which estimates the EOO for a species by calculating the area of a
minimum convex polygon drawn around the range polygons. See instructions above for adding tools to the ArcGIS
toolbox.
1) Map the species’ range using the methods described in this document.
2) Ensure that the Presence, Origin and Seasonal fields of the shapefile’s Attribute Table are completed. The
tool only calculates the EOO around polygons with Presence (1,2), Origin (1,2) and Seasonal (1,2,3) values.
Your polygons will need these values filled in for the tool to work.
3) Double-click on the tool in the Toolbox and complete the EOO Calculator window as follows:
a. Species Range: select the species shapefile for which you want to calculate the EOO
b. Species Field: select BINOMIAL
c. Output Geodatabase: Navigate to EOO Calculator v1.0>ToolData>eoo_geodatabase.gdb and click
Add or create your own geodatabase and navigate to and add that instead. EOO polygons for each
species along with area calculation will be stored in this geodatabase.
d. Use IUCN spatial attributes: this box is checked by default and ensures that the EOO is only
calculated around data with the recommended attribute values (these are Presence 1 or 2 AND
Origin 1 or 2 AND Seasonal 1, 2 or 3). The fields must exist in the input data or tool will fail. If the box
is unchecked the EOO will be calculated using all the spatial data for the species.
e. A small pop-up window will track the progress of the tool. Close it when it has finished.
4) Upon completion, the tool should add another layer to your Table of Contents that is titled something like
Arthroleptis_bioko_EOO_proj and its polygon should cover all the range polygons of the species. Open the
Attribute Table to find the EOO in km2.
a. If the layer is not automatically added, click on the Add Data button and navigate to the folder
containing the geodatabase for this tool, click on it and you should see a list of filenames similar to
Arthroleptis_bioko_EOO_proj. Select the species you want the EOO for and click Add.
Calculating area of occupancy (AOO)
In the absence of specific guidance on how to consistently calculate AOO and without an AOO Calculator tool, we
provide the following description of how the Amphibian RLA has understood and applied AOO to its assessments.
In contrast to EOO, the value of AOO in Red List assessments is to provide a measurement for range-restricted
species. If your species is a habitat specialist or its range is very circumscribed, then consider calculating its AOO. We
continue to use the methodology of the GAA for the calculation of this value in that we use the combined area of its
range polygons as a proxy for AOO.
Please bear in mind that this value assumes adequate survey effort such that you are certain the species only occurs
in known localities.
1) Map the species’ range using the methods described in this document.
2) Often the range polygon(s) of a habitat specialist or very circumscribed species will also represent its AOO, in
which case the Amphibian RLA recommends that you use the combined area of its range polygons as a proxy
for AOO. Follow the steps below to calculate the area of your polygons.
a. To calculate a more accurate polygon area we must avoid any distortions from the WGS84
coordinate system by changing the coordinate system of the data frame to the World Cylindrical
Equal Area projection.
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i. Right-click on Layers in the Table of Content (see image at
right). Scroll down to and select Properties…
ii. Open the Coordinate System tab; navigate to Projected
Coordinate Systems>World>Cylindrical Equal Area (world).
Select Cylindrical Equal Area (world), click the Apply
button and close the window.
b. Calculate the area of the shapefile polygons in the Attribute Table:
i. If the field Area_Km2 (or similar) doesn’t already exist in
your Attribute table, create it by clicking the Options
button
and selecting Add Field…; complete the popup window as follows:
1. Name: Area_km2
2. Type: Double
ii. Right-click on the heading of your new field and select
Calculate Geometry (you don’t have to be in an editing session, so click OK when that
window pops up); complete the pop-up window as follows:
1. Property: Area
2. Coordinate System: World Cylindrical Area
3. Unit: Square kilometres
c. If there is more than one polygon in the shapefile, add up all the values in the Area_Km2 field and
use that as your AOO.
Smoothing a polygon
If your range polygon is angular and you don’t know enough about the species to redraw it into a more
accurate/natural shape (other locations, habitat preferences, etc), then we ask that you smooth its edges. This is
more of an aesthetic step than technical requirement, so we have chosen units that minimize how much area is
added to the polygon. If you are concerned about how much area was added to your polygons in the process, please
get in touch with the Amphibian RLA central coordination team.

Open the GAA smoothing tool in ArcToolbox or ArcCatalog, click on BuffSmooth
o Feature Layer: the shapefile you want to smooth
o Distance: Linear unit: 1 km
o Smoothing Tolerance: 10km
Creating a circle of 10km2
A circle with an area of 10km2 is used to represent the range of a species for which only a single locality is known and
for which no habitat preferences are known. By IUCN convention, this is usually a circle with a radius of 10 km
resulting in a circle of 314.2 km2. However, the Amphibian RLA has created its own exception to this convention,
requiring a circle with an area of 10 km2 instead. We feel the resulting area best reflects the situation of species for
which only a single point is known.
To create this circle (until a shortcut for your toolbox is created):


Follow the steps above for creating a new polygon
As you create the circle, watch the measurements which automatically appear at the bottom of the ArcMap
window (which are probably in metres). Stop when you have created a circle of appropriate area.
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