Calculating Area of Occupancy & Range Extent (EOO) With GeoCAT-1
Calculating Area of Occupancy & Range Extent (EOO) With GeoCAT-1
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a. Import data directly from GBIF, iNaturalist, Picasa, or Flicker using the tool
b. Add points (or remove) manually to the map.
c. Or Upload Data. Or do a combination of all three.
i. Data Upload Requirements: (See Appendix to obtain data from Biotics 5)
▪ Coordinate fields must be named Latitude and Longitude.
▪ Must use point data.
▪ Coordinates must be in Decimal Degrees (may need to convert to decimal degrees
from degrees minutes seconds: DD= (degrees)+(minutes/60)+(seconds/3600) and
remember to multiple by -1 if the direction is South or West).
▪ File must be saved as .csv
▪ File must be closed before uploading.
ii. Common Data Sources
1. Element Occurrence centroids (See Appendix to obtain data from Biotics 5)
2. Specimen Data
3. Observation Data
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3. To calculate Range Extent (Extent of Occurrence) and Area of Occupancy, within the ANALYSIS AND
SOURCES section to the right, mark the checkbox which Enables EOO/AOO.
GeoCAT Output for EOO (Range Extent or Extent of Occurrence) and AOO (Area of Occupancy) are in sq
km. Area of Occupancy is calculated with the default cell width of 2 km, which is a 4 sq km grid cell. To
get the number of grid cells, divide area of occupancy by four.
4. Options to save or download data, make collaboration easy:
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Where and how do I enter AOO and Range Extent in Biotics and the rank calculator?
Tool Field Number/lette Units Methods
r to Enter
Biotics EGR: Appropriate range n/a n/a
Section: Range/Distribution for Range Extent
Field: Rating within Range
Extent section
Biotics EGR: Range Extent Select n/a
Section: Range/Distribution from
Field: Estimate within drop
Range Extent section down
Biotics EGR: Appropriate range 4 sq km Calculated using 4
Section: Range/Distribution, for # of grid cells grid cell sq km grid cells
Area of Occupancy Field: (divide AOO by 4)
Rating as number of 4 sq
km grid cells (most often)
Biotics OR if using 1 sq km grid cells Appropriate range 1 sq km Calculated using 1
(linear habitats) Rating as for # of grid cells grid cell sq km grid cells
number of 1 sq km grid (= area of grid
cells cells)
Biotics EGR: Area of Select n/a
Section: Range/Distribution Occupancy from
Field: Estimate within Area drop
of Occupancy section down
Rank Calculator Range Extent Appropriate range n/a n/a
for Range Extent
Rank Calculator Area of Occupancy Appropriate range n/a n/a
for # of grid cells
(enter either 4 sq
km grid cells or 1
sq km grid cells
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Appendix I. Preparing spatial EO data for use in GeoCAT - Method using centroids
for each EO part
1. Create a shapefile (not a feature class, as you will need the dbf) of the EO polygons. You should
exclude EOs ranked X and possibly those ranked H, F, U, or X, as Range Extent and AOO should be
based on the element’s current distribution.
3. Change EOs with multiparts into singleparts (so each part's centroid can ultimately become a point
in a later step). If you have any EOs with multiparts, you will notice the number of rows in the
attribute table is more in the resulting output of this step.
On right of screen, click Catalog\System Toolboxes\Data Management Tools\Features\Multipart to
single part. Save as your previous file name "singlepart"
7. Open excel, find the .dbf file of the shapefile and open it. Only the Latitude and Longitude fields are
needed for GeoCat, so delete any fields that you wish besides these. Save as a CSV file. Make a
separate CSV file for each species if your table contained multiple species. You may also wish to
make different versions containing only certain EOs. For example, it may be helpful to make a
version that includes only the EOs not ranked X or no ranked HXUF, if you did not exclude these in
your initial export.
8. Open GeoCAT. Start a new project. Upload Data under "Add New Source" choose "Import GeoCAT
.CSV"
Browse, select the CSV file for one species, Import
In upper box, click Enable EOO/AOO.
The results are shown on screen. Copy these values into a document or spreadsheet.
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Note: if you have information on other locations, specimens etc., you may manually add them
(green dot tool on left) and EOO/AOO will recalculate. To change to a different CSV file, click the x
on the lower right of the CSV "source" and click yes to "do you want to delete these points".
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Appendix II. Preparing EO data from Central Biotics for use in GeoCAT - Method
using centroid of EO only (if already calculated and stored in Biotics - tabular)
1. Run a query in Biotics that returns the pertinent element and EO information including latitude and
longitude. Possible example below.
2. Prepare the query by editing the EGT ID or working list name.
3. Run the query in Biotics Query Builder.
SELECT
case when (length(EO.latitude)=7) and EO.latitude like '______N' and
(LENGTH(trim(TRANSLATE(substr(EO.latitude,1,6), '0123456789',' '))) is null) then
round(to_number(substr( EO.LATITUDE,1,2)) + (to_number(substr(
EO.LATITUDE,3,2))/60) + (to_number(substr( EO.LATITUDE,5,2))/3600),5)
when (length(EO.LATITUDE)=7) and EO.LATITUDE like '______S' and
(LENGTH(trim(TRANSLATE(substr(EO.LATITUDE,1,6), '0123456789',' '))) is null) then
-1* round(to_number(substr( EO.LATITUDE,1,2)) + (to_number(substr(
EO.LATITUDE,3,2))/60) + (to_number(substr( EO.LATITUDE,5,2))/3600),5)
else null end LATITUDE,
case when (length(EO.LONGITUDE)=8) and EO.LONGITUDE like '_______E' and
(LENGTH(trim(TRANSLATE(substr(EO.LONGITUDE,1,7), '0123456789',' '))) is null) then
round(to_number(substr( EO.LONGITUDE,1,3)) + (to_number(substr(
EO.LONGITUDE,4,2))/60) + (to_number(substr( EO.LONGITUDE,6,2))/3600),5)
when (length(EO.LONGITUDE)=8) and EO.LONGITUDE like '_______W' and
(LENGTH(trim(TRANSLATE(substr(EO.LONGITUDE,1,7), '0123456789',' '))) is null) then
-1* round(to_number(substr( EO.LONGITUDE,1,3)) + (to_number(substr(
EO.LONGITUDE,4,2))/60) + (to_number(substr( EO.LONGITUDE,6,2))/3600),5)
else null end LONGITUDE,
ELEMENT_GLOBAL.ELEMENT_GLOBAL_ID,
eo.eo_id,
eo.principal_eo_shape_id,
D_CLASSIFICATION_STATUS.CLASSIFICATION_STATUS_CD cl,
SCIENTIFIC_NAME.SCIENTIFIC_NAME gname,
ELEMENT_GLOBAL.G_RANK,
DelimList('SELECT DECODE(s.nation_id,139,''MX'','''')
|| s.subnation_code || ''('' || s_rank || '')'' || '' ch:'' || substr (s_rank_change_date,
1,4) || '' rv:'' || substr (s_rank_review_date, 1,4)
AS subnatl_dist '
|| ' FROM element_subnational, subnation s, taxon_subnatl_dist tsd WHERE
element_subnational.subnation_id = s.subnation_id
and element_subnational.element_subnational_id = tsd.element_subnational_id
and tsd.d_dist_confidence_id = 1 /****confident****/
and element_subnational.element_national_id IN '
|| '(SELECT element_national_id FROM element_national WHERE element_global_id='
|| element_global.element_global_id || ') ORDER BY s.nation_id desc, SUBNATL_DIST ',
', ') AS subn_srk_conf_ch_rv_yr,
nation.iso_nation_cd natn,
subnation.subnation_code subn,
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a. You can save different versions for analysis (EOs not ranked X, etc.). It is highly
recommended that extirpated (X and X?) are excluded. Others should be excluded based on
the knowledge of the element in review.
Appendix III. Preparing SF data from a Local Biotics for use in GeoCAT
1. Run a query in a Local Biotics that returns SF centroids. Two possible examples below were provided
by Frank Price of FNAI.
2. Prepare the query.
a. Edit the SName.
b. Edit the codes in the last line tell it what to exclude. It is highly recommended that
extirpated (X and X?) are excluded. Others should be excluded based on the knowledge of
the element in review.
15 F
16 H
17 X
18 F?
19 H?
20 X?
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3a. Run this query in Biotics Query Builder which uses the sci_name function, which not all programs
may have (see #3b for alternative).
select
SOURCE_FEATURE_ID
, gv.x LONGITUDE
, gv.y LATITUDE
from
SOURCE_FEATURE_REP_PROJ
, table(sdo_util.getvertices(
mdsys.sdo_cs.transform(
SDO_GEOM.SDO_CENTROID(SOURCE_FEATURE_REP_PROJ.shape,0.005)
, 0.005, 4326)
)) gv
WHERE source_feature_id IN
(SELECT source_feature_id FROM source_feature WHERE sci_name(element_subnational_id) = 'Najas
filifolia')
AND source_feature_id NOT IN
(SELECT source_feature_id FROM
eo LEFT OUTER JOIN eo_source_feature eo_sf
ON eo.eo_id = eo_sf.eo_id
WHERE d_basic_eo_rank_id IN (16,17,20))
3b. Run this alternative query in Biotics Query Builder which does not use the sci_name function.
select
SOURCE_FEATURE_ID
, gv.x LONGITUDE
, gv.y LATITUDE
from
SOURCE_FEATURE_REP_PROJ
, table(sdo_util.getvertices(
mdsys.sdo_cs.transform(
SDO_GEOM.SDO_CENTROID(SOURCE_FEATURE_REP_PROJ.shape,0.005)
, 0.005, 4326)
)) gv
WHERE source_feature_id IN
(
SELECT source_feature_id
FROM source_feature SF
LEFT OUTER JOIN ELEMENT_SUBNATIONAL EST
ON SF.ELEMENT_SUBNATIONAL_ID = EST.ELEMENT_SUBNATIONAL_ID
LEFT OUTER JOIN SCIENTIFIC_NAME SN
ON EST.SNAME_ID = SN.SCIENTIFIC_NAME_ID
WHERE SN.SCIENTIFIC_NAME = 'Najas filifolia'
)
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Changelog
12 Nov 2021:
• Updated query in Appendix 2 (moved the latitude and longitude to the first 2 columns for
GeoCAT import (can just save your data as csv file and import)
• Added query in new appendix (3) to provide an example for local biotics export of SF centroids
for GeoCAT analysis. Query provided by Frank Price.
• Clarifications: within the Identifiers Section Major Habitat is for Animals Only.
• Removed from requirements document
o Last Literature Search: Enter the date by selecting from calendar icon if you thoroughly
reviewed literature.
13 Oct 2021:
• Amanda updated preferred citation for EOs, including the attributes. “If needed, cite
information found in EOs this way (NatureServe Network 2021). Add the reference in the
References Table: NatureServe. 2021. NatureServe Network Biodiversity Location Data.
NatureServe, Arlington, Virginia. (U21NAT01HQUS)”
• Amanda updated the definition of Range Extent addressing the exclusion of unsuitable habitat in
range extent calculations. The definition was updated to align with the definition in Biotics Help,
but further clarification should be pursued.
FORMER: Extent of occurrence is defined as the area contained within the shortest continuous
imaginary boundary which can be drawn to encompass all the known, inferred or projected sites
of present occurrence of a taxon, excluding cases of vagrancy. This measure may exclude
discontinuities or disjunctions within the overall distributions of taxa (e.g., large areas of
obviously unsuitable habitat) (but see 'area of occupancy'). Extent of occurrence can often be
measured by a minimum convex polygon (the smallest polygon in which no internal angle
exceeds 180 degrees and which contains all the sites of occurrence).
CURRENT: Range Extent (Extent of occurrence) is defined as the area contained within the
shortest continuous imaginary boundary that can be drawn to encompass all the known,
inferred, or projected sites of present occurrence of a taxon or ecosystem, excluding cases of
vagrancy. While this measure may exclude discontinuities or disjunctions within the overall
distribution of a taxon or type (e.g., large areas of obviously unsuitable habitat), such exclusions
are discouraged except in extreme cases because these disjunctions and outlying occurrences
accurately reflect the extent to which a large range size reduces the chance that the entire
population of the taxon will be affected by a single threatening process. Risks are spread by the
existence of outlying or disjunct occurrences irrespective of whether the range extent
encompasses significant areas of unsuitable habitat. (See also 'area of occupancy'.) Range Extent
is measured by a minimum convex polygon (the smallest polygon in which no internal angle
exceeds 180 degrees and which contains all the sites of occurrence).
• ‘Extent of Occurrence’ was updated to ‘Range Extent’ throughout the document to be
consistent with NatureServe Terminology.
1 Mar 2021:
• Dave Almquist (FNAI) revised Appendix I of the GeoCat instructions to exclude unnecessary
steps.
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• Amanda fixed link for [DM]. This now correctly links you to the instructions for submitting a help
desk ticket.
• 23 March 2021: A new rule is added to the Style Guide: ”Do not name private companies or
landowners, especially when referring to negative practices on their land.”
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