BioGIS Guide
1
BIOGIS TOOLS .................................................................................................................................... 3
1.1
SELECT TOOL .................................................................................................................................. 4
1.1.1
Build a query based on your selection criteria. ..................................................................... 4
1.1.1.1
1.1.1.2
1.1.1.3
1.1.1.4
1.1.1.5
1.1.1.6
1.1.1.7
1.1.1.8
1.1.2
1.1.2.1
1.1.2.2
1.1.2.3
1.1.2.4
1.1.2.5
1.1.3
1.1.4
1.1.4.1
1.1.4.2
Choose a field from a list .................................................................................................................4
Select an object from a categorical field ..........................................................................................6
Add an object to the query ...............................................................................................................7
Remove an object from the query....................................................................................................7
Add a selection criterion ..................................................................................................................8
Set limits of a continuous field .........................................................................................................9
Filter out records............................................................................................................................ 10
Select records based on record date ............................................................................................. 11
Select records based on spatial location ............................................................................ 12
Predefined polygon ........................................................................................................................ 12
Coordinate based query ................................................................................................................ 13
Custom polygon............................................................................................................................. 14
Switch between Map and Satellite view ......................................................................................... 16
Zoom in and out............................................................................................................................. 17
View the number of records and species included in the query ......................................... 18
Save selection criteria and load saved selection criteria .................................................... 19
Save selection criteria in a file ....................................................................................................... 19
Load selection criteria file .............................................................................................................. 20
1.2
MAP TOOL ..................................................................................................................................... 21
1.2.1
Map operations.................................................................................................................... 21
1.2.1.1
1.2.1.2
1.2.1.3
1.2.1.4
1.2.1.5
1.2.1.6
1.2.1.7
1.2.1.8
1.2.1.9
1.2.1.10
1.2.1.11
Move map center ........................................................................................................................... 21
Zoom ............................................................................................................................................. 21
Point information............................................................................................................................ 21
Polygon information ....................................................................................................................... 21
Zoom to BioGIS extent .................................................................................................................. 23
Zoom to selected records extent ................................................................................................... 23
Zoom to analyzed records extent .................................................................................................. 23
Zoom to BioGIS extent .................................................................... Error! Bookmark not defined.
Zoom to selected records extent ..................................................... Error! Bookmark not defined.
Zoom to analyzed records extent .................................................... Error! Bookmark not defined.
Switch between Map and Satellite view ......................................................................................... 23
1.2.2
Layers .................................................................................................................................. 24
1.3
ANALYZE RECORDS ....................................................................................................................... 25
1.3.1
View the distribution of records based on a chosen field. ................................................... 25
1.3.1.1
1.3.1.2
1.3.2
1.3.2.1
1.3.2.2
Count records based on a field ...................................................................................................... 25
List records based on a field .......................................................................................................... 27
Explore analyzed records .................................................................................................... 28
List records in a specific bin........................................................................................................... 28
View records of a specific condition in the Map tool. ..................................................................... 28
1.4
MODELS........................................................................................................................................ 30
1.4.1
Niche Profile ........................................................................................................................ 30
1.4.2
Environmental niche modeling ............................................................................................ 31
1.4.2.1
Overview ....................................................................................................................................... 31
1.4.2.2
Scientific notes .............................................................................................................................. 31
1.4.2.3
About the models in BioGIS........................................................................................................... 32
1.4.2.3.1 BIOCLIM................................................................................................................................... 32
1.4.2.3.2 ENFA ........................................................................................................................................ 33
1.4.2.3.3 Mahalanobis ............................................................................................................................. 33
1.4.2.4
Using the models ........................................................................................................................... 33
1.5
SPECIES RICHNESS ........................................................................................................................ 35
1.5.1
Overview ............................................................................................................................. 35
1.5.2
Operating the Species Richness tool .................................................................................. 37
1.5.2.1
1.5.2.2
Initial settings ................................................................................................................................. 37
Species richness window .............................................................................................................. 38
1.6
DAMAGE CALC .............................................................................................................................. 41
1.6.1
Overview ............................................................................................................................. 41
1.6.2
Concept and assumptions ................................................................................................... 41
1.6.3
The species distribution model in Damage Calc ................................................................. 42
1.6.4
Operating the Damage Calc ................................................................................................ 43
1.6.4.1
Settings ......................................................................................................................................... 43
1.6.4.1.1 Predefined polygon: ................................................................................................................. 45
1.6.4.1.2 Custom polygon: ...................................................................................................................... 45
1.6.4.1.3 Switch between Map and Satellite view:................................................................................... 47
1.6.4.1.4 Zoom in and out: ...................................................................................................................... 48
1.6.4.2
Results .......................................................................................................................................... 49
1.6.5
1.6.5.1
1.6.5.2
1.6.5.3
2
The Damage Calc metrics ................................................................................................... 49
General .......................................................................................................................................... 49
For each species ........................................................................................................................... 49
For each taxonomic group ............................................................................................................. 50
BIOGIS DATA ..................................................................................................................................... 51
2.1
DATABASES OF RECORDS .............................................................................................................. 51
2
1 BIOGIS TOOLS
BioGIS site has a set of tools for presenting and analyzing spatial biodiversity data (species
records). The following guide will allow you to explore the wide capabilities of BioGIS. The
different tools are arranged in different tabs in the top of the page and the user can switch
between them by clicking on the required tab.
The Select Tool is BioGIS’s central feature allowing the user to build an advanced query with
flexible selection operations for effective data mining. Most of the tools in BioGIS are based on
the Select Tool. The basic structure of BioGIS tools is shown below:
Select tool
Build a query based on
your selection criteria
For example:
• Select a species or a
taxonomic group
• Define query area
• Limit record dates
• Select data s ources
Map tool
Analyze records
Analyze records based on
different fields
For example:
• Count records based on a
specific field
• List records by species
Models
Explore the distribution of
a species based on its
potential niche
For example:
• Analyze the niche profile of
a species
• Generate a predicted
distribution map based on
environmental variables
Damage Calc
Species richness
Estimate the importance of
an area for the biodiversity
Create a species accumulation
curve
3
Use a variety of display
features for spatial data
For example:
• Show selected records
• Show GIS layers
• Show BioGIS records by
group
• Show projections of
distribution models
• Get record information
• Summarize species data for
user-defined polygons
1.1
Select tool
To select a set of records based on desired criteria click the Select Tool tab. By default, the
Select Tool includes in the query all records present in the BioGIS database.
1.1.1 Build a query based on your selection criteria.
1.1.1.1 Choose a field from a list
Click on the marked (red circle) arrow to view a list of available fields (use the scroll bar to view
all available fields) and click on the required field, for example – Species (which is also the
default field).
4
5
1.1.1.2 Select an object from a categorical field
Write the name of the object (autocomplete) for the query or select from an alphabetic list of
available objects by clicking left mouse button (the list of available objects updates according to
the user selection). A rectangle with the name of the selected object will appear under Selected
objects.
6
1.1.1.3 Add an object to the query
Repeat the previous step. A rectangle with the object name will appear under Selected objects.
The selection will be a conjunction between the objects (equivalent to logical OR).
1.1.1.4 Remove an object from the query
Click on in the object’s rectangle.
7
1.1.1.5 Add a selection criterion
Click on
+ to add a selection criterion. The selection will be a disjunction with the already
existing criteria (equivalent to logical AND).
8
1.1.1.6 Set limits of a continuous field
After choosing a continuous field (for example, Mean annual rainfall), set the selection limits
by dragging the grey rectangles (left = minimum, right = maximum) with the left mouse button or
by manually changing the numbers in the boxes.
9
1.1.1.7 Filter out records
Select all records that do not fulfill a criterion by clicking the Is not field instead of the Is field in
the selection criterion line.
10
1.1.1.8 Select records based on record date
Check boxes From and/or To and fill in the dates using the calender.
11
1.1.2 Select records based on spatial location
1.1.2.1 Predefined polygon
Choose the query area by selecting a polygon from a list.
12
1.1.2.2 Coordinate based query
1. Select a coordinate field (for example, Latitude, Longitude, X, Y). You can add two selection
criteria for the query (for example: Latitude + Longitude).
2. Set the coordinate limits by dragging the grey rectangles (left = minimum, right = maximum)
with the left mouse button or by manually changing the numbers in the boxes.
13
1.1.2.3 Custom polygon
Create your own query area by drawing a polygon on the map.
1. Choose the Custom from the polygon list.
2. Set the vertexes of the polygon by clicking the vertex location in the map. The borders of your
selection area will be defined by the sides of the created polygon (three vertexes are
sufficient for defining your selection area).
3. Refine your polygon by moving vertex’s location. Use the left mouse button to drag the
balloon of the vertex.
4. Clear selection area by clicking on
5. Repeat step 2 for creating a new polygon.
Step 1
14
Step 2
Step 4
Step 3
15
1.1.2.4 Switch between Map and Satellite view
Click on Map or Satellite tab in the selection area window.
16
1.1.2.5 Zoom in and out
Click on the scroll bar buttons in the Selection area window to zoom in (+) and zoom out (-) or
use the mouse toggle.
17
1.1.3 View the number of records and species included in the query
The number of records and number of species included in the query update automatically
according to the selection operations.
18
1.1.4 Save selection criteria and load saved selection criteria
1.1.4.1 Save selection criteria in a file
1. Click on Save selection.
2. Save file in your computer using the new window (.bgq extension).
3. Continue according to your usual browser downloading procedure.
Step 2
Step 1
19
1.1.4.2 Load selection criteria file
1. Click on Load selection (double click for Explorer users).
2. Browse and choose a previously saved file.
3. Selection criteria will be set in the Select tool to those saved in the file (see previous figure).
Step 2
Step 1
20
1.2
Map tool
The Map tool allows a variety of display and query operations. Click on the Map tool tab. The
tool is useful for visual exploration of the data available in BioGIS and for viewing analyses
performed in other BioGIS tools on a map.
1.2.1 Map operations
1.2.1.1 Move map center
Click and drag the
button to move map center to the desired location.
1.2.1.2 Zoom
To zoom in click on
and click left mouse button on a location on the map that you wish to
enlarge (alternatively, click and drag left mouse button to extend a rectangle to be enlarged).
You can also click on the scroll bar buttons to zoom in (+) and zoom out (-) or use the mouse
toggle.
1.2.1.3 Point information
To show information on a record click on
and then click on a location on the map. A table
showing information on the closest record will appear (including environmental variables). Click
on
to exit the table.
1.2.1.4 Polygon information
To show information on species within a polygon:
1. Click on
.
2. Click left mouse button to add a vertex to the polygon (at least 3 vertexes are required
for a polygon).
3. Refine vertex location by dragging the vertex balloon.
4. When the polygon is ready, click on
within the polygon.
5. Click on
to open a table showing information on species
to exit the table.
21
Step 1
Step 3
Step 2
22
Step 4
1.2.1.5 Zoom to BioGIS extent
To set the map extent to the default extent (Israel), click on
.
1.2.1.6 Zoom to selected records extent
To set the map extent to that of the selected records (see 1.1 Select tool), click on
.
1.2.1.7 Zoom to analyzed records extent
To set the map extent to that of the analyzed records (see 1.3 Analyze records), click on
1.2.1.8 Switch between Map and Satellite view
Click on Map or Satellite tab to switch background map.
23
.
1.2.2 Layers
To display a required map layer, click on the relevant checkbox. Uncheck to remove layer.
Change display color by clicking on the layer’s colored rectangle and choosing a desired color.
24
1.3
Analyze records
To analyze records based on different fields click on the Analyze records tab. The operations
in the Analyze records are preformed on the selected records (defined in the Select tool).
1.3.1 View the distribution of records based on a chosen field.
1.3.1.1 Count records based on a field
1. Choose a field from a list (use the scroll bar to view all available fields).
2. Set Results type to Count.
3a. Set Bins to Number, alternatively 3b. Set Bins to Size.
4a. Set number of bins, alternatively 4b. Set size of bins.
5. Set range of chosen field.
6. Click on
to run analysis.
Note that 3a, 3b, 4a, 4b and 5 are available only for a continuous field.
Step 1
25
Step 2
Step 4a
Step 3a
Step 5
Step 6
26
1.3.1.2 List records based on a field
1. Choose a field from a list (use the scroll bar to view all available fields).
2. Set Results type to List (List by species will organize the list by species).
3. Click on
to run analysis.
Step 2
Step 1
27
1.3.2 Explore analyzed records
1.3.2.1 List records in a specific bin
Click on
to list the records in a specific condition (category or a bin in a continuous field).
Click on
to view details of a specific record in the list.
Click on
to go back to previous detail level or on
to go forward in detail levels.
1.3.2.2 View records of a specific condition in the Map tool.
Click on
next to a specific condition (category or a bin in a continuous field). This will
open the Map tool and the records of the selected condition will appear on the map
(Analyzed records layer). Click on Analyze Records tab to switch back to Analyze
Records.
28
29
1.4
Models
This tool is useful for exploring the distribution of a species based on its potential niche.
Two types of analysis are available, Niche profile and Environmental niche modeling.
1.4.1 Niche Profile
To analyze the niche profile of a selected species (or another taxonomic unit) click the Models
tab and then Niche profile.
This operation produces tables describing the records of the selected species (or another
taxonomic unit) with respect to a number of ecological variables (“niche axes”). For continuous
variables (such as Altitude, Mean annual rainfall, Mean January temperature), five statistics are
calculated based on the selected records: average, maximal and minimal values, range, and
standard deviation. For categorical variables (such as Soil and Lithology), all values found in the
set of selected records (i.e., the various soil types and rock types) are displayed.
Note: It should be emphasized that the results of the Niche Profile are derived from the set of
selected records, and do not necessarily reflect the “true” niche of the selected species.
30
1.4.2 Environmental niche modeling
1.4.2.1 Overview
This tool generates a predictive distribution map of a selected species using environmental
niche modeling, a numerical method that combines observations of species occurrence with
environmental estimates.
BioGIS uses three models for environmental niche modeling: BIOCLIM, ENFA, Mahalanobis.
Environmental niche modeling involves two stages. The first stage is the extraction of the
“environmental envelope” of a species (or another taxonomic unit) from the data. The
environmental envelope is the range of the species distribution within a multidimensional space
determined by a set of environmental variables. In the second stage, the environmental
envelope is projected from the multidimensional environmental space into a two-dimensional
geographic space (i.e., a map). Thus, the outcome of an environmental niche model is a
predictive map indicating the potential distribution of a species using data on the environmental
characteristics of the sites where the species was recorded.
1.4.2.2 Scientific notes
 It should be emphasized that a niche model predicts the potential distribution of a
species with respect to particular environmental variables, rather than the actual range
of distribution. Thus, the main purpose of niche modeling is to evaluate the apparent
environmental suitability of various geographic regions for the existence of species of
interest.
 The degree to which a map generated by a niche model reflects the actual distribution
range of a particular species depends on the relative importance of the environmental
variables on which the model is based as determinants of the species distribution. Thus,
reliable predictions are expected only for species with distribution ranges strongly
affected by the selected environmental variables.
 The quality of an environmental niche map is strongly influenced by the quality of the
data used for the development of the model. Both errors in the original data (e.g., in
geographic coordinates) and various kinds of biases (e.g., lack of data for certain
climatic combinations) may significantly reduce the quality of the model’s predictions.
Note: Records associated with relatively large polygon sites are not recommended to be
used for predictive purposes because of their low spatial accuracy. Such records can
be excluded from the analysis using the field Spatial accuracy in the advanced Select
tool.
 Since values of the climatic variables are determined for both the recording sites and the
grid cells of the map using interpolation processes, the quality of model predictions is
also influenced by the accuracy of the climatic surfaces obtained from the interpolation
processes.
 Details on the analytical procedures used for generating the climatic maps used in
BioGIS and their accuracy can be found in: Kurtzman, D. & R. Kadmon. 1999. Mapping
of temperature variables in Israel: a comparison of different interpolation methods.
Climate Research, 13:33-43.
31
1.4.2.3 About the models in BioGIS
Short descriptions for each model are provided (see example for the BIOCLIM model.
1.4.2.3.1 BIOCLIM
The BIOCLIM model defines the ecological niche of a species as the bounding hyper-box that
encloses all the records of the species in the climatic space (Busby, 1991). Thus, it creates a
rectilinear “envelope” in the environmental space, defined by the most extreme (minimum and
maximum) records of the species for each environmental variable. In addition, to reduce the
sensitivity of model predictions to outliers, the species records for each variable are sorted and
the records that lie within a certain percentile range of the data are used for construction of the
model. The predictive map generated by BioGIS consists of two distinct regions: “Core” and
“Periphery.” The “Core” consists of grid cells characterized by climatic conditions falling in the
5th-95th percentile values of all climatic variables. The “Periphery” is determined by the
minimum-maximum values of all variables. The predictive map is displayed in the Map tool with
the Core and Periphery regions marked by different colors.
Busby, J.R. (1991) BIOCLIM — A Bioclimate Analysis and Prediction System. Nature
Conservation: Cost effective biological surveys and data analysis. Nature conservation (ed. by
C.R.Margules and M.P. Austin), pp. 64–68. CSIRO, Melbourne.
Example
According to the BioGIS database, a niche model constructed for Quercus calliprinos
(Palestine oak) based on all sites and the three variables Mean annual rainfall, Mean
August temperature and Minimal January temperature, has the following climatic
envelope:
Minimum
5th percentile
95th percentile
Maximum
Mean annual
rainfall [mm]
250
431
893
1201
Mean August
temperature [oC]
21.1
21.8
25.8
28.8
Minimal January
temperature [oC]
-1.5
-0.6
2.5
3.3
Thus, the “core” predictive map of Quercus calliprinos will consist of all squares of 1x1
km in Israel that satisfy the following conditions:
 Rainfall is in the range 431 - 893 mm, and
 Mean August temperature is in the range 21.8 - 25.8oC, and
 Minimal January temperature is in the range –0.6 – 2.5oC.
32
1.4.2.3.2 ENFA
The ENFA (Ecological Niche Factor Analysis) model uses a modified principal component
analysis for presence only data of a species (Hirzel et al., 2002). It calculates a measure of
habitat suitability based on the analysis of marginality (i.e., how the species mean differs from
the global mean) and environmental tolerance (i.e., how the species variance compares to the
global variance).
Hirzel, A.H., Hausser, J., Chessel, D. & Perrin, N. (2002) Ecological-niche factor analysis: How
to compute habitat-suitability maps without absence data? Ecology, 83, 2027–2036.
1.4.2.3.3 Mahalanobis
The Mahalanobis model ranks potential sites by their Mahalanobis distance to a vector
expressing the mean environmental conditions of all the records in the environmental space. A
certain distance threshold is then used to define the boundaries of the ecological niche. This
algorithm produces an elliptic envelope that explicitly accounts for possible correlations between
the environmental variables (Farber & Kadmon, 2003).
Farber, O. & Kadmon, R. (2003) Assessment of alternative approaches for bioclimatic modeling
with special emphasis on the Mahalanobis distance. Ecological Modeling, 160, 115–130.
1.4.2.4 Using the models
The following steps are required to generate an environmental niche model:
1. Select a species (or another taxonomic unit) using Select tool (see 1.1 Select tool).
2. Select a model – click on the Models tab and then choose one of the models: BioCLIM,
ENFA, Mahalanobis
3. Select the relevant environmental variables by checking the boxes next to the required
environmental variables (you can select more than one variable).
4. Click on
to run the model. The Map tool will open with the projected distribution map.
Step 1
Select a
species
Step 2
Select a model
33
Step 4
Step 3
Select
environmental
variables
34
1.5
Species richness
1.5.1 Overview
The Species Richness tool evaluates to what degree a selected area was sufficiently
sampled. Since data on the distribution of any species are always partial and biased, this tool
is important for evaluating the reliability of query results for a selected area. In essence, this
tool evaluates the "completeness” of the list of species in a defined area. By analyzing species
accumulation curves over time or over records, it is possible to evaluate whether the selected
area was sufficiently sampled assuming that new species are hard to find in sufficiently
sampled areas. Species accumulation curves show the rate at which new species are found
within a defined area over time or over records and can be extrapolated to provide an estimate
of species richness. The "completeness” of the sampling effort in a defined area is determined
by evaluating whether the accumulation curve has reached an asymptote and by comparing the
observed number of species to the number predicted by the fitted curve. This tool is also useful
for planning priorities for future sampling effort in the field.
The application can plot the cumulative number of species recorded as a function of sampling
effort (number of records or number of sites). Since the order in which samples are included in
a species accumulation curve will influence the overall shape, a smooth accumulation curve
can be produced by repeating a process of randomly adding the samples to the accumulation
curve and then plotting the mean of these permutations and 95% confidence interval.
A regression function can then be fitted to the curve.

One of the following models are applied for fitting a regression function:
1. Michaelis-Menten:
y
x
x
2. Exponential:
y    (1  e    x x)

A relative error is calculated:
35
1
( max   min )
2
Re l.Er 

If the relative error (RE) exceeds 50%, the fit will be considered a failure (a null result).

an R2 score for the fit is calculated:
 f (x )  y 
2
R2  1
i
i
 y
i
 ( y )
2
i
i

The estimated number of species based on the fit function is shown along with the
observed number of species and the observed/estimated ratio.
For the analysis to be carried out there is a limitation of 4 samples (minimum) within the selected
area.
36
1.5.2 Operating the Species Richness tool
1.5.2.1 Initial settings
Before starting the Species richness tool use the Select tool (see 1.1 Select tool) to define
the area of interest. It is recommended to perform the analysis on a specific taxonomic group, or
separately for each group. The Select tool can be used also to narrow the Species richness
analysis to specific environmental conditions (for example, to examine the “completeness” of
sampling effort in Hamra soils).
To select a taxonomic group, click on the Select Tool tab.
Click on the marked (red circle) arrow to view a list of available fields (use the scroll bar to view
all available fields) and click on the Group. Insert a group name (for example, Birds) under
value.
To define the area of interest, see 1.1.2 Select records based on spatial location. Note that
species richness analysis for record-rich large areas might involve long running time.
To open the Species Richness window click on the Species Richness tab.
37
1.5.2.2 Species richness window
The Species Richness window opens after clicking on the Species richness tab.
To define the type of accumulation curve, click on ▼ and choose between: Records, Locations,
Years and Dates.
For accumulation curves based on Records or Locations enter the number of permutations
(random reorder of the samples). The default number of permutations is 100 (recommended).
If you choose accumulation curves based on Years or Dates, a temporal range will open so that
you can limit the range of dates.
Click on
to produce the accumulation curve.
38
To fit a regression curve click on ▼to select a regression function.
In this example the curve is still not in saturation, indicating possible lack of sufficient sampling
effort in the area. The next figure shows a more saturated accumulation curve indicating a much
better sampling effort.
39
40
1.6
Damage Calc
1.6.1 Overview
The purpose of this tool is to support decision makers and planners in evaluating the
contribution of any area within Israel to the biodiversity in Israel. This tool estimates the potential
damage to biodiversity as a result of habitat loss. The estimate is based on a comparison of
species distributions between a target area and a reference area. The target area is the area
to be evaluated or the area in risk for damage and the reference area is a broader area of
interest to which the biodiversity is compared (Israel or a region within Israel). For example, if a
new settlement is planned in the Negev, Damage Calc can estimate the potential biodiversity
damage in relation to the biodiversity in: the entire country, the Negev, or in a defined
geographical region (for example, a square of 20X20 km surrounding the settlement).
For each species in the database, a spatial map of its potential niche is created by the use of
the BIOCLIM species distribution model (see 1.4.2 Environmental niche modeling) using
species records and climatic GIS data. The species potential niche area in the target area is
compared with the potential niche area in the reference area. The results of the calculation are
summarized for each systematic group.
The method can be used to evaluate the uniqueness of a selected area in terms of species
composition and its contribution to nature conservation. Damage Calc can be used for
comparing consequences for biodiversity of different planning scenarios, thus, can help in
decision making and conservation planning.
1.6.2 Concept and assumptions
The Damage Calc tries to estimate the risk to biodiversity from habitat loss in a target area. For
example, the target area can be an area planned for building a new city. The concept is based
on the following assumptions:
1. Species distribution is well-represented by the species distribution model used (BIOCLIM in
Damage Calc).
2. Complete habitat loss is expected in the target area so that species richness in the target
equals zero.
3. There are no indirect effects from the planned action in the target area influencing the species
distribution.
As these assumptions do not apply fully for many planning scenarios, the user must interpret
the results of the analysis with caution and consider them as estimates for potential damage.
We illustrate the concept of the Damage Calc using the following simplified figure. The area of
the distribution models of four species A, B, C and D is marked with green (the models are
based on records of four species). The target area is within the red frame and the reference
area is within the blue frame.
Species A will not be included in the damage calculation.
Species B is not expected to suffer any damage.
Species C is expected to suffer partial damage.
41
Species D is expected to become extinct.
A
Reference
B
Target
D
C
1.6.3 The species distribution model in Damage Calc
This application uses species records from the BioGIS database (presence-only data). For each
species, all grid cells (cell size = 1 km2) within Israel containing a record are identified. For each
species a raster distribution map is created where cells are coded “1” if they contain a record
and “0” if they do not). A BIOCLIM (see 1.4.2.3.1 BIOCLIM) model is run on the raster data of
the species distribution and the climatic data used as the factors affecting the potential niche
distribution of the species. The climatic data from the HUJ GIS center consists of:
1. Mean annual rainfall
2. Mean daily temperature of the coldest month (January)
3. Mean daily temperature of the hottest month (August)
4. Mean maximum temperature of the hottest month (June)
5. Mean minimum temperature of the coldest month (January)
The result of the BIOCLIM model (excluding 10% outliers) is a raster map of the potential
climatic niche of the species.
Notes:
1. If part of the target area is outside the reference area then the program uses only the
overlapping area. In case there is no intersection between the target area and the
reference area, an error message is displayed.
2. The BIOCLIM model will not run for species with less than 6 raster cells containing
presence records. In these cases, the calculation of the species distribution area within
the target area and the reference area will be based only on the cells that contain
presence records.
42
1.6.4 Operating the Damage Calc
The Damage Calc tool can be operated from any window in BioGIS.
Note: The Damage Calc tool operates independently of the Select tool.
Operating the Damage Calc involves two steps:
1. Settings – Defining the reference area and the target area
2. Results – Viewing the calculation metrics
1.6.4.1 Settings
Click on the Damage Calc tab and then click on Settings
43
Use the appropriate map for defining your Reference area and your Target area.
The same principles apply for setting the Target area and the Reference area.
We will demonstrate how to define the Target area. The Reference area can be defined in the
same way. Remember that the Reference area should contain the Target area (if the Target
area has an area outside the Reference area – this area will be excluded from the target area
for the damage calculation).
44
1.6.4.1.1 Predefined polygon:
Choose the Target area and Reference area by selecting a polygon from a list. After defining
your Target area and Reference area click on
Results.
to start the damage calculation and switch to
1.6.4.1.2 Custom polygon:
Create your own Target area by drawing a polygon on the map.
1. Choose the Custom from the polygon list.
2. Set the vertexes of the polygon by clicking on the vertex location in the map. The borders of
your selection area will be defined by the sides of the created polygon (three vertexes are
sufficient for defining your Target area).
3. Refine your polygon by moving vertex’s location - drag the balloon of the vertex using the left
mouse button.
4. Clear selection area by clicking on
5. Repeat step 2 for creating a new polygon
Click on
to start the damage calculation and switch to Results.
After defining your Target area and Reference area click on
and switch to Results.
45
to start the damage calculation
Step 1
Step 2
46
Step 2
Step 3
1.6.4.1.3 Switch between Map and Satellite view:
Click on Map or Satellite tab in the Reference or Target windows.
47
1.6.4.1.4 Zoom in and out:
Click the scroll bar buttons in the view of the Target area and Reference area windows to zoom
in (+) and zoom out (-) or use the mouse toggle. To fit the map scale and map center between
the Target area and Reference area, use the blue arrows.
48
1.6.4.2 Results
The Results window shows the Damage Calc metrics (see 1.6.5 The Damage Calc metrics for
a detailed explanation).
1.6.5 The Damage Calc metrics
The calculation is based on species distribution maps created by the BIOCLIM model. For each
species the program counts the number of cells that the BIOCLIM model predicts presence in
the target area and in the reference area.
The following metrics are shown:
1.6.5.1 General
Reference area – size of the reference area (km2)
Target area – size of the reference area (km2)
Percentage of target area – 100 * Target area / Reference area
1.6.5.2 For each species
Reference - the number of cells that the species is predicted to be present in the reference area
Target - the number of cells that the species is predicted to be present in the target area
Israel - the number of cells that the species is predicted to be present in Israel
%damage - 100 * Target / Reference. If this result is 100%, then the species is considered
extinct.
49
1.6.5.3 For each taxonomic group
Reference
# Species – the number of species in reference area (based on species predicted distributions)
% Damaged – percent of species in reference area expected to be damaged (Percent damage
> 0%).
Target
# Species – the number of species in target area (based on species predicted distributions)
Extinct
# Species – the number of species that are expected to get extinct (Percent damage = 100%).
(based on species predicted distributions)
Average damage
All – Average Percent damage for all species in the taxonomic group
Damaged - Average Percent damage for species in the taxonomic group that their distribution
is damaged (Percent damage > 0%).
Median damage
All – Median Percent damage for all species in the taxonomic group
Damaged - Median Percent damage for species in the taxonomic group whose distribution is
damaged (Percent damage > 0%).
A histogram shows the distribution of Percent damage for each taxonomic group.
50
2 BIOGIS DATA
2.1
Systematic
Group
Databases of records
Source
Record type
Site type
HUJ
Bryophytes collections
specimen
point or
polygon
Vascular
plants
observation
polygon
Vascular
plants
A. Danin's
grid database
A. Danin’s
point
database
Vascular
plants
HUJ
Herbarium
Vascular
plants
Vascular
plants
INPA
database
Israeli Gene
Bank for
Agricultural
Crops
Vascular
plants
#
Records
Contact
person
Ilana
1,702 Herrnstadt
Avinoam
125,504 Danin
Avinoam
39,766 Danin
observation
point
specimen
point or
polygon
observation
point
specimen
point or
polygon
Rivka
1,657 Hadas
SPNI
observation
point
9,459 Uri Ramon
Snails
snails — HUJ
collections
specimen
point or
polygon
Joseph
1,957 Heller
Snails
HUJ
collections
specimen
point or
polygon
Henk
5,415 Mienis
Butterflies
Israeli
Lepidopterists
Society
observation
point or
polygon
Dubi
3,554 Benyamini
Fish
HUJ
collections
specimen
point or
polygon
Daniel
1,077 Golani
Hagar V.
17,252 Leschner
Linda
Olsvig84,521 Whittaker
51
How to cite
The National Natural History Collections
at the Hebrew University of Jerusalem
(2012) Bryophytes - HUJ Herbarium.
BioGIS (database),
http//:www.biogis.huji.ac.il
Israel National Herbarium (2012)
Vascular plants - HUJ Herbarium. BioGIS
(database), http//:www.biogis.huji.ac.il
Danin, A. (2012) Vascular plants - A.
Danin’s point database. BioGIS
(database), http//:www.biogis.huji.ac.il
Danin, A. (2012) Vascular plants - A.
Danin’s grid database. BioGIS
(database), http//:www.biogis.huji.ac.il
Israel Nature and Parks Authority (2012)
Vascular plants - INPA database. BioGIS
(database), http//:www.biogis.huji.ac.il
Israel Plant Gene Bank (2012) Vascular
plants - Israel Plant Gene Bank. BioGIS
(database), http//:www.biogis.huji.ac.il
Society for the Protection of Nature in
Israel (2012) Vascular plants - SPNI
database. BioGIS (database),
http//:www.biogis.huji.ac.il
The National Natural History Collections
at the Hebrew University of Jerusalem
(2012) Marine snails - HUJ Colllections.
BioGIS (database),
http//:www.biogis.huji.ac.il
Heller, J. (2012) Land snails - HUJ
collections, BioGIS (database),
http://www.biogis.huji.ac.il
Israeli Lepidopterists Society (2012)
Butterflies - Israeli Lepidopterists
Society, BioGIS (database),
http://www.biogis.huji.ac.il
The National Natural History Collections
at the Hebrew University of Jerusalem
(2012) Fish - HUJ Colllections. BioGIS
Fish
INPA
database
observation
point
Reptiles
HUJ
collections
specimen
point or
polygon
Reptiles
INPA
database
observation
point
Birds
INPA
database
observation
point or
polygon
Birds
TAU
collections
specimen
point or
polygon
Mammals
HUJ
collections
specimen
point or
polygon
Mammals
INPA
database
observation
point
Mammals
TAU
collections
specimen
point or
polygon
Mammals
SPNI
observation
point or
polygon
Bats
TAU
collections
specimen
point or
polygon
Bats
SPNI
observation
point or
polygon
Bats
A. Tsoar's
database
specimen or
observation
point
(database), http//:www.biogis.huji.ac.il
Linda
Israel Nature and Parks Authority (2012)
OlsvigFish - INPA database. BioGIS (database),
764 Whittaker
http//:www.biogis.huji.ac.il
The National Natural History Collections
at the Hebrew University of Jerusalem
(2012) Reptiles - HUJ Colllections.
Boaz
BioGIS (database),
2,548 Shacham
http//:www.biogis.huji.ac.il
Linda
Israel Nature and Parks Authority (2012)
OlsvigReptiles - INPA database. BioGIS
1,905 Whittaker
(database), http//:www.biogis.huji.ac.il
Linda
Israel Nature and Parks Authority (2012)
OlsvigBirds - INPA database. BioGIS
69,185 Whittaker
(database), http//:www.biogis.huji.ac.il
The National Collections of Natural
History at Tel Aviv University (2012)
Menachem Birds - TAU Colllections. BioGIS
4,161 Goren
(database), http//:www.biogis.huji.ac.il
The National Natural History Collections
at the Hebrew University of Jerusalem
(2012) Mammals - HUJ Colllections.
Rivka
BioGIS (database),
1,230 Rabinovich http//:www.biogis.huji.ac.il
Linda
Israel Nature and Parks Authority (2012)
OlsvigMammals - INPA database. BioGIS
17,618 Whittaker
(database), http//:www.biogis.huji.ac.il
The National Collections of Natural
History at Tel Aviv University (2012)
Menachem Mammals - TAU Colllections. BioGIS
2,972 Goren
(database), http//:www.biogis.huji.ac.il
Society for the Protection of Nature in
Mammalian Israel (2012) Mammals - SPNI database.
center,
BioGIS (database),
3,327 SPNI
http//:www.biogis.huji.ac.il
The National Collections of Natural
History at Tel Aviv University (2012)
Menachem Bats - TAU Colllections. BioGIS
522 Goren
(database), http//:www.biogis.huji.ac.il
Society for the Protection of Nature in
Mammalian Israel (2012) Bats - SPNI database.
Center,
BioGIS (database),
3,786 SPNI
http//:www.biogis.huji.ac.il
Tsoar, A. (2012) Bats - A. Tsoar's
database. BioGIS (database),
767 Asaf Tsoar
http//:www.biogis.huji.ac.il
52