We`ll describe how to use shapes to search for species in any world area, and to analyze environmental conditions in one area.
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8.- Working with shapes (Version ModestR 5.3 or higher)
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Step by step tutorial:
Working with shapes in ModestR
2. What do you need for this tutorial:
1. ModestR v5.3 or higher
2. Environmental data already integrated in
ModestR (if you have not done that yet, tutorial “How to
integrate and use environmental data in ModestR” can help you
doing that; available in ModestR web site)
3. ModestR database with distribution maps
4. About 45 minutes*
ModestR software can be freely downloaded from http://www.ipez.es/ModestR
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
*Processing times can vary depending on the size of ModestR database and number of environmental variables
3. We’ll describe how to work with vector layers based
on georeferenced shapes in ModestR, introducing
some features using global geospatial data of river
basins.
Follow the next steps!
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
4. The first step is to run MRFinder and go to menu File >> Open Database to open your ModestR database containing
taxonomical information and distribution maps of several species*
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*If you don’t have a ModestR database yet, follow the tutorial “How to create
a ModestR database” (available in ModestR web site) to create a new one.
In this example, we used the database created in the Tutorial “Using some
ModestR tools to browse ITIS taxonomy database and check taxonomic data
using GBIF “
5. ModestR integrates two global geographic databases (ModestR shapes) based on vector layers composed of georeferenced
shapes: World Basins and World Countries (administrative divisions). Users could also add their own databases.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Go to menu Layers >>Add
predefined shapes
In this tutorial, we use
geospatial data of
global river basins
6. Shapes are hierarchically organized, from upper levels (e.g., main river basins) to lower levels (e.g., small sub-basins).
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
BROWSER (HIERARCHICAL TREE)
ACTIVE PREVIEW
The user can move
through the levels
using the browser
(tree) or the active
preview, by double-
clicking on the
wanted polygon to
go into the
corresponding sub-
level
Double- Click on the
African continent
7. Now, basins of the African continent are shown. User can go to another sub-level or select any of the displayed basins to be
added to the map and processed in later steps.
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8. When the user select a river basin, the tree and the active preview are always synchronized, so that it is easy to know the
name of the basin as well as its location in the map. In this example, we select three basins.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
To select an element
in the active preview,
right click in the
desired element and
click on Select
element on the pop
up menu.Click on Close button to add the selected basins to the map.
9. The selected basins are shown and zoomed in the World map. In MRFinder, shapes define an area to search for species
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Click on Search
button to search
for species in the
selected basins
10. MFFinder provide different search options using a tabbed panel. In this example, we run the search using land habitat
option.
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Click on Search button
to continue
Habitat: User can select
the habitats in the
selected areas where
species will be searched.
Species: User can
delimit the rank or
species to be searched.
If the filter is empty, all
the species included in
the database are
searched.
Grouping and simplify:
Users can choose to
search in each region
separately or in all
regions as a whole.
There is an also an
option to simplify the
search with complex
selections
11. When the species search in completed, MRFinder shows the Filter/Export tabbed panel. Results are organized in a
hierarchical tree with the complete taxonomy.
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Search results are
shown using a
hierarchical tree
with the complete
taxonomy
12. The Filter/Export tabbed panel provide three options to filter the search results: Taxonomy filter, Rare species filter and
Categories filter. Final results are shown in tab Filtered results organized in a hierarchical tree with taxonomic information.
In this example, we did not apply any filter.
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Tabs with different filter options. More
details in ModestR manual (Section 3.8)
User can manually check if
any species or taxon is
present in the filtered results
13. The Filter/Export tabbed panel provides different options to export the filtered results. For instance, users can obtain a
summary of the species found in each basin. A richness map wherein each basin is coded by color according to its total
species richness is obtained by click on Close button
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Click on Export maps to obtain:
To grouped summary: summary of the species found in each
basin
To presence data: species locations and associated
environmental data
Click Close to
see the
richness map
Click on Export Metric
to compute metrics,
including richness,
rarity, AOO index, EOO
index, path index or
latitudinal range index
14. Richness map and its corresponding scale are shown in MRFinder after the user click on Close button of Filter/Export panel.
To save the map as image: File >> Export >> Current Map View as Image. If you want to
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15. MRFinder also provides a method to estimate the area of shapes (river basins in this example). A report is generated in CSV
format with both the total area and the area for each type of habitat within each shape.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
16. A shape can also be used as a pattern to clip a raster. The clipping facility is useful for obtaining rasters of environmental
variables for a specific area. A repot with a summary of areas and statistics for each shape and variable is also generated.
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17. ModesR also provides tools to evaluate the environmental quality of shapes (river basins in this example). The first step is to
run MapMaker and create an environmental layer*Once the environmental layer is created, add the shapes (river basins) to
the map. Go to menu Layers >> Shapes >> Add shapes and follow the previous instructions (slides 5-8). Then, shapes added to
the map will be shown semitransparent by default. For example: Oceania’s shape.
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Now we can calculate the environmental conditions of the
areas corresponding to the shapes, according to the
environmental layer previously built.
18. Next, a dialog with the whole data map of the current environmental layer will be shown. In this dialog you can select one
of the shapes previously added to the map.
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By default, the data map
of the whole
environmental layer is
shown
Clicking on the Export
button, a report
including this type of
graph, as well as other
data, is exported for
each shape of the left list
19. MapMaker will show the parts of the whole environmental layer corresponding to the environmental conditions present in
the selected shape, providing an insight of the diversity of the environmental conditions in this area and its relationship
with the whole environmental conditions.
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Select one of the shapes
previously added to the
map to see its specific
data map. For example:
New Zelaland
Only the conditions present in the
selected shape are shown in the
displayed data map.
This can provide an overview of the
kind of environmental conditions
present in this area, regarding its place
within the polar coordinates system.
The gray background represents the
whole environmental layer, allowing
users to see the selected area within
the whole map.
20. In addition to data corresponding to a specific region, the density of its environmental conditions can also be displayed,
providing an overview of which conditions are more frequent in the selected shape. It is useful for comparing regions.
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In the right tabbed
panel, select the
Region density map.
The conditions present in
the selected shape are
shown as a density graph.
Areas with a warmer
color (green, yellow, red)
indicate more frequent
conditions than areas
with colder colors (blue).
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Data can be projected to the corresponding geographic area to be displayed in the world map by clicking on the Show
button. For example: Australia.
22. It was the
Step by step tutorial:
Working with shapes in ModestR
Thank you for your interest.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/º
You can find this one and other tutorials in
http://www.ipez.es/ModestR
By the ModestR team
Colaborators:
Estefanía Isaza Toro