We describe how to create an environmental layer in ModestR, integrating several environmental variables in a single space. Environmental layers can be used to estimate distribution of a species, to visualize its niche, and to compare environmental conditions of different areas, among other things.
6.- Creating environmental layers 2D (Version ModestR 5.3 or higher)
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Step by step tutorial:
Creating 2D environmental layers 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. Internet connection
4. About 45 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR
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3. We’ll describe how to create an environmental layer
in ModestR, integrating several environmental
variables in a single space. Environmental layers can
be used to estimate distribution of a species, to
visualize its niche, and to compare environmental
conditions of different areas, among other things.
Follow the next steps!
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4. The first step is running ModestR and going to menu Mapping/Niche of occurrence/Create new environmental layer.
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Go to menu
Mapping/Niche of
occurrence/Create
new environmental
layer 2D
5. The first step to create an environmental layer is selecting the environmental variables that will be part of it. In some way,
an environmental layer represents way of visualizing and working with multiple environmental dimensions in a simpler way.
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Environmental data is not provided with
ModestR. It should be the user who adds those
data.
For details of how to integrate environmental
data in ModestR, see the step-by-step tutorial
“How to integrate and use environmental data
in ModestR” or the ModestR user’s manual, in
the Modestr website.
For this example we are selecting some terrestrial
variables such as althymetry or VI (vegetation index). You
must select at least two variables, but an environmental
layer may typically involve 4 or more variables.
You should use variables that mostly cover the same
geographic area.
Then click on Continue button.
6. In the next step, Variance Inflation Factor can be optionally calculated, in order to detect collinearities between variables,
and, eventually, delete variables that can be redundant. This step is optional, and you can just skip and continue.
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For this example we’ll neither calculate VIF nor
delete variables.
A value that already appears is the minimal
relative % of coverage of each variable regarding
the other ones. If one variable has a low value
(e.g.< 50%) this usually indicates that there are
many missing values for the geographic areas
where the other variables do have values. An
extreme case would be if you selected terrestrial
and marine variables, that will not have the same
geographic coverage, then they should not be
used in the same environmental layer.
Click on Continue button.
7. In the next step, the polar coordinates system that will constitute the environmental layer is depicted.
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The default assignation of
the variables to each axis of
the polar coordinates
system is done basing on
the correlation of each
variable with each other,
trying this way to maximize
data dispersion, and
therefore a more visually
descriptive environmental
layer.
You can optionally select
variables in the list and
change their position using
those buttons.
Click on Continue button.
Each variable is an axe of
this polar coordinates
system. In this step you
may optionally change the
order of the axes, but you
mostly accept the default
order and continue to the
next step.
8. In the next step, the environmental layer is generated and shown both on the map and in the polar coordinates system.
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Here the current environmental data
are projected on polar coordinates
system. The result is a bidimensional
and more easily understandable
representation of the different
environmental conditions that occur in
the world, according to a compound of
variables (those selected to build this
layer). A color scale is assigned the
polar coordinates system, and used to
visualize the correspondence with the
geographic areas.
Click on Continue button.
9. Finally, the new environmental layer can be optionally saved to be used later. A report can also be exported.
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Enter a name and a description
for the new layer and click on
Save layer to save it.
You can optionally export a
report of the environmental
layer, that contains several files
such as the polar data map, the
X and Y rasters and other ones.
Click on Load layer to load it in MapMaker.
MapMaker will then automatically use this
layer for any subsequent operation that
requires an environmental layer.
You can change the currently loaded
environmental layer going to menu
Mapping/Niche of occurrence/Load
environmental layer.
Currently loaded layer (if any) is shown in the
bottom status bar.
10. Now we’ll see some things that can be done using an environmental layer. Such as showing the environmental conditions
of a geographic area within the whole shape. For this example, we’ll use ModestR predefined selections.
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The first step is selecting the
target area. In this example, we’ll
use predefined selections that
are already integrated in
ModestR
Go to menu Layers >> Shapes >>
Add shape.
11. A dialog box shows the collection of predefined selections integrated in ModestR. To add a predefined selection to the
map, just select it in the tree or in the active map.
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The active map shows
the selected areas. It
also allows going into
an area or selecting it
using the right mouse
button.
For this
example, we’re
adding some
basins of Africa.
To do that, we’ll
open the
“World Basins”
node in the tree
and next the
“Basins of
Africa”. Then
we’ll select
some of them.
Click on Close to continue
12. Selections (called shapes in ModestR) added to the map will appear by default as semitransparent shapes.
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You can place
the mouse over
any selection to
see its name
13. Now we can calculate the environmental conditions of the areas corresponding to those selections, according to the
environmental layer previously built.
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Go to menu Mapping/Niche of occurrence/Polar data maps for shapes
14. Next, a dialog with the whole data map of the current environmental layer will be show. In this dialog you can select one of
the selections 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 area of the left list,
to a folder.
15. MapMaker will show the parts of the whole environmental layer corresponding to the environmental conditions present in
the selected area. This provide an insight of the diversity of the environmental conditions in this area, and its relationship
with the whole environmental conditions.
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In the data map displayed only the
conditions present in the selected
area are shown.
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
to see the selected area within the
whole map.
Select one of the
selections
previously added
to the map to see
its specific data
map
16. Selecting different areas and showing their maps can provide an insight of their global differences regarding their
environmental conditions. As an environmental layer is a compound of several variables, it provides a more global overview
that comparing the values of each variable one by one for each area.
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Select another
selection to
see its specific
data map.
The data map
displayed clearly
shows that there are
environmental
differences between
this area and the
previous one.
This provides a
simple and intuitive
way of visualizing
and understanding
environmental
differences between
several areas.
17. Besides data corresponding to a specific region, the density of its environmental conditions can also be displayed. This can
provide an overview of which conditions are more frequent in this region, and can be useful to compare several regions.
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In the right tabbed
panel, select the
Region density map.
In the graph displayed the
conditions present in the
selected area are shown in
the form of a density graph.
Zones with a warmer color
(green, yellow, red) indicate
more frequent conditions
than zones with colder colors
(blue).
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The same data, but projected to the corresponding geographic area, can be displayed by clicking on the Show button
Clicking on the Show button,
the corresponding data for
the selected area (either
from the density map or
from the data map) will be
shown in the world map as
raster data.
Now close the dialog box to
go back to the main map.
Then go to menu
Layers/raster
templates/Clear raster
templates to clear the map.
19. Now we’ll see another utility of environmental layers: estimate the potencial niche of a species. That is what is called
“niche of occurrence” in ModestR.
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The first step will be to add occurrences of a species to the map. We can download them from GBIF, for example. To do that, go to menu
File >> Import >> Occurrences from online GBIF database.
20. Now we’ll see another utility of environmental layers: estimate the potencial niche of a species. That is what is called
“niche of occurrence” in ModestR.
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Then write “Ursus arctos” in the
species name, for example, and click
on the Accept button.
21. The “Niche of Occurrence” can be calculated from occurrence data, such as those downloaded from GBIF or imported from
CSV files.
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Once data downloaded from GBIF,
you have to select habitats to be
accepted for this species.
For this example, we’ll select “Land”
Then click on the Accept button.
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The “Niche of Occurrence” feature works by looking for environment similarities to infer the areas favorable to a species. To
do that, it uses an environmental layer, to measure the distance between the environmental conditions where the species
already has confirmed presences, and the other conditions that appear in the layer.
Now data is added to
the map. Samples
that fall outside of
the habitats selected
for the species will
appear in another
color (by default
black).
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Once occurrence data added to the map, we can do a density map using the “niche of occurrence” approach.
Go to Mapping >>
Niche of occurrence >>
Density map.
24. If no environmental layer is currently loaded, a list will appear to let you to select one. If any was already loaded, it will be
used.
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If no environmental layer is
currently loaded, a list will
appear to let you to select
one.
If a layer is already loaded,
(which is shown in the
bottom status bar)
MapMaker will automatically
use this layer.
You can change the currently
loaded environmental layer
going to menu
Mapping/Niche of
occurrence/Load
environmental layer.
Density map uses a
kernel density approach
to determine the
environmental areas
with higher density of a
species in the polar
coordinates system of
an environmental layer.
Several parameters can be
adjusted, but most of the
times, default options are OK
(as usual in ModestR! )
Just click on the Run button.
25. Therefore, environmental areas (not geographic!) where the species is already present will have more density, and then
environmental areas nearest those ones, which will have a high density, can be considered also favorable to the species.
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Polar density map show
the environmental areas
with higher density of
the species in the
environmental layer.
Areas with higher
density will be
considered favorable to
the species. They form
the “niche of
occurrence” of the
species.
Click on the Close button
to go back, to the map.
26. The geographic niche of occurrence is just a projection of the areas with higher density in the environmental layer into the
geographic space.
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The same density information is shown in the map, but, obviously, translated to the geographic space. The geographic areas that have
the environmental conditions with higher density of the species in the environmental layer will appear here highlighted.
27. Besides density, we can calculate and add the niche of occurrence as presence areas to the map. Go to menu Layers >>
Raster templates >> Clear raster templates to clear the map.
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Go to Mapping >> Niche of occurrence>> Distribution map.
28. The areas added are those with higher density of the species in the environmental layer.
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Several parameters can
be adjusted, but most
of the times, default
options are OK (as
usual in ModestR! )
Select Add area option to
add the presence areas to
the map.
Then click on the Run button.
29. This is an example of the result. Of course, results depend from the species, and, particularly from the variables used to
build the environmental layer. More information in the ModestR user manual available at www.ipez.es/ModestR
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The geographic areas that have the environmental conditions with higher density of the species in the environmental
layer are added to the map.
30. It was the
Step by step tutorial:
Creating 2D environmental layers in
ModestR
Thank you for your interest.
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You can find this one and other tutorials in
http://www.ipez.es/ModestR
By the ModestR team
Colaborators:
Estefanía Isaza Toro