10.- Creating environmental layers 3D (Version ModestR 5.3 or higher)

MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Step by step tutorial:
Creating 3D environmental layers in ModestR:

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
ModestR software can be freely downloaded from http://www.ipez.es/ModestR

We’ll describe how to create a 3D 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!

¿When am I going to use a 3D environmental layer?
 Every time I want to evaluate the conexion between stratification or
mixing and biological, chemical or physical phenomena.
¿What do I need to work with 3D environmental
layers in ModestR?
 Environmental layers at each depth of interest. ModestR will convert the
set of layers in a single one: 3D one.
Before starting with this tutorial, please take a look of the tutorial No. 9
(Adding NOAA's Word Ocean Atlas data to ModestR)

The first step is running ModestR and going to menu Mapping>> Niche of occurrence >>Create new environmental layer >>
3D.

To create a 3D environmental layer, select 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.
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.
See also “Step by step tutorial 9- Adding NOAA's
Word Ocean Atlas data to ModestR.”
For this example we are selecting WOA 2013
marine environmental variables such as
temperature, oxygen and nitrate. 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.

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.
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.

In the next step, the polar coordinates system that will constitute the environmental layer is depicted.
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.

In the next step, the environmental layer is generated and shown both on the map and in the polar coordinates system.

In the next step, the environmental 3D layer is generated and shown both on the map and in the polar coordinates system.
Here the current environmental data are projected on polar coordinates system.
The result is a tridimensional representation of the different marine
environmental conditions that occur in the world.

Finally, the new environmental layer can be optionally saved to be used later. A report can also be exported.
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.

Now we will load this new layer in MapMaker, to be able to use it inmediately after.

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.
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 Samples from online GBIF
database.
Then write “Lepidochelys olivacea” in the species name, and
select “All” for the “Kind of records to download” option.
Then, click on the Accept button.

The “Niche of occurrence” can be calculated from occurrence data, such as those downloaded from GBIF or imported from
CSV files.
Once data downloaded from GBIF, you have to select habitats to be accepted for this species. For this example, we’ll select “Sea”
Then click on the Accept button.

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).

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.
Select the type of Z dimension
to be used = the meaning you
want to give to Z. You have five
options: Depth, Date&Time,
Year, Other Z value, Custom. At
the moment, you’ll choose
Depth.
All occurrences will be used to
perform calculations, whether
they have Z value or not. For
occurrences without Z value
you can select which
substitutive value will be used.
Depth (Z) range for NOO calculation:
Select the Z range to be used to
perform calculations. This also
determines which occurrences will
be used. Only occurrences with a Z
value within the selected range will
be used. Options you have:
1.Use full compounded layer range:
the whole range of the
environmental variables will be
used.
2.Use range of occurrences Z: only
species Z range (according to
occurrences Z values) will be used.
3.Use custom values: a custom range
entered by the used will be used.

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.

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.
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 3D View button
to visualize the 3D results.

Here you can see the 3D environmental layer for the Lepidochelys olivacea, based on kernel density estimation. For
additional information >> ModestR User’s Manual.

The geographic niche of occurrence is just a projection of the areas with higher density in the environmental layer into the
geographic space. Here you can see the density information for Lepidochelys olivacea, projected in a 2D map.
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.

It was the
Step by step tutorial:
Creating 3D environmental layers 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 Estefanía Isaza Toro
Collaborator of the ModestR Team

10.- Creating environmental layers 3D (Version ModestR 5.3 or higher)

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