17. An example using ModestR to assess species distribution in different climatic change scenarios (Version ModestR 5.6 or higher)

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Step by step tutorial:
An example using ModestR to
model species distribution in
different climatic change
scenarios

What do you need for this tutorial:
1. ModestR v.5.6 or higher installed
2. Internet connection
3. About 40 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR

We’ll describe how to use ModestR to
assess species distribution in different
climatic change scenarios. To do that, we’ll
use the 3D Niche capability of ModestR,
taking time as 3th dimension. Follow the
next steps!

For this tutorial we’ll use a climate change scenario from
WorldClim. In order to follow the tutorial, you already have
this climate change scenario integrated in ModestR.
If you still haven’t done this, please see Tutorial 16 in the
ModestR Tutorials page

First step of NOO3D is loading occurrences from a species. With ModestR you can
download data from GBIF or import them from a CSV file. For this example we’ll use a
sample file with occurrences from a virtual species generated using the “virtualspecies”
package from R, using the variables BIO2, BIO8 and BIO15 of WorldClim
Here is the suitability map of this
species. As you can see, it has been
limited to a rectangular area in France

1) Select menu “Options / Preferences”
2) To use Spanish format (default):
 Decimal separator  “ , “
 Field separator  “ ; “
To use English format :
 Decimal separator  “ . “
 Field separator  “ , “
For this tutorial you’ll find a sample file “VirtualSpecies_Original_for_Tutorial_17”.
You can choose it between two CSV options: Format Spanish / Format English
You may select the format depending on the configuration in the "Options / Preferences" menu of the "CSV Exportation
Options" section of any of the ModestR applications.
For example in ModestR DataBase Manager you can find it:

2) Go to menu “File/Import/Occurrence
data from CSV file” then select the
downloaded CSV file
Download the file “VirtualSpecies_Original_for_Tutorial_17” from next link:
CSV in Spanish Format / CSV in English Format
Then import it from MapMaker
1) Run ModestR MapMaker

When importing occurrences to ModestR, you have to select the valid habitats for the species
1) In the dialog box just
check the “Land” habitat
2)Then click on “Accept”
3) Once the import
completed, click on
“Accept”

Once occurrences imported, you can zoom on the area. ModestR checks the habitats and indicates when
occurrences are in an invalid habitat for the species using another color. Those occurrences are shown but are
not used in any analysis or calculation
Invalid occurrences (here in black) are
occurrences located in habitats not valid for the
species. As we indicated that only land was valid
for this species, invalid occurrences are those
located in marine or freshwater habitats.

NOO3D can be used to calculate a density map that shows species suitability , of to calculate a distribution.
We’ll first start with the density map
1) Go to menu Mapping/Niche of occurrence/Density Map

Next step is creating or selecting an existing 2D or 3D CEL (Compounded Environmental Layer).
A CEL will bind together several enviromental variables in a single multidimensional variable. In this case we’ll
create a new 3D CEL using the WorldClim data we have imported previously
1) Select “Create a new 3D CEL”
More details about what are compounded
environmental layers can be found in ModestR
User’s Manual on ModestR website.
A tutorial about compounded environmental layers
creation can also be found at
http://www.ipez.es/ModestR/Manual_Tutorial.html
2) Click “Accept”
If other previously created and stored
CEL’s exist, they will be show here

When creating a 3D CEL, only 3D datasets will be displayed among the candidate variables.
You have to select the whished variables you want to work with.
1) For this example, in the dialog box
that will be shown, select all the
variables from a WorldClim climate
change scenario (i.e. those for RCP26,
or RCP45…)
By default, NOO3D modelling will be done
for the whole range covered by the
selected variables, which in this case are
the years from 2000 to 2070.

You also have to select the geographical extent you want to work with
2) Select “Extent of Occurrence”
as geographical extent .
By default, alpha
shape is used.
3) Click on “Preview” to see the Extent of
Occurrence to be used in the World map.
4) Click on “Continue”

1) Click on “Calculate VIF “
In the next step you can calculate VIF (Variance Inflation Factor)
of the variables to detect collinearity and, optionally, delete
some variables that may be redundant

You can select a variable an delete it from the list.
VIF will be recalculated with the remaining variables. You can
continue deleting other variables, until VIF is considered acceptable
(tipically when VIF<30)
For this example we’ll keep only BIO2, BIO4, BIO8, BIO9, BIO15,
BIO18 and BIO19. Delete all other variables
VIF of each variable is shown
VIF >30 is shown in red.
2) Select a variable and click on “Delete selected“
(keep only BIO2, BIO4, BIO8, BIO9, BIO15, BIO18 and BIO19)
Note.- to select several variables keep Ctrl key pressed while
selecting.

In the next step you can calculate the relative relevance of each variable regarding the species distribution using a
Instability Index (see https://doi.org/10.1016/j.ecoinf.2016.11.004 for more information). This can help you selecting the
most relevant variables for the species
1) Select “Use all occurrences” and uncheck the
option “Use occurrences Z value if exists”
2) Select “Use custom Z value” then select 2000 as value. This means
that all current occurrences are manually assigned to year 2000.
In other context, for example when modelling species in a depth
range, we’ll most likely use the depth value of each occurrence.
3) Select “EOO” to use only the values of
the variables within the EOO
4) Click on “Analyse”
Z meaning is set by default to “Year”
because this is the Z meaning we
previously assigned to the variables
we imported.

Contribution of each variable will appear
Most relevant variables
will be automatically
selected.

In the next step variables are optimally ordered in the polar space using they correlation matrix.
You can eventually reorder variables, but the most of the time you’ll just continue
Click on “Continue”

In the next step, the 3DCEL is generated and shown 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 environmental
conditions that occur in the world for each year..
2) Click on “3D View” to
open a 3D viewer and
show the 3DCEL in a 3D
view.
1) Click on those cursor
buttons to see the
different layers of the
3DCEL. There is one layer
for each year of the used
variables

In the last step, you can optionally save this 3D CEL to be used later. Or you can just load it for the current worksession.
For this example we’ll save it to use it later
1) Enter a name
2) Click on “Save layer”
3) When save completed,
click on “Continue”

This Z value indicates here which year (thus, which
environmental data) corresponds to the current species
occurrences. For example, if we assign them 2000, that
means that the occurrences should be considered as
corresponding to the environmental data assigned to Z
(Year)=2000 in the 3D CEL we are using.
This indicates that NOO3D will generate a model for the whole
range of years included in the 3DCEL (2000,2050, 2070).
In other contexts, for example when modelling species in a depth
range, we’ll most likely use the depth range where the species is
present, but not the whole depth range available.
1) Select “Use all occurrences”
and uncheck the option “Use
occurrences Z value if exists”
Z meaning is set to Year because this is the Z meaning
we previously assigned to the variables we imported.
2) Select “Use custom Z value”
to the current occurrences
Once a 3DCEL selected or built, we can perform the NOO3D for the species.
We’ll have to set that the Z axis is Year and assign a Z value to the current occurrences, as in
this context they don’t have a value. In other contexts, for example when modelling species in
a depth range, we’ll most likely use the depth value of each occurrence

2) Click “Run” to calculate density
1) Set “Smoothing” to 3
NOO3D uses a kernel density function to calculate the suitability of the species.
Therefore a smoothing parameter can be adjusted to take into account the
environmental tolerance of the species. The more a species is tolerant, the
higher we may adjust smoothing. Typical values range between 1 and 3

Results will be displayed both in the world map, showing geographic density, and in the dialog box, showing polar density map
You can see the density for each Z (year)
value of the 3D CEL using the button bar
You can also open the 3D view using the
3D View button
Probability and density rasters can
be saved to files using this button

If you click the 3D View button you’ll see a 3D viewer with the niche density data of the species

Going back to MapMaker, you can move the dialog box to be able to show the world map, and see the species
suitability for different years
1) Drag the dialog box to a side
to be able to see the world map
2) Click on those cursor buttons to
see the different layers of the
3DCEL. There is one layer for each
year of the used variables
You can see in the world map the
density for each Z (year) value of
the 3D CEL using the button bar to
change year

Close the dialog box and go back to main MapMaker window. We’ll now calculate Distribution map
1) Go to menu
“Mapping/Niche of occurrence/ Distribution map”

Thanks to having saved previously the 3DCEL we built, we’ll now just have to select it to calculate NOO3D distribution
2) Select the previously saved CEL
3) Click on “Accept”

The parameters to set are the same than for the density map
This indicates that NOO3D will generate a model for the whole
range of years included in the 3DCEL (2000,2050, 2070).
In other contexts, for example when modelling species in a depth
range, we’ll most likely use the depth range where the species is
present, but not the whole depth range available.
1) Select “Use all occurrences” and
uncheck the option “Use occurrences
Z value if exists”
Z meaning is set to Year because this is the Z meaning
we previously assigned to the variables we imported.
2) Select “Use custom Z value” to
the current occurrences

5) Click on “Run”. You’ll be asked to enter a file
name to save results. Then calculation will start
4) Set “Smoothing” to 3
Kernel density hull options
“Add area” option (by default) indicates that the
estimated area will be added to the distribution map. The
other option, “Hull simulation”, adds just a shape only
for visualization purposes, not as part of the species
distribution.
Range can be “Full layer” or “EOO”.
In this case, as the CEL we are using
is already limited to the EOO, we
can leave the defaults

Once ended, results will include a file that can be opened with MRMapping
MRMapping is another application of ModestR that
can show several distribution maps at the same time,
while MapMaker is intended to work with a single
distribution map
Click to “Open MRMapping”

The file generated for MRMapping contains a distribution map for each Z value (year) of the 3D CEL used to calculate
niche. In this case, this means a distribution map for each year for which we added environmental data to the 3D CEL
Zoom to France
Uncheck valid occurrences to
only see the range distribution
The distribution of the species
for each year is displayed with a
different color

Go to menu “Edit / Distribution list editor”
Double click on land colors to modify
them
Use those checkboxes to show / hide
individual distribution maps
Select a distribution and use those
buttons to change their display order
You can modify the distribution colors and order to explore the species distribution by year
The list of distributions is shown here

You can also use slideshow feature to see how species niches will change in time
Go to “View / Slideshow”
A floating toolbar will be displayed, to easily move around the distribution maps
for each Z value (year), much like moving from a slide to another in a slideshow

The procedure previously described is useful when working with one or few species, and when we want to see the results
of each step, test several parameters, etc.
But when working with many species, it may be more useful to use DataManager application from ModestR, that
allows working with databases of hundreds or thousands of species. In DataManager you can perform NOO3D in batch
mode and obtain for example the distribution of many species for different years

It was the Step by step tutorial:
An example using ModestR to model species distribution in
different climatic change scenarios
Thank you for your interest.
You can find this one and other tutorials in http://www.ipez.es/ModestR
By the ModestR team

17. An example using ModestR to assess species distribution in different climatic change scenarios (Version ModestR 5.6 or higher)

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