11.- Calculating species distribution for different periods with ModestR (Versión ModestR 5.3 or higher)

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Step by step tutorial:
Calculating species
distribution for different
periods with ModestR

What do you need for this tutorial:
1. ModestR v.5.3 or higher installed
2. Internet connection
3. About 25 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR

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

To calculate species distribution in different periods in time, we’ll need environmental data for those periods.
We have sets of those variables for 3 different years, that we just
number as year 0, 1 and 2 (you can number them at your
convenience). Of course, Altitude may be the same for all three
years; but in this case, we’ll need to have 3 files, one for each year,
even if they contain the same data.
We need to have those data in separated files ESRI ASC formats, for
example, and name them using this format:
name[year].ASC
For this example, let’s suppose we have data for:
 Anual mean temperature
 Anual mean precipitation
 Altitude

2. Next step will be to arrange those files in folders; one
folder for each variable, to obtain a structure like this:

3. Run ModestR MapMaker and go to Layers/Manage environmental variables to open variable manager window.
1. Go to Layers / Manage enviromental variables

2. Select the root node on the tree
3. Right-Click to show context menu
and select “Add new folder”

4. Type a name
(For this example we’ll enter “Niche3DExample”)
5. Click OK

The new folder will appear on the tree

4. Now, open a Windows Explorer (also called File Explorer), select the three folders that contain the environmental data.
Then drag them and drop them over the new folder.
1. Select the three folders
2. Drag them
3. And drop them on the new folder
Windows Explorer

The environmental variables will be imported and added to the tree.
ModestR will automatically assign a Z value
to each variable using the number in square
brackets from the corresponding filename.

5. Now we’ll have to convert each variable folder to a 3D dataset, which is a type of dataset containing several data for
the same variable, for different Z values (where Z can be for example depth, or time, as in this case).
1. Select the Niche3DExample node
and right-click
2. Select Convert all subfolders to 3D
datasets in the contextual menú

Done! Now we have three 3D datasets. We can close this window.
3D icon identifies a 3D dataset

6. Next step is creating a 3D CEL (Compounded Environmental Layer) that will bind together the variables added
before in a single multidimensional variable.
1. Go to menu Mapping/Niche of
occurrence/Create new compounded
environmental layer (CEL)/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

When creating a 3D CEL, only 3D datasets will be displayed among the candidate variables.
Note: unlike in this example you’ll usually employ more
than just three variables to calculate species niche, to
obtain more significant results.
2. For this example, in the dialog box
that will be shown, select the three
3D datasets added before
3. Click on Continue button.

1
For the sake of simplicity, we’ll just use default settings. Thus, we’ll simply click Continue in each step until last one.
2
3
Of course, displayed graph will
depend on the data you used,
and won’t have to match the
one shown here.
4. Click Continue button

In the last step, we’ll save this 3D CEL to be used later. Finally, we’ll click Close to go back to MapMaker main window.
5. Enter a name for the CEL (here
“Modestr 3D CEL example”)
6. Click Save 3D Layer
7. Click Close

Example of how the environmental layer would be displayed depending on the data used.

Now we’ll test this 3D CEL to calculate species distribution at several periods of time.
8. Click on Clear raster

7. Then we’ll first download species occurrences from GBIF (you can also import them from a CSV file)
2. Then select Samples from online GBIF database
1. Go to File/Import

Enter the scientific name of a species. Of course, select a species that lives in the habitats corresponding to the
environmental data imported before (i.e. select a marine species if you imported environmental variables for marine
areas)
3. Species name
4. Click Accept
For test purposes, we suggest to use a common (not too
rare) species, in order to have a number of occurrences
high enough to calculate a niche. Then click on Accept.
Download task will start immediately.

Once data downloaded, you have to select the correct habitat for the species. Typically land or sea.
5. Select the correct habitat for the species
6. Click Accept

8. Once we have occurrences from a species, we can calculate its niche for different time periods using the previously
created 3D CEL. We’ll start by Density map.
1. Go to menu Mapping/Niche of
occurrence/ Density map

You may have to select the 3D CEL to be used (depending on it was already loaded or not).
2. Select the 3D CEL example created
3. Click Accept

4. Set that the Z axis is
time
6. Click Continue
5. Assign a Z value to
the current occurrences
This Z value indicates here which time (thus, which
environmental data) corresponds to current species
occurrences. For example, if we assign them the 0, that
means that the occurrences should be considered as
corresponding to the environmental data assigned to Z
(time)=0 in the 3D CEL we are using.
Then we’ll have to set that the Z axis is time and have to assign a Z value to the current occurrences

7. Click Run to calculate density

Results will be displayed both in the world map, showing geographic density, and in the dialog, showing polar density map.
8. You can see the density for each Z
(time) value of the 3D CEL using the
button bar
9. You can also open the 3D view
using the 3D View button

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

9. Going back to MapMaker, we’ll now calculate Distribution map.
1. Go to menu Mapping/Niche
of occurrence/ Distribution map

2. Set that the Z axis is
time
4. Click Continue
3. Assign a Z value to
the current occurrences
This Z value indicates here which time (thus, which
environmental data) corresponds to current species
occurrences. For example, if we assign them the 0, that
means that the occurrences should be considered as
corresponding to the environmental data assigned to Z
(time)=0 in the 3D CEL we are using.
Then we’ll have to set that the Z axis is time and have to assign a Z value to the current occurrences

Then select Add area option, and Run. You’ll be asked to select a folder to save results. Then calculation will start.
5. Select Add area option
6. Click Run

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
7. Click to Open MRMapping

10. The file generated for MRMapping contains a distribution map for each Z value of the 3D CEL used to calculate
niche. In this case, this means a distribution map for each period for which we added environmental data to the 3D CEL.
Each one of those distribution maps
is displayed with a different color

1. Go to menu Edit / Distribution list editor
2. Modify colors
3. Show / Hide individual distribution maps
4. Change their display order

This way you can see how species distribution will change in time.
5. Go to View / Slideshow A floating toolbar will be displayed, to easily move around the distribution
maps for each Z value, much like moving from a slide to another in a slideshow

It was the Step by step tutorial:
Calculating species distribution for different
periods with ModestR
Thank you for your interest.
You can find this one and other tutorials in http://www.ipez.es/ModestR
By the ModestR team
Colaborators:
Estefanía Isaza Toro

11.- Calculating species distribution for different periods with ModestR (Versión ModestR 5.3 or higher)

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