22.- Using Maxent in ModestR (Version ModestR 6.0 or higher)

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Step by step tutorial:
Using Maxent in ModestR

What do you need for this tutorial:
1. Maxent (we’ll explain how to get it)
2. ModestR 6.0 or later
3. Internet connection
4. About 25 minutes

We’ll describe how to configure
ModestR to be able to calculate species
distributions using Maxent.
Follow the next steps!

First of all, if you still don’t have Maxent program, you have to download it from this link:
https://biodiversityinformatics.amnh.org/open_source/maxent/
Uncompress the .zip file you will download in a folder (you may create a specific folder for this).
The files you’ll find in this folder are:

Maxent is a Java program. That is, it needs Java to be installed in you computer in order to run properly.
If you don’t know if you already have Java installed, you can perform this simple test: double-click on the “maxent.bat”
file in order to run it. If after some seconds a window like the one below appears, that’s OK, Java is installed and you can
run Maxent. Otherwise, maybe you need to install Java. Java can be got from: https://www.java.com › download

Run ModestR MapMaker program.
1) Run ModestR MapMaker

In order to calculate the distribution of a species using Maxent, we first need species occurrences. We may add them
manually, import them from a CSV file, an existing ModestR database, or from GBIF online database. To perform this last
one, select File/Import/Occurrences from online GBIF database.
2) Go to menu “File/Import/Occurrences
from online GBIF database”

In the dialog box that will appear we will enter the species name. For example “Panthera onca”.
3) Type the species name in
the textbox
4) Click “Accept”

The next step will query GBIF database how many occurrence records there are for the selected species. It will display
this information and ask you to confirm you want to continue downloading.
5) Just click on the Accept button to continue
downloading occurrence data from GBIF
Downloading of occurrence records will be done. Wait a few
minutes. When download finished, click on accept and continue.

Select the valid habitats for the species. In this case, it is the Land habitat. This information will be used by MapMaker to
automatically check occurrences validity.
7) Check the Land habitat
By default, occurrences will autochecked. That is, ModestR will
automatically check occurrences validity regarding the habitat
There are other options to clean imported
data. Now we’ll just use the default
settings.
But all those options are explained in the
ModestR User’s Manual available in the
ModestR website

Once imported, MapMaker will display a brief summary of the imported, valid and invalid occurrences.
You can also save a CSV file with all downloaded data, including GBIF
information about data sources, rights and citation information

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Now imported data are shown on the map. By default samples are automatically checked regarding species valid habitats,
and displayed using different colors.

We now can apply Maxent on this species. Go to Mapping/Run Maxent SDM
1) Go to menu “Mapping/Run Maxent SDM”

The first time we use Maxent from ModestR, an error message will be displayed, because you need to indicate where to
find Maxent program. Click on Accept.

Now select the maxent.jar file you downloaded previously. And that’s OK! Hereinafter ModestR will be able to use Maxent.
3) Click “Open”

In the next step we have to select the environmental variables to be used to calculate species distribution using Maxent.
For this example we’ll use the WorldClim dataset, but any other terrestrial variables may be used. If you don’t have any
variables integrated in ModestR, you can follow “Step by step tutorial 14- Adding WorldClim data to ModestR”.
5) Click “Continue”
4) Select some variables. For this example we selected
variables 01, 03, 09, 10, 12 and 13 from WorldClim
The geographical extent to be used to calculate species
distribution will be “Full extent”. That is, all the area covered by
the selected environmental variables

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.
But for this example we don’t do it, we just continue.
You can find more information about this option in the “Step by
step tutorial 20- Calculating species niche with Niche of
Occurrence (NOO) in ModestR”
6) Click “Continue”

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. But for this example we just continue.
7) Click on “Continue”

Finally, we can set the most relevant Maxent options. The defaults are those of Maxent. More details about Maxent settings
can be found in the Maxent documentation in https://biodiversityinformatics.amnh.org/open_source/maxent/
If you want to save Maxent output, select a
specific folder. Otherwise result will only be
displayed in ModestR

Maxent will be run from ModestR with the current species data and the selected environmental variables. This can take
some time.

Once completed, results will be shown in MapMaker map.

The right scale
indicates the suitability
level that corresponds
to the color scale in
the map.

This is the suitability map, but we may want to obtain a presence map, transforming suitabilities from a certain threshold to
presences. This can be done going to menu Layers/Rasters/Convert current raster to distribution.
1) Go to menu “Layers/Raster/Convert
current raster to distribution”

You should set the way the threshold will be established.
4) Click on “Accept”
You may select a range of suitability
values that will be considered presences
3) Select the species habitats.
In this case, it’s Land
2) Or you may select that the threshold
should be automatically fixed using the
minimum suitability value where a
confirmed presence (occurrence) already
exists

Once finished, if you selected an automatic threshold based on the minimum suitability on a confirmed presence, the
threshold value will be shown.

Then the presence areas will be added to the map.

Let’s see now other options that are made easier thanks to using ModestR to run Maxent. First of all, undo the last changes
to go back to the map with occurrences only.
5) Click on the “Undo Button”

Let’s apply Maxent again on this species. Go to Mapping/Run Maxent SDM
1) Go to menu “Mapping/Run Maxent SDM”

But now we’ll select to limit the potential area (Geographical extent) to the Extent Of Occurrence (EOO). ModestR allows
several methods to calculate EOO. We leave the default, which is alpha-shape.
For more details about EOO, see “Step by step tutorial 4- Data cleaning and hulling”.
3) Select Extent Of Occurrence
as Geographical extent
2) Select some variables. For this example
we selected variables 01, 05, 10, 14 and 16
from WorldClim
Default is alpha-shape

ModestR will “cut” the environmental variables to limit them to the EOO.

Next steps (calculate VIF and Instability Index) have no changes. For this example we’ll just continue.
5) Click on “Continue” 6) Click on “Continue”

In the last step we can set the most relevant Maxent options and also select a folder to save Maxent output. Try this option
selecting a folder. Take into account that you have to select an empty folder, to avoid overwriting.
If you want to save Maxent output, select
a specific folder. Otherwise result will
only be displayed in ModestR

Once completed, results will be shown in MapMaker map. It can be seen that now the suitability area is limited to the EOO
of the species, in turn of being worldwide.

You can hide occurrences to better see the suitability data.
8) Use those checkboxes
to show/hide occurrences

Let’s undo the last changes to go back to the map with occurrences only.
Use those checkboxes to
show/hide occurrences
9) Click on the “Undo Button”

Now we want to calculate Maxent but limiting the geographical extent to the river basins where the species is present.
To do that, go to menu Layers/Shapes/Add river basins with occurrences
1) Go to menu “Layers/Shapes/Add river basins with occurrences”

We can select different ways of selecting those basins. For this example we’ll use the default option, which is selecting the
smaller contiguous basins where the species is present (that is, where there is an occurrence).
You can find more information about this feature in the “Step by step tutorial 15- Locating species occupied river basins”

After a small time, the basins will appear as shapes in the map. In MapMaker those shapes are only for visualization
purposes, they are independent from the species distribution.

But now we’ll select to limit the potential area to the shape, which correspond to the shapes of the river basins we added
to the map.
2) Select some variables. For this example
we selected variables 01, 05, 10, 14 and 16
from WorldClim
3) Select Shape as
Geographical extent

ModestR will “cut” the environmental variables to limit them to the current shapes.

Next steps (calculate VIF and Instability Index) have no changes. For this example we’ll just continue.

In the last step we can set the most relevant Maxent options and also select a folder to save Maxent output.
If you want to save Maxent output, select
a specific folder. Otherwise result will
only be displayed in ModestR

Once completed, results will be shown in MapMaker map. It can be seen that now the suitability area is limited to the river
basins where the species is present.

We may hide shapes to better see the suitability map.
Use this button to show/hide
shapes in the map

As we’ve seen before, we can obtain a presence map, transforming suitabilities from a certain threshold to presences.
This can be done going to menu Layers/Rasters/Convert current raster to distribution.
1) Go to menu “Layers/Rasters/Convert
current raster to distribution”

You should set the way the threshold will be established. For this example we’ll use a range of 0.5 to 1.
2) Indicate a range between 0.5 and 1
3) Select the species habitats.
In this case, it’s Land
4) Click on “Accept”

Until here we have seen how to use Maxent in MapMaker to work with a single species. But you can work with many
species very easily using DataManager. For this, you need to have a database with species and occurrence data for those
species. You can find how to create a database and download data from GBIF for many species all at once in the
“Step by step tutorial 1- How to create a database”
To apply Maxent, select the species you want in the database tree then go to menu Mapping/Calculate-Apply Maxent.
2) Go to menu “Mapping/Calculate-Apply Maxent”
1) Run ModestR DataManager

The first step, like in MapMaker, is selecting the environmental variables to be used and the geographical extent. The
options are quite the same than in MapMaker: full extent, EOO, the river basins where the species is present, or an
arbitrary shape (i.e. countries, regions, etc.)
Previously saved settings
or last used settings can
be retrieved clicking on
this button
Depending on the selected
Geographical extent, specific
options may appear on a right
panel
Select the Geographical extent

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.

In the next step you can enable or disable the option of using a
variable contribution analysis to select, for each species, the most
relevant variables. If you disable it, all previously selected variables
will be always used for every species.
Enable or disable the option of using
a variable contribution analysis

In the next step you can set Maxent options and Maxent output folder. An empty folder is required, to avoid overwriting or
confusion with previous results.
Maxent output folder
Maxent options

You can also decide if you want just to generate Maxent output or also import those results to the current database. If yes,
you have to set the way suitabilities will be transformed to presences, fixing the threshold settings.
Import those results to
the current database
Select the species habitats
You must select a range of
suitability values that will be
considered presences
You may select that, whenever
species data already exists in the
database, the threshold should be
automatically fixed using the
minimum suitability value where a
confirmed presence (occurrence)
already exists

Finally, you can set if you want to export a map image of the Maxent results for each species.
All those settings can be saved in ModestR to easily use them in later worksessions.
6) Click on “Start”
Settings can be
saved clicking here
Export map image
of the Maxent
Click on this button to set image
map settings, such as region to be
exported, grids, scale, etc.

Maxent will be run from ModestR for each one of the selected species. This can take some time.

Once finished, you can see a summary in the right panel of DataManager.
Here the list of correctly
processed species is shown
If you selected to import Maxent results to the database,
the threshold applied to each species will be shown here.
Also other messages, errors or warnings will be shown
here.
You can right-click with the mouse over this list and select
“Copy to clipboard” to copy all messages to another
application (such as Notepad) in order to easily read them

If you choose to import Maxent results to the database, presence areas were added to each species, like seen previously in
MapMaker.

In the selected output folder you will find Maxent results. Go to Maxent manual for more information about this output.
You can visualize .ASC files (rasters) with MapMaker,
using menu Layers/Shapes/Load raster from ESRI ASC
/GeoTiff files

If you selected to export image maps, you will also find an “Image_maps” folder with the image of the Maxent suitability
map for each species.

It was the Step by step tutorial:
Using Maxent in ModestR
Thank you for your interest.
You can find this one and other tutorials in http://www.ipez.es/ModestR
By the ModestR team

22.- Using Maxent in ModestR (Version ModestR 6.0 or higher)

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