3.- Integrating environmental data in ModestR (Version ModestR v5.3 or higher)

Step by step tutorial:
Integrating and using
environmental data in
ModestR
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/

What do you need for this tutorial:
1. ModestR v5.3 or higher
2. Internet connection
3. About 20 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR

In this tutorial we’ll describe how to
integrate environmental data coming in
ASC raster format in ModestR, and how
to use it. Follow the next steps!

Environmental data can be integrated in ModestR and used for several purposes. Not only for visualization, but also for data
exportation, data cleaning or niche calculation. Moreover, ModestR allows working with environmental data in different ways,
for example to generate clipped environmental data for a specific area.

1Tyberghein L., Verbruggen H., Pauly K., Troupin C., Mineur F. & De Clerck O. Bio-ORACLE: a global environmental dataset for marine species
distribution modeling. Global Ecology and Biogeography (DOI: 10.1111/j.1466-8238.2011.00656.x).
ModestR:
 Can integrate and use environmental data in ASCII grid format (see format description:
https://en.wikipedia.org/wiki/Esri_grid ). If you have data in this format, you can directly integrate it ModestR.
 netCDF format is also partly supported. As netCDF files can contains several rasters in different projections and formats,
the compatibility with ModestR will depend on the internal format used in the file.
 Supports precisions equal or greater than 1’, but in practice, it is strongly recommended to work with precisions around
5’ to avoid a significant performance degradation.
Environmental data collections: Bio-Oracle
You can also find different websites that offer environmental data collections in this format, for example the Bio-Oracle
dataset1. If you’ll use Bio-Oracle dataset for this example, we recommend you to download the 90°N-90°S Real Values.
Then just decompress all the files in a folder.
To access Bio-Oracle de datasets: http://www.bio-oracle.org/

1Tyberghein L., Verbruggen H., Pauly K., Troupin C., Mineur F. & De Clerck O. Bio-ORACLE: a global environmental dataset for marine
species distribution modeling. Global Ecology and Biogeography (DOI: 10.1111/j.1466-8238.2011.00656.x).
Environmental data collections: Example with Bio-Oracle1
1. To access Bio-Oracle datasets: http://www.bio-oracle.org/
2. Go to Download manager and apply the following criteria:
a) Period of layers: Present.
b) Depth of layers: Surface.
c) Format of file(s): ASCII grid file (.asc).
d) Layers to download:
 Temperature.
 Salinity.
 Nitrate.
 Phosphate.
 Silicate.
3. It’s highly recommended to create a specific folder for theses variables:
Marine.

1. Run ModestR MapMaker application. Then go to menu Layers/Manage environmental variables (In ModestRv2.0 this option
is located in the Options menu item. In more recent releases it is found in the Layers menu item).
Go to menu
Layers/Manage
environmental
variables

1. An Environmental variables management dialog box will be displayed. Then click on the Import button.
Click on the Import
button to explore
the format options
you can work with.
In this tutorial, we’ll
explain how to use
data in .ASC format.
Data with netCDF
formats will be
explain in Tutorials
11 and 12.

2. There are two ways to add environmental data: by importing a folder of Windows that contains the data, or by adding the
folder to the Environmental Variables root and then import the files into it.
1. Click on Add folder
button.
2. A dialog box will be
shown. In this dialog
box, you can enter
the folder name.
Example: Marine
3. After clicking OK,
you’ll see the new
folder in the
Environmental
Variables list.
First option:
creating the
folder*.
*folders where called “types” in previous versions

2. After creating the folder, you can import the datasets. As we said, in this tutorial, we’ll explain how to use .ASC data.
1. Select the
folder created.
2. Click on the Import
button and three
options will show up. In
this example, we’ll
import multiple .ASC
files.
The folder is just
a label or tag that
ModestR will
associate to data
for organization
purposes. It has
no effect on data
neither in its
usage. Assigning
different folder to
different data can
helps you to
identify and find
them more easily.

2. The next step is to select the raster files that contain environmental data you want to integrate in ModestR.
After selecting the variables you’re
interested in, click on the Open button.
The importing process depends on how
many variables you want to import, and
the size of the files.

3. Once the files are imported, you can modify the variables settings by clicking on the Edit button and adding the
information you want.
1. Verify the
variables
are in the
Marine
folder.
2. Click on the Edit
button to enable
the Environmental
variable settings
After updating
the information,
click on the Save
button and
close.

4. Now we’ll see some of the uses of environmental data once integrated in ModestR. There are to options to visualize
environmental information. By adding data rasters or loading raster from ESRI ASC file.
To visualize with the first option: Adding data rasters.
Layers >> Rasters >> Add Environmental data raster.
After selecting the variable you want to visualize,
click on Accept button.

5. Environmental data for the selected variable will be loaded and shown on the map. A scale will also be shown at the left
side. Independently from that, you can work on MapMaker in the usual way (zooming, adding presence areas, editing
maps..). Environmental data displayed doesn’t affect habitual MapMaker behavior.

6. If you load a distribution map or add presence data, they will be displayed over the environmental data. If you export a
map to an image file when displaying environmental data on MapMaker, it also be visible on the resulting image.
Samples are displayed
over the environmental
data
Click on the button to
export the current map view to
an image file (JPG or BMP). For
this example you can just
accept default settings. As
you’ll see, resulting image
includes currently displayed
environmental data.
In the Tutorial No 2
you can find how to add
occurrence data from GBIF, for
example.

7. You can hide or remove environmental data from the map by clicking on the corresponding button of the toolbar.
To visualizer another variable, just repeat the previous steps: click on the button and select an environmental variable.
Use this button to remove
environmental data from the
MapMaker map.

8. Besides visualization, ModestR also haves features to clip environmental data. Let’s see it through an example. Please
repeat the previously described steps to display an environmental on MapMaker.
Click on the button to add an
environmental variable to the map.
In the dialog box that will be shown,
check the wanted variable on the
tree. For example, sstmean (if you
are using Bio-Oracle data).

9. Let’s suppose you want to clip and export environmental data for a specific area you’ll directly select on the map using the
Freehand tool.
1. Select the
Freehand tool
on the right
tool panel.
2. Draw an arbitrary area on
the map, taking care of
including marine zones (Bio-
Oracle environmental data
we are using in this example
only include marine areas)
Click with the right mouse button
over the selected area and select
Add as shape.
This option will convert the
selection in a shape (for
visualization purposes)

10. Once added the visual template that demarcates the wanted area, you just have to go to File/Export/Environmental
data/For visual templates and select which environmental data you want to clip.
Go to File/Export/ Environmental
data/For each shape.
For this example we’ll only select one variable, but in fact you can select several
variables to be clipped according to the visual template. MapMaker will generate one
new file for each one.

10. Clipped environmental data will be exported to the folder you select, in the previously mentioned ASCII format
In the tree that is
displayed, select the
variables to be
clipped. For this
example, select the
same variable that is
displayed: sstmean.
Then click on
Accept.
Select the folder where
clipped data will be
saved.
Take into account that
existing files with the
same name will be
overwritten!

11. The exporting data process will take a few seconds, and after that you can open the resulting raster file with MapMaker.

12. The other way to use the environmental data as raster: Loading raster from ESRI ASC file.
Continuing with the previous example in MapMaker: go to menu Layers/Raster templates/Load raster from ESRI ASC file.

13. Select the file generated in the previous step and finally the clipped raster will be shown in the map.
Select the clipped raster and
click on the Open button.

14. If you have environmental data for land areas, you can also use predefined visual templates to easily add a visual template
and then clip data for a specific region, country, continent, etc.
You can add a predefined
visual template by clicking in
Layers >> Shapes >> Add
shapes. Or by clicking
directly on the Add shapes
icon in the tool bar.
In this example we are using environmental data for land areas (they are not included in Bio-Oracle dataset,
but you may find some in other web sites o related international programs satellite sensors like Moderate
Resolution Imaging Spectroradiometer MODIS ).

15. In the preselection tree, you can select a country, a whole continent, etc. To verify the area, you can drag the mouse over
the maps. Here, we selected Africa and then click on Close button.

16. The visual template is added to the map: Africa and its territories with yellow borders.

15. Then you can add the environmental raster, exactly as you did before: Layers >> Rasters >> Add Environmental data raster.

15. Then, you can:
1. Clip and save the raster for each shape: In this case will save each African country in separated files.

15. The process will time some time, depending on the size of the shape.

15. After exportation, you can visualize the variables you exported for African countries: Layers >> Rasters >> Load raster from
ESRI ASC file. A dialog box will show you the options you have, after selecting the country of interest, click on Accept.

15. Finally you can see the raster you selected, with the environmental information.
This option allows you to visualize
each raster (country in this case).
You may not be able to select
more than option.
If you want to visualize Africa
entirely (for example), you need
to follow different steps.

16. If you want to visualize the entire African environmental raster.
1. Load the area of interested shape as
you did before: Layers >> Shapes >>
Add shapes.
2. Add the environmental raster: Layers
>> Rasters >> Add Environmental data
raster.
3. A dialog box will ask you for the folder
where you want to save the files.
Select the one you prefer.
4. After finishing the exportation process,
click on Ok button.
5. Repeat the step 2, but selecting the
file you exported, usually is the last
one you created (verify the Date of the
file).

17. Finally, you can visualize just the african environmental raster.

Besides visual templates, you can also clip environmental data for a species presence areas.
The steps are quite the same:
 Go to File/Export/ Environmental data/For presence areas and select which environmental data you want to clip. Environmental data
will be clipped to the presence areas of the current map.
In this example, you must generate the presence areas from occurrences, by applying the alpha shape method to estimate Extent Of
Occurrence - EOO. This makes easy to obtain environmental data for the EOO of a specific species. You can check the Tutorial No.4: How
to use data cleaning, EOO estimation and environmental of occurrence features in ModestR.
The steps are: Mapping>> Hull transformation >> Alpha shape >> Add as presence area.

Now, export the presence areas as you did before, selecting the environmental variable you want to export:
Export >> Environmental data >> For presence areas >> Select the variable >> Save.

Finally, to visualize the environmental variable, load it as you did before: Layers >> Rasters >> Load raster from ESRI ASC file.
To see the environmental more clear, we recommend you to uncheck the Valid option in the in the MapMaker
panel.

Finally, to visualize the environmental variable, load it as you did before: Layers >> Rasters >> Load raster from ESRI ASC file.
Now, delete all presence areas: Edit >> Delete all presence areas.

Environmental variables, once integrated in ModestR as previously described, can also be used to:
 Data cleaning and niche of occurrence estimation should use environmental variables previously integrated in ModestR
(Tutorial No. 4).
While in MapMaker you can perform an operation on a single map, in DataManager you can easily apply it to all maps of a
group (a class, an order…) in a single step.

DataManager also gives you the option to export all maps of a whole class as images (JPG) , including in them
environmental data. Or generate clipped environmental data for each one of a whole set of species in a single
step.
But all those options
are explained in the
ModestR User’s
Manual available in
the ModestR website.

It was the
Step by Step tutorial:
Integrating and using environmental
data 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 the ModestR team
Colaborators:
Estefanía Isaza Toro

3.- Integrating environmental data in ModestR (Version ModestR v5.3 or higher)

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