2.- How to create and edit a map using GBIF data (Version ModestR v5.3 or higher)

Step by step tutorial:
How to create and edit a map
downloading data from GBIF
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/

What do you need for this tutorial:
1. ModestR software installed (this
tutorial is done with Modestr V.5.3)
2. Internet connection
3. A ModestR database (see first step by
step tutorial “How to create a database”)
4. About 20 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR

We’ll describe how to create a new map
downloading data from GBIF, how to
edit it, and how to store it in a ModestR
database. Follow the next steps!

1. Run ModestR MapMaker and select an existing database using the File/Select database menu option.
Select the database
MapMaker will work
with. In this example
we’ll assume you’re
using the
“MyModestRDatabase”
created in the step by
step tutorial nº1 “How
to create a ModestR
database”)

2. Let’s suppose you want to download occurrence records from GBIF. Then select File/Import/Occurrences from
online GBIF database
Other options already exist such as importing occurrence
data from a CSV file, from KML files, shapefiles, etc.
All those options are explained in the ModestR Tutorial No. 1
available in the ModestR website.

3. In the dialog box that will appear we will select the species from the database.
Other options already
exist to select which
kind of records to
download from GBIF,
and to use synonyms.
All those options are
explained in the
ModestR User’s Tutorial
available in the
ModestR website.
Click on the Select
from database
button to select the
species to be
downloaded.
You can also directly
type the species
name in the textbox.

4. The taxonomy tree of the database will be displayed. Now you can select the species to be downloaded from GBIF.
Click on the
Enable/Disable search
button to show the
search options.
You can also directly
select the species from
the tree.

3.Click on the Select
button to select the
species and close this
dialog box.
2.Select the species
“Carcharhinus
acarenatus” in the
search results.
5. You can easily search for the species and select it to continue download process.
1.Type the first letters
of the species:
“Carcharhinus”

6. Now you are ready to start downloading by clicking on the Accept button.
Just click on the Accept
button.
Selected species name
appears on the text
box.

7. According the past selecting criteria, an information message will show you the confidence level related to the species
name selected.
Click on the Yes button to accept downloading occurrence data for the
proposed the species.

8. 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.
Just click on the Accept
button to continue
downloading occurrence
data from GBIF.

9. Downloading of occurrence records will be done. Wait a few minutes. When download finished, click on accept and
continue.

10. Select the valid habitats for the species. In this case, it is the Sea habitat. This information will be used by MapMaker
to automatically check occurrences validity.
Check the Sea habitat
and the Accept button
to continue
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.
By default, occurrences will
autochecked. That is, ModestR will
automatically check occurrences
validity regarding the habitat.

11. Once imported, MapMaker will display a brief summary of the imported, valid and invalid occurrences.

12. You can also save a CSV file with all downloaded data, including GBIF information about data sources, rights and
citation information.

13. Now imported data are shown on the map. By default samples are automatically checked regarding species valid
habitats, and displayed using different colors. Let’s zoom on a zone where the species is present.
2. Click on one
corner of the
wanted zone and
drag to the
opposite corner to
select the zone.
3. Click with the
right button of
the mouse and
select Zoom
1. Select the
Zoom tool on
the left
toolbar

14. Repeat the last action until you see occurrences with more precision.
Zoom on the area
several times if
needed.

15. Now we are seeing occurrences with more precision. Let’s suppose that you have found several occurrences that are
clearly out of the valid habitats of the species and you want to delete them.
Let’s suppose you want to
delete those occurrences.
By default, occurrences are
automatically checked
regarding species valid
habitats, and displayed
using different colors.
Valid occurrence
Invalid
occurrence

16. You can simply delete any samples selecting an area in the map and using the Freehand tool to select them and next
the Delete samples feature.
2. Select an
area that
contains the
occurrences to
be deleted
1. Select the
Freehand
tool
3. Right-click with
the mouse and
select Selected
occurrences and
next Delete
occurrences.
Alternatively you can
use the Delete
occurrences button.

1. Occurrences have
been deleted
17. The selected occurrences will be deleted from the map. But let’s suppose you made a mistake. Then, you will undo last
modifications using the Undo button or the Edit/Undo menu.
2. Undo last
modifications using
the Undo button or
the Edit/Undo menu.

1. Pccurrences have been
restored
18. Occurrences will be restored. In fact, you decided that you’d rather relocate the occurrences in turn of deleting
them. To do that, you can use the Edit occurrence tool.
3. Click on the occurrence
to be moved and drag it to
its new positon. Then
release the mouse button.
While you drag the
occurrence you can
immediately see, by its
color, if it is located in a
valid habitat (only if it is an
habitat autovalidated
occurrences)
2. Select Edit occurrence
tool.

19. The Edit occurrence tool can also be used to delete a single occurrence. Just select the occurrence and press the
Delete key.
1. Select Edit
occurrence tool.
2. Select the
occurrence and press
the Delete key. The
occurrence is removed.
You can also right-click
on the occurrence to
be deleted and select
the Delete occurrence
option in the
contextual menu.

20. But remember that you can also just let stay the invalid occurrences in the map if you want. ModestR will store them
but will always left them out when doing any map processing or calculation. So you are not obliged to delete them.
Moreover, ModestR
will always recheck
occurrence validity if
there are
modifications in the
world map used as
reference.
If, for example, a new
lake is added to the
ModestR world map,
all occurrences will
be automatically
rechecked.

3. Right-click with the
mouse and select
Selected occurrences
and next Manually
validate occurrences,
and finally Only not
valid.
21. Another possibility is to manually validate an occurrence. Let’s suppose that you want to consider that all the
occurrences shown as invalid near Australia are in fact valid. In this case you can validate them manually. ModestR
will always consider them as valid regardless of where they are located.
1. Select
the
Freehand
tool
2. Select an area
that contains
the occurrences
to be validated

22. Now the occurrences that were invalid have been manually validated. If you zoom on the area, you will see that
those occurrences have a different color that the automatically validated occurrences.
Here automatically
validated occurrences are
light green, while manually
validated occurrences are
brown (colors depend on
your ModestR settings).
Even if less usual, the opposite
operation can also be done: you
can manually invalidate
occurrences. Those occurrences
will be stored in the map, but
they will not be took into
account for any calculation or
processing.
ModestR will always consider
them as invalid regardless of
where they are located.

23. To make easier to distinguish them, you can modify occurrence color and transparency going to Options/Preferences.
2. By default new
settings will be
saved for the next
time you run
MapMaker.
1. Just click on the
color rectangles to
modify the color of
the different types
of occurrences in
the map.

24. You can also manually add occurrences if you want. If you use habitat autovalidated occurrences, you can drag the
occurrence and immediately see if it is located in a valid habitat before placing it in the map.
1. Select the Add
occurrence tool
3. Click on the
position where you
want to add a new
occurrence. You can
drag the sample and
immediately see, by
its color, if it is
located in a valid
habitat before
placing it in the map
(only if you use
habitat
autovalidated
occurrences).
2. Select the valid
habitats. In this
case, just Sea.

25. Once the map edited, you can store it in the database. Just click on the corresponding button!
Click on the button
of the toolbar to
save the current
map in the database
The map will be saved in the current
working database, replacing the existing
map, if any. Remember that you can easily
change the working database going to the
menu File/Select database.
You can also go to menu
File/Save/To ModestR Maps
Database

It was the
Step by step tutorial:
How to create and edit a map
downloading data from GBIF
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

2.- How to create and edit a map using GBIF data (Version ModestR v5.3 or higher)

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