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MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Step by step tutorial:
Doing a multiple distributions map and
calculating spatial overlapping in MRMapping
What do you need for this tutorial:
1. ModestR v2.1 or higher (previous versions still not include
MRMapping)
2. A ModestR database already created and
populated with species distribution data (see our
tutorial “How to create a ModestR database” for details about how to create
a ModestR database, or use the ModestR “Elasmobranchii” sample database
available in ModestR website)
3. Internet connection
4. About 30 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
We’ll describe how to create maps that can
include data from several species, grouped
by any rank (class, order, family…), using
MRMapping, and how to calculate spatial
overlappings.
Follow the next steps!
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
If you still don’t have a ModestR database, you can download a sample database.
First of all, start MRMapping, and select a ModestR database that already contains species distribution data, going to
menu File/Select database, and then selecting the wanted database.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
1. Download a sample
database:
www.ipez.es/ModestR
>> Download >>
Databases >> ModestR
Elasmobranchii
database.
2. Decompress the zip file.
3. Select the
decompressed file from
MRMapping:
Menu>>File>>Select
Database.
4. This database only has
the taxonomy, please
import the GBIF data
samples as you did in
Tutorial No.2.
Now you can easily add to the map a species dataset from the selected database. Just go to the menu File/Add/Maps
from ModestR database.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Go to File/Add/Maps from ModestR database
A tree view of the database will be shown, where you can easily navigate though the different levels (classes, orders,
families, genuses and species).
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
By default, each selected species will
be added as a distinct individual
series data to the map.
Expand any branch(es) and
selected two different species,
whether or not from the same
branch.
Click on “Select” button
You can, for example, go to the species level of
the same or of different branches, and select two
different species by using the corresponding
checkboxes.
This counter displays how many species are
currently selected. This is useful to know how
many species are involved when you selected a
whole rank (e.g. a family, an order…).
Both selected species will be shown on the map. For this example we are using species with occurrence data. So each
occurrence is shown in the map as a colored point, but you can also see the occurrence area like colored areas.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Note: occurrences are usually named ‘samples’ in ModestR
To change map settings, go to Edit/Distribution list editor menu.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Go to Edit/Distribution list
editor menu.
Here are displayed the colors
assigned to samples, land and sea
presence areas (those two last
colors are used in range maps).
To change colors of a series data just double-click on the name of the wanted series (in this example, each series
corresponds to a species).
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
To modify the
color of the valid
samples, for
example, click on
the
corresponding
colored square.
A color-selection
box will be
displayed. Select
the new color
and accept. The
corresponding
samples will be
immediately
updated in the
map.
A dialog box will be
displayed where you
can change any color
just by clicking on it.
Double-click on the name of the
wanted series
If you are using range maps (such as “Elasmobranchii” sample database), you should modify presence areas colors (e.g. sea color) in turn of sample colors.
Once you have changed the colors to your liking, you can export the map as an image.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Go to File/Export/Current map view as image menu option.
Let’s go to Legend tab, and:
1. Check the “Add legend to map” option.
2. Then click on the Preview button. A preview of the
image to be exported will be shown on the default
image viewer of your system.
3. Close this preview, and click on the Accept button
to export the image to a file.
When you export an image, the
current map view is exported. So you
can zoom to a specific area, for
example, then export this view.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
A dialog box will be displayed where you can set the dimensions and format of the image to be exported, add a grid or
a legend..
The exported image will probably look like this one (if you’re using “Elasmobranchii”).
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Now let’s see how to do more complex maps, grouping presence data by ranks (orders, families, genuses…).
First of all, we’ll start a new map, going to File/New menu option.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Go to File/New menu
option to create a new
map.
Then go to File/Add/Maps from ModestR database menu option, to select several species distribution maps to add.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Go to File/ File/Add/Maps
from ModestR database
menu option.
Then go to File/Add/Maps from ModestR database menu option, to select several species distribution maps to add.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Expand any
branch(es) and
selected for
example a whole
class, or one or
two orders.
Change the Add mode to “Group by”, and select to group selected species by families, for example.
Click on “Select” button.
If the selection you have
done includes many
species, a message may be
displayed warning that the
operation may take some
time.
MRMapping will collect the
data of every selected
species and group them by
the category you have
selected.
Resulting map will show a different color for the data of each category you have selected (orders, families, genuses…)
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Resulting map will show a different color for the data of each category you have selected (orders, families, genus).
Go to Edit/Map list editor menu as you did before.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
A dialog box with the list of
different datasets currently
shown in the map will be
displayed.
In this example, data has been
grouped by families. So here we
can see that each family is a
dataset, and, as previously
explained, we can double click
on any dataset name to modify
colors and other settings.
You can also easily delete one or more datasets from the map.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Then click on the
Del button to
delete the checked
datasets.
Map will be
immediately
updated.
Use the checkboxes
on the left of the
datasets to select
them.
You can modify the order in which datasets are displayed on the map, thus modifying how they overlap. Order column
indicates the order in which the datasets are displayed. The order nº1 indicates the topmost dataset, that is, the
dataset that is painted above all the others. The order nº 2 is the next one, etc. So you may want to change this order
to do that a dataset shall be more visible than another one.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Once all settings done, click on
“Close” button to close this dialog
box.
To do that, just select the wanted
dataset, and change its relative
order using the buttons Top, Up,
Down and Bottom.The map will be
immediately updated.
Verify that the
Show option is
unchecked.
You can decide to add more data in any moment, just by going again to File/Add/Maps from ModestR database menu
option, and selecting new data. There is no restriction in the way you may add data: you can now add a single species,
or a whole family, etc. Finally you can export resulting going to File/Export/Current map view as image menu option,
as explained before.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
There are more things you can do un MRMapping, such as adding environmental data or visual templates. More
information about environmental variables in Tutorial No. 3
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
This is an example of a map generated with MRMapping with surface temperature as marine environmental layer.
If you use range maps (e.g. those from “Elasmobranchii” sample database available in ModestR website), you can also
calculate spatial overlapping between the distributions you have added to the map.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
You will have three options:
1. Geographic overlapping.
2. Environmental overlapping.
3. Areas summary report.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Geographic overlapping option: exporting and map processing steps.
✓ Short report only calculates global spatial overlapping between each pair of
distributions.
✓ Full report also provides information about occupied surface of each
distribution and overlapping by habitat type.
Select the option you’re interested in and wait until the map processing step
finishes.
Geographic overlapping option: saving and analyzing steps.
✓ Save the .csv file in the folder and click Ok.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Environmental overlapping option: exporting and saving steps. To estimate the environmental overlapping, you need
to create the environmental layer before (Tutorial No. 3).
✓ Short report only calculates global spatial overlapping between
each pair of distributions.
✓ Full report also provides information about occupied surface of
each distribution and overlapping by habitat type.
Select the option you’re interested in and save the .file in the folder
and click Accept.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Areas summary reports: This option generates a report in CSV format with the areas in km2 of each type of habitat
where the species is present..
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
✓ Then, you can open
the file with any
spreadsheet.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Areas summary reports: Total Area Of Occupancy of the species: Total.AOO. Total area for each habitat type occupied
by the species: Sea.Area, Land.Area, Large.Rivers.Area, Small.Rivers.Area, Lentic.waters.Area, etc. Minimum and
maximum coordinates where the species is present. Min.Longitude, Max.Longitude, Min.Latitude, Max.Latitude.
It was the
Step by step tutorial:
Doing a map in MRMapping
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

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5.- Doing a map in MRMapping (Version ModestR v5.3 or higher)

  • 1. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Step by step tutorial: Doing a multiple distributions map and calculating spatial overlapping in MRMapping
  • 2. What do you need for this tutorial: 1. ModestR v2.1 or higher (previous versions still not include MRMapping) 2. A ModestR database already created and populated with species distribution data (see our tutorial “How to create a ModestR database” for details about how to create a ModestR database, or use the ModestR “Elasmobranchii” sample database available in ModestR website) 3. Internet connection 4. About 30 minutes ModestR software can be freely downloaded from http://www.ipez.es/ModestR MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 3. We’ll describe how to create maps that can include data from several species, grouped by any rank (class, order, family…), using MRMapping, and how to calculate spatial overlappings. Follow the next steps! MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 4. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ If you still don’t have a ModestR database, you can download a sample database.
  • 5. First of all, start MRMapping, and select a ModestR database that already contains species distribution data, going to menu File/Select database, and then selecting the wanted database. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ 1. Download a sample database: www.ipez.es/ModestR >> Download >> Databases >> ModestR Elasmobranchii database. 2. Decompress the zip file. 3. Select the decompressed file from MRMapping: Menu>>File>>Select Database. 4. This database only has the taxonomy, please import the GBIF data samples as you did in Tutorial No.2.
  • 6. Now you can easily add to the map a species dataset from the selected database. Just go to the menu File/Add/Maps from ModestR database. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Go to File/Add/Maps from ModestR database
  • 7. A tree view of the database will be shown, where you can easily navigate though the different levels (classes, orders, families, genuses and species). MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ By default, each selected species will be added as a distinct individual series data to the map. Expand any branch(es) and selected two different species, whether or not from the same branch. Click on “Select” button You can, for example, go to the species level of the same or of different branches, and select two different species by using the corresponding checkboxes. This counter displays how many species are currently selected. This is useful to know how many species are involved when you selected a whole rank (e.g. a family, an order…).
  • 8. Both selected species will be shown on the map. For this example we are using species with occurrence data. So each occurrence is shown in the map as a colored point, but you can also see the occurrence area like colored areas. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Note: occurrences are usually named ‘samples’ in ModestR
  • 9. To change map settings, go to Edit/Distribution list editor menu. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Go to Edit/Distribution list editor menu. Here are displayed the colors assigned to samples, land and sea presence areas (those two last colors are used in range maps).
  • 10. To change colors of a series data just double-click on the name of the wanted series (in this example, each series corresponds to a species). MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ To modify the color of the valid samples, for example, click on the corresponding colored square. A color-selection box will be displayed. Select the new color and accept. The corresponding samples will be immediately updated in the map. A dialog box will be displayed where you can change any color just by clicking on it. Double-click on the name of the wanted series If you are using range maps (such as “Elasmobranchii” sample database), you should modify presence areas colors (e.g. sea color) in turn of sample colors.
  • 11. Once you have changed the colors to your liking, you can export the map as an image. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Go to File/Export/Current map view as image menu option.
  • 12. Let’s go to Legend tab, and: 1. Check the “Add legend to map” option. 2. Then click on the Preview button. A preview of the image to be exported will be shown on the default image viewer of your system. 3. Close this preview, and click on the Accept button to export the image to a file. When you export an image, the current map view is exported. So you can zoom to a specific area, for example, then export this view. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ A dialog box will be displayed where you can set the dimensions and format of the image to be exported, add a grid or a legend..
  • 13. The exported image will probably look like this one (if you’re using “Elasmobranchii”). MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 14. Now let’s see how to do more complex maps, grouping presence data by ranks (orders, families, genuses…). First of all, we’ll start a new map, going to File/New menu option. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Go to File/New menu option to create a new map.
  • 15. Then go to File/Add/Maps from ModestR database menu option, to select several species distribution maps to add. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Go to File/ File/Add/Maps from ModestR database menu option.
  • 16. Then go to File/Add/Maps from ModestR database menu option, to select several species distribution maps to add. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Expand any branch(es) and selected for example a whole class, or one or two orders. Change the Add mode to “Group by”, and select to group selected species by families, for example. Click on “Select” button. If the selection you have done includes many species, a message may be displayed warning that the operation may take some time. MRMapping will collect the data of every selected species and group them by the category you have selected.
  • 17. Resulting map will show a different color for the data of each category you have selected (orders, families, genuses…) MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 18. Resulting map will show a different color for the data of each category you have selected (orders, families, genus). Go to Edit/Map list editor menu as you did before. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ A dialog box with the list of different datasets currently shown in the map will be displayed. In this example, data has been grouped by families. So here we can see that each family is a dataset, and, as previously explained, we can double click on any dataset name to modify colors and other settings.
  • 19. You can also easily delete one or more datasets from the map. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Then click on the Del button to delete the checked datasets. Map will be immediately updated. Use the checkboxes on the left of the datasets to select them.
  • 20. You can modify the order in which datasets are displayed on the map, thus modifying how they overlap. Order column indicates the order in which the datasets are displayed. The order nº1 indicates the topmost dataset, that is, the dataset that is painted above all the others. The order nº 2 is the next one, etc. So you may want to change this order to do that a dataset shall be more visible than another one. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Once all settings done, click on “Close” button to close this dialog box. To do that, just select the wanted dataset, and change its relative order using the buttons Top, Up, Down and Bottom.The map will be immediately updated. Verify that the Show option is unchecked.
  • 21. You can decide to add more data in any moment, just by going again to File/Add/Maps from ModestR database menu option, and selecting new data. There is no restriction in the way you may add data: you can now add a single species, or a whole family, etc. Finally you can export resulting going to File/Export/Current map view as image menu option, as explained before. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 22. There are more things you can do un MRMapping, such as adding environmental data or visual templates. More information about environmental variables in Tutorial No. 3 MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ This is an example of a map generated with MRMapping with surface temperature as marine environmental layer.
  • 23. If you use range maps (e.g. those from “Elasmobranchii” sample database available in ModestR website), you can also calculate spatial overlapping between the distributions you have added to the map. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ You will have three options: 1. Geographic overlapping. 2. Environmental overlapping. 3. Areas summary report.
  • 24. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Geographic overlapping option: exporting and map processing steps. ✓ Short report only calculates global spatial overlapping between each pair of distributions. ✓ Full report also provides information about occupied surface of each distribution and overlapping by habitat type. Select the option you’re interested in and wait until the map processing step finishes.
  • 25. Geographic overlapping option: saving and analyzing steps. ✓ Save the .csv file in the folder and click Ok. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 26. Environmental overlapping option: exporting and saving steps. To estimate the environmental overlapping, you need to create the environmental layer before (Tutorial No. 3). ✓ Short report only calculates global spatial overlapping between each pair of distributions. ✓ Full report also provides information about occupied surface of each distribution and overlapping by habitat type. Select the option you’re interested in and save the .file in the folder and click Accept. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 27. Areas summary reports: This option generates a report in CSV format with the areas in km2 of each type of habitat where the species is present.. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ ✓ Then, you can open the file with any spreadsheet.
  • 28. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Areas summary reports: Total Area Of Occupancy of the species: Total.AOO. Total area for each habitat type occupied by the species: Sea.Area, Land.Area, Large.Rivers.Area, Small.Rivers.Area, Lentic.waters.Area, etc. Minimum and maximum coordinates where the species is present. Min.Longitude, Max.Longitude, Min.Latitude, Max.Latitude.
  • 29. It was the Step by step tutorial: Doing a map in MRMapping 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