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Step by step tutorial:
Adding NOAA's Word Ocean
Atlas 2018 data to ModestR
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Download Word Ocean Atlas data specifically formated for ModestR from ModestR website:
http://www.ipez.es/ModestR/Datafiles.html >> Data Files >> NOAA’s World Ocean Atlas 2018
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Before all, read this:
This tutorial explains how to import specific data from WOA to ModestR.
But if what you want is to import objectively analyzed means for the WOA measured variables for all decades, you
don’t need to follow this tutorial. You can just download those data from ModestR website, then follow tutorial 9
which is more straightforward:
Then follow tutorial 9.
What do you need for this tutorial:
1. ModestR v.5.3 or higher installed
2. Internet connection
3. About 15 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 download and
install Word Ocean Atlas 2018 data
(from NOAA) in ModestR . Follow the
next steps!
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Go to NOOA’s World Ocean Atlas 2018 data: https://www.nodc.noaa.gov/OC5/woa18/woa18data.html (*)
Then select the variable you want to download (if you want to download several ones, you should repeat this process
for each one).
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Next you have to select the resolution grid (5°, 1° or 1/4°degree) and the format. In the format select NetCDF. You
may also select the decadal period. Finally, select the time period. For this tutorial we’ll select Annual.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Now you have to select the way to access data. We’ll select HTTPServer. The download will start.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
As explained in the tutorial nº3 “How to integrate and use environmental data”, run ModestR MapMaker or
DataManager and go to the Layers >> Manage environmental variables menu. A dialog box will be opened. Follow the
steps:
1.Click on the Add
button in th Folders
bar
2. Enter a folder
name
3. The new folder will be added to
the variables tree. Click over it to
select it.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Now we’ll import the downloaded file to the new folder we created. Follow the steps:
1.Click on the
Import button
3.A dialog box will open to select
the file to be imported. Select the
file previously downloaded with
WOA data.
2.Then select the
single NetCDF file
option in the menu
that appears
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
A NetCDF file can contains several variables packaged, along with metadata. ModestR will detect this and show a dialog
box to allow selecting which data has to be imported.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Placing the mouse cursor over any variable in the list a popup will appear showing the available information about the
variable.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
1. Place the mouse
cursor over any
variable
2. A popup will appear
showing the available
information about the
variable.
ModestR also allows you to see metadata that may describe the data contained in the file.
1.Click on the
Metadata button
2.A window will appear showing file
metadata.
In those metadata we can read for example that the variable named “t_an” is the ‘Objectively analyzed mean fields for
sea_water_temperature at standard depth levels’. For this example we’ll only import this variable.
1.For this example
leave checked only
the variable t_an
2.Select as Z value the depth.
WOA contains data for
each variable along a
wide range of depths.
They are all packaged in
the NetCDF file. Here
we can see that there
are data for each
variable at 102 different
depth value.
3. Accept
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
The importation process will start. It may take some time, depending on the number of variables to be imported.
A new node will appear on the tree, with the same name than the imported folder
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
importation, a new folder with
me of the imported variable will
r. Clicking on it to expand it, we
ee all the data imported. In this
here are data for several depths.
As we selected ‘depth’ as Z value in t
previous step, each variable as the
corresponding value assigned.
This is specially useful when worki
with 3D species distributions (s
ModestR Tutorials 17 and 19)
Selecting a variable in the tree will
display all its information on the right
panel.
Close to go back to MapMaker m
Now we can already use the imported data. For example, to show it in a Map.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
In MapMaker go to
>>Rasters>>Add environmental
aster
2. Then select a variable in the tree an
click on Select.
This should be the result:
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Let’s go back to the Environmental Variable Manager. Select Layers >> Manage environmental variables menu option.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
To be able to use this variable for 3D analyses, you have to indicate to ModestR that this folder corresponds to a 3D
variable. That is, this folder contains the same variable but for several depths (Z values). To do that, select the folder
and convert it to a 3D dataset.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
1. Select the folder
corresponding to the
variable and right-click
to see a menu
2. In the contextual
menu, select Convert
folder to 3D dataset
An icon will indicate that the folder is now considered as a 3D dataset. If you import more variables from WOA, you
should repeat the same steps with the other folders, to convert them to 3D datasets.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
3D icon identifies
a 3D dataset.
That’s it! Now you can import other WOA variables repeating those same steps.
And you can also create 3D compounded environmental layers (CEL’s) and calculate species distribution models along
depth dimension, using those 3D datasets too, as explained in the tutorials of ModestR.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
-See Tutorial 10 “Creating environmental layers 3D” to create 3D
compounded environmental layers (3DCEL’s). 3DCEL’s allows to
estimate species distributions in 3D (i.e. along depth or time.
- See Tutorial 19 “Calculating 3D species distribution in marine habitats
with ModestR “to estimate species distributions along depth.
It was the
Step by step tutorial:
Adding NOAA's Word Ocean Atlas
2018 data to 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

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23. Importing NOAA's World Ocean Atlas WOA2018 data to ModestR

  • 1. Step by step tutorial: Adding NOAA's Word Ocean Atlas 2018 data to ModestR MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 2. Download Word Ocean Atlas data specifically formated for ModestR from ModestR website: http://www.ipez.es/ModestR/Datafiles.html >> Data Files >> NOAA’s World Ocean Atlas 2018 MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ Before all, read this: This tutorial explains how to import specific data from WOA to ModestR. But if what you want is to import objectively analyzed means for the WOA measured variables for all decades, you don’t need to follow this tutorial. You can just download those data from ModestR website, then follow tutorial 9 which is more straightforward: Then follow tutorial 9.
  • 3. What do you need for this tutorial: 1. ModestR v.5.3 or higher installed 2. Internet connection 3. About 15 minutes ModestR software can be freely downloaded from http://www.ipez.es/ModestR MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 4. We’ll describe how to download and install Word Ocean Atlas 2018 data (from NOAA) in ModestR . Follow the next steps! MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 5. Go to NOOA’s World Ocean Atlas 2018 data: https://www.nodc.noaa.gov/OC5/woa18/woa18data.html (*) Then select the variable you want to download (if you want to download several ones, you should repeat this process for each one). MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 6. Next you have to select the resolution grid (5°, 1° or 1/4°degree) and the format. In the format select NetCDF. You may also select the decadal period. Finally, select the time period. For this tutorial we’ll select Annual. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 7. Now you have to select the way to access data. We’ll select HTTPServer. The download will start. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 8. As explained in the tutorial nº3 “How to integrate and use environmental data”, run ModestR MapMaker or DataManager and go to the Layers >> Manage environmental variables menu. A dialog box will be opened. Follow the steps: 1.Click on the Add button in th Folders bar 2. Enter a folder name 3. The new folder will be added to the variables tree. Click over it to select it. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 9. Now we’ll import the downloaded file to the new folder we created. Follow the steps: 1.Click on the Import button 3.A dialog box will open to select the file to be imported. Select the file previously downloaded with WOA data. 2.Then select the single NetCDF file option in the menu that appears MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 10. A NetCDF file can contains several variables packaged, along with metadata. ModestR will detect this and show a dialog box to allow selecting which data has to be imported. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 11. Placing the mouse cursor over any variable in the list a popup will appear showing the available information about the variable. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ 1. Place the mouse cursor over any variable 2. A popup will appear showing the available information about the variable.
  • 12. ModestR also allows you to see metadata that may describe the data contained in the file. 1.Click on the Metadata button 2.A window will appear showing file metadata.
  • 13. In those metadata we can read for example that the variable named “t_an” is the ‘Objectively analyzed mean fields for sea_water_temperature at standard depth levels’. For this example we’ll only import this variable. 1.For this example leave checked only the variable t_an 2.Select as Z value the depth. WOA contains data for each variable along a wide range of depths. They are all packaged in the NetCDF file. Here we can see that there are data for each variable at 102 different depth value. 3. Accept MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 14. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ The importation process will start. It may take some time, depending on the number of variables to be imported.
  • 15. A new node will appear on the tree, with the same name than the imported folder MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ importation, a new folder with me of the imported variable will r. Clicking on it to expand it, we ee all the data imported. In this here are data for several depths. As we selected ‘depth’ as Z value in t previous step, each variable as the corresponding value assigned. This is specially useful when worki with 3D species distributions (s ModestR Tutorials 17 and 19) Selecting a variable in the tree will display all its information on the right panel. Close to go back to MapMaker m
  • 16. Now we can already use the imported data. For example, to show it in a Map. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ In MapMaker go to >>Rasters>>Add environmental aster 2. Then select a variable in the tree an click on Select.
  • 17. This should be the result: MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 18. Let’s go back to the Environmental Variable Manager. Select Layers >> Manage environmental variables menu option. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
  • 19. To be able to use this variable for 3D analyses, you have to indicate to ModestR that this folder corresponds to a 3D variable. That is, this folder contains the same variable but for several depths (Z values). To do that, select the folder and convert it to a 3D dataset. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ 1. Select the folder corresponding to the variable and right-click to see a menu 2. In the contextual menu, select Convert folder to 3D dataset
  • 20. An icon will indicate that the folder is now considered as a 3D dataset. If you import more variables from WOA, you should repeat the same steps with the other folders, to convert them to 3D datasets. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ 3D icon identifies a 3D dataset.
  • 21. That’s it! Now you can import other WOA variables repeating those same steps. And you can also create 3D compounded environmental layers (CEL’s) and calculate species distribution models along depth dimension, using those 3D datasets too, as explained in the tutorials of ModestR. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/ -See Tutorial 10 “Creating environmental layers 3D” to create 3D compounded environmental layers (3DCEL’s). 3DCEL’s allows to estimate species distributions in 3D (i.e. along depth or time. - See Tutorial 19 “Calculating 3D species distribution in marine habitats with ModestR “to estimate species distributions along depth.
  • 22. It was the Step by step tutorial: Adding NOAA's Word Ocean Atlas 2018 data to 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