step by step tutorial 9 adding noaas word ocean atlas data to modestr

Step by step tutorial: Adding NOAA's Word Ocean

Atlas data to ModestR

MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/

http://www.ipez.es/ModestR/

What do you need for this tutorial:

1. ModestR v.5.1 or higher installed2. Internet connection3. About 15 minutes

ModestR software can be freely downloaded from http://www.ipez.es/ModestR


http://www.ipez.es/ModestR



We’ll describe how to download and install Word Ocean Atlas (from NOAA)

data in ModestR . Follow the next steps!



1. Download Word Ocean Atlas data specifically formated for ModestR from ModestR website:http://www.ipez.es/ModestR/Datafiles.html


1. Go to Datafiles section

2. Download Word OceanAtlas data for ModestR

http://www.ipez.es/ModestR/Datafiles.html


2. Create a folder in your computer, called “WOA 1º Objectively analyzed mean All Decades” and decompressdownloaded file in this folder.


Decompress

Downloaded file

Folder contents once filedecompressed


3. Run ModestR DataManager, go to the Layers/Manage environmental variables menu option.


Manage environmental variables

Here the current database tree is usually shown. For this tutorial, no specific database is needed.


4. If you already have added other environmental variables, they will appear on the tree. Otherwise, only the root willbe shown.


Already existing variables (if any) will be shown under the root

Root will always appear


5. Select the root node, click on the Import button on the bottom bar, then on the Folder option on the contextualmenu that will be shown.


1. Select the root node on the tree

2. Click on the Import button

3. Click on Folder option on the contextualmenu


6. On the dialog box that will appear, select the folder that you previously created on step 2 , then click Accept.


1. Select the folder where decompresseddata are (created in step 2)


7. Importation process will be performed.



8. A new node will appear on the tree, with the same name than the imported folder


A new node will always appear


9. Expand the node to see the subfolders and variables imported. Each subfolder contains all the variables of the sametype for each depth.


1. Click on the “+” to expand the node andsee subfolders 2. Click on the “+” to expand a subfolder

and see variables within


10. Select a variable to see its details in the right panel. Each imported variable have an associated Z Valuecorresponding to its depth. This value has been extracted automatically by ModestR from the variable filename duringimportation.


1. Select a variable on thetree

2. Details about the variable are shown onthe right panel.In this case the Z Value corresponds to thedepth


11. To be able to use variables for 3D analyses, you have to indicate to ModestR that each folder corresponds to a 3Dvariable. That is, each folder contains a same variable but for several depths (Z values).To do that, select each folder and convert it to a 3D dataset.


1. Select a folder, such as “ApparentOxygenUtilization”

2. Click with the right button over it to display thecontextual menu

3. Select Convert type to 3D Dataset


12. An icon will indicate that the folder is now considered as a 3D dataset. Repeat the same steps with the otherfolders.


3D icon identifies a 3D dataset.

1. Following the same steps, convertall the folders to 3D datasets


13. Now you can create 3D compounded environmental layers (CEL’s) using those 3D datasets, for example. Here we’lljust describe a simple example; run MapMaker and follow those steps:


More details about what are compoundedenvironmental layers can be found in ModestRUser’s Manual on ModestR website.A tutorial about compounded environmental layerscreation can also be found athttp://www.ipez.es/ModestR/Manual_Tutorial.html

1. Go to menu Mapping/Niche ofoccurrence/Create new compoundedenvironmental layer (CEL)/3D CEL


http://www.ipez.es/ModestR/Manual_Tutorial.html

14. When creating a 3D CEL, only 3D datasets will be displayed among the candidate variables. For this example, justselect 5 variables among the WOA data imported before.


1. For this example we are selecting 5 variables from WOA. You must select at least two variables, but a CEL may typically involve 4 or more variables.

2. Click on Continue button.


15. In the next step, Variance Inflation Factor can be calculated, in order to detect collinearities between variables,and, eventually, delete redundant variables. This step is optional, and for this example we’ll just skip and continue.


1. For this example we’ll neither calculate VIF nor delete variables.



16. In the next step, the polar coordinates system that will constitute the environmental layer is depicted. Eachvariable is an axe of this polar coordinates system. In this step you may optionally change the order of the axes, but forthis example we’ll just skip and continue.


1. The default assignation of the variables to each axis of the polar coordinates system is done basing on the correlation of each variable with each other, trying this way to maximize data dispersion, and therefore a more visually descriptive environmental layer.



17. In the next step, the CEL is generated and shown both on the map and in the polar coordinates system. For a 3DCEL, you can visualize each Z value (Z = depth in this case). You can also show a 3D view of the CEL.


1. Here the current environmental data are projected on polar coordinates system. The result is a bidimensional and more easily understandable representation of the different environmental conditions that occur in the world, according to a compound of variables (those selected to build this layer).

2. You can use those buttons to go across the several Z values (here Z=depth) of this 3D CEL

3. Click on the 3D View button to open the external viewer


18. The 3D CEL viewer allows you to interactively explore the 3D CEL in an easy way


1. In the left panel a 3D view is displayed. You can rotate it, zoom and move it using the mouse.

2. In the right panel a 2D view of the Z layer currently highlighted in the left panel is displayed. Just move the mouse over the 3D graph on the left to select the layer to be displayed on the right panel


19. Close the 3D viewer and go back to MapMaker. Then continue to the last step of CEL creation.




20. In the last step you can eventually export a report about the CEL, and save the CEL in order to use it later. CEL’s canbe used to calculate species niche or species environmental overlaps (see User’s Manual for more details).



It was theStep by step tutorial:

Adding NOAA's Word Ocean Atlas 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



step by step tutorial 9 adding noaas word ocean atlas data to modestr

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