step by step tutorial - using time as 3rd dimension to calculate species niche in modestr

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Step by step tutorial: Calculating species niche for

different periods with ModestR

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


What do you need for this tutorial:

1. ModestR v.5.2 or higher installed2. Internet connection3. About 25 minutes

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


http://www.ipez.es/ModestR



We’ll describe how to calculate species niche for different periods. To do that,

we’ll use the 3D Niche capability of ModestR, taking time as 3th dimension.

Follow the next steps!



1. To calculate species niche in different periods in time, we’ll need environmental data for those periods.

For this example, let’s suppose we have data for:• Anual mean temperature• Anual mean precipitation• Altitude

We have sets of those variables for 3 different years, that we just number as year 0, 1 and 2 (you cannumber them at your convenience. Of course, Altitude may be the same for all three years; but in this case,we’ll need to have 3 files, one for each year, even if they contain the same data.

We need to have those data in separated files ESRI ASC format,and name them using this format:

name[year].ASCSo we’ll have those files:



2. Next step will be to arrange those files in folders; onefolder for each variable, to obtain a structure like this:



3. Run ModestR MapMaker and go to Layers/Manage environmental variables to open variable manager window.

1. Go to Layers / Manage enviromental variables



2. Select the root node on the tree

3. Right-Click to show context menuand select “Add new type”



4. Type a name(For this example we’ll enter “Niche3DExample”)

5. Click OK



The new type will appear on the tree



4. Now, open a Windows Explorer (also called File Explorer), select the three folders that contain the environmental data. Then drag them and drop them over the new type.

1. Select the three folders2. Drag them

3. And drop them on the new type

Windows Explorer



The environmental variables will be imported and added to the tree.

ModestR will automatically assign a Z valueto each variable using the number in squarebrackets from the corresponding filename.



5. Now we’ll have to convert each variable folder to a 3D dataset, which is a type of dataset containing several data forthe same variable, for different Z values (where Z can be for example depth, or time, as in this case).

1. Select the Niche3DExample nodeand right-click

2. Select Convert all subtypes to 3Ddatasets in the contextual menú



Done! Now we have three 3D datasets. We can close this window.

3D icon identifies a 3D dataset



6. Next step is creating a 3D CEL (Compounded Environmental Layer) that will bind together the variables addedbefore in a single multidimensional variable.

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

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


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


When creating a 3D CEL, only 3D datasets will be displayed among the candidate variables.

Note: unlike in this example you’ll usually employ morethan just three variables to calculate species niche, toobtain more significant results.

2. For this example, in the dialog box that will be shown, select the three3D datasets added before

3. Click on Continue button.



1

For the sake of simplicity, we’ll just use default settings. Thus, we’ll simply click Continue in each step until last one.

2

3

Of course, displayed graph willdepend on the data you used,and won’t have to match theone shown here.

4. Click Continue button



In the last step, we’ll save this 3D CEL to be used later. Finally, we’ll click Close to go back to MapMaker main window.

5. Enter a name for the CEL (here“Modestr 3D CEL example”)

6. Click Save 3D Layer

7. Click Close



Example of how the environmental layer would be displayed depending on the data used.



Now we’ll test this 3D CEL to calculate species niche at several periods of time.

8. Click on Clear raster



7. Then we’ll first download species occurrences from GBIF (you can also import them from a CSV file)

2. Then select Samples from online GBIF database

1. Go to File/Import



Enter the scientific name of a species. Of course, select a species that lives in the habitats corresponding to theenvironmental data imported before (i.e. select a marine species if you imported environmental variables for marineareas)

3. Species name

4. Click Accept

For test purposes, we suggest to use a common (not toorare) species, in order to have a number of occurrenceshigh enough to calculate a niche. Then click on Accept.Download task will start immediately.



Once data downloaded, you have to select the correct habitat for the species. Typically land or sea.

5. Select the correct habitat for the species

6. Click Accept



8. Once we have occurrences from a species, we can calculate its niche for different time periods using the previously created 3D CEL. We’ll start by Density map.

1. Go to menu Mapping/Niche ofoccurrence/ Density map



You may have to select the 3D CEL to be used (depending on it was already loaded or not).

2. Select the 3D CEL example created

3. Click Accept



4. Set that the Z axis istime

6. Click Continue

5. Assign a Z value tothe current occurrences

This Z value indicates here which time (thus, whichenvironmental data) corresponds to current speciesoccurrences. For example, if we assign them the 0, thatmeans that the occurrences should be considered ascorresponding to the environmental data assigned to Z(time)=0 in the 3D CEL we are using.

Then we’ll have to set that the Z axis is time and have to assign a Z value to the current occurrences



7. Click Run to calculate density



Results will be displayed both in the world map, showing geographic density, and in the dialog, showing polar density map.

8. You can see the density for each Z(time) value of the 3D CEL using thebutton bar

9. You can also open the 3D viewusing the 3D View button



If you clicked the 3D View button you’ll see a 3D viewer with the niche density data of the species.



9. Going back to MapMaker, we’ll now calculate Distribution map.

1. Go to menu Mapping/Nicheof occurrence/ Distribution map



2. Set that the Z axis istime

4. Click Continue

3. Assign a Z value tothe current occurrences

This Z value indicates here which time (thus, whichenvironmental data) corresponds to current speciesoccurrences. For example, if we assign them the 0, thatmeans that the occurrences should be considered ascorresponding to the environmental data assigned to Z(time)=0 in the 3D CEL we are using.

Then we’ll have to set that the Z axis is time and have to assign a Z value to the current occurrences



Then select Add area option, and Run. You’ll be asked to select a folder to save results. Then calculation will start.

5. Select Add area option

6. Click Run



Once ended, results will include a file that can be opened with MRMapping.

MRMapping is another application of ModestRthat can show several distribution maps at thesame time, while MapMaker is intended towork with a single distribution map

7. Click to Open MRMapping



10. The file generated for MRMapping contains a distribution map for each Z value of the 3D CEL used to calculate niche. In this case, this means a distribution map for each period for which we added environmental data to the 3D CEL.

Each one of those distribution mapsis displayed with a different color



1. Go to menu Edit / Distribution list editor

2. Modify colors

3. Show / Hide individual distribution maps

4. Change their display order



This way you can see how species niches will change in time.

5. Go to View / Slideshow A floating toolbar will be displayed, to easily move around the distributionmaps for each Z value, much like moving from a slide to another in a slideshow



It was the Step by step tutorial:

Calculating species niche for different periods with ModestR

Thank you for your interest.

You can find this one and other tutorials in http://www.ipez.es/ModestR

