how to integrate and use environmental data in modestr

Step by step tutorial: Integrating and using environmental data in

ModestR

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What do you need for this tutorial:

1. ModestR v2.1 or higher 2. Internet connection3. About 20 minutesModestR software can be freely downloaded from http://www.ipez.es/ModestR


http://www.ipez.es/ModestR



In this tutorial we’ll describe how to integrate environmental data coming in ASC raster format in ModestR, and how

to use it. Follow the next steps!



Environmental data can be integrated in ModestR and used for several purposes. Not only for visualization, but also for data exportation, data cleaning or niche calculation. Moreover, ModestR allows working with environmental data in different ways, for example to generate clipped environmental data for a specific area.



If you have data in this format, you can directly integrate itModestR. You can also find different websites that offerenvironmental data collections in this format, as forexample the Bio-Oracle dataset1 that you can find inhttp://www.oracle.ugent.be/ . If you’ll use Bio-Oracledataset for this example, we recommend you to downloadthe 90°N-90°S Real Values. Then just decompress all thefiles in a folder.Take into account that ModestR doesn’t copyenvironmental data files you add to it. It just stores links tothose files. Therefore, it is important that, once added toModestR, you don’t move neither delete those files.Otherwise, ModestR will not be able to find and usethem.In the next steps we’ll explain how to integrate them inModestR.


1Tyberghein L., Verbruggen H., Pauly K., Troupin C., Mineur F. & De Clerck O. Bio-ORACLE: a global environmental dataset for marine species

distribution modeling. Global Ecology and Biogeography (DOI: 10.1111/j.1466-8238.2011.00656.x).

ModestR can integrate and use environmental data in ASCII grid format (see http://en.wikipedia.org/wiki/Esri_grid forformat description). It supports precisions equal or greater than 1’; but, in practice, it is strongly recommended to workwith precisions around 5’ to avoid a significant performance degradation.

http://www.oracle.ugent.be/


http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2011.00656.x/abstract

http://en.wikipedia.org/wiki/Esri_grid

Now, run ModestR MapMaker application. Then go to menu Layers/Manage environmental variables (In ModestRv2.0 this option

is located in the Options menu item. In more recent releases it is found in the Layers menu item). A dialog box will be displayed. Then click on the Import button.


Click on the Import button.

Go to menu Layers/Manage environmental variables


The next step is to select the raster files that contain environmental data you want to integrate in ModestR.


Click on Select files button.

A dialog box will be shown.In this dialog box, go to the folder where the files to be imported are located and select all the files you want to integrate in ModestR.

Remember that you can use the Control or Shift key to select several files in Windows.

Once your selection made, click on the Open button (or its equivalent according to your system language).


Once the files selected, you’ll have to assign a type to them. The type is just a label or tag that ModestR will associate to data for organization purposes. It has no effect on data neither in its usage. Assigning different types to different data can helps you to identify and find them more easily.


For this example, you can assign the “Marine” label to those data. Just write “Marine” in the Type textbox.

Then click on the Save button.


Now data is already integrated in ModestR. Each variable will appear on the tree under the type label you assigned to it.


The “Marine” type has been created and all selected files are added as variables under this type.

If you select a variable in the tree you can see its data in the left panel.


As we imported several files in a single step, all variable fields have been fulfilled by default. But you can modify any variable fields if you want, to introduce more accurate and complete data. Here’s an example:


Search and select the sstmeanvariable in the tree (for example), clicking on it.

Click on the Edit button

Now you can modify variable name, description, etc.For example, you can write “Sea surface temperature” in the Description field; and enter “ºC” in the Units field.

Once all modifications made, click on the Save button to save changes.

Finally, close this dialog box.


Now we’ll see some of the uses of environmental data once integrated in ModestR. For example for visualization purposes:


Click on the button to add an environmental variable to the map.

Check the wanted variable on the tree. For example, sstmean (if you are using Bio-Oracle data)

Even if it is not mandatory, for a more accurate visualization, you can select the habitat where the variable data should be displayed. This avoids “bleeding effects” due to coarse precision of environmental data.

Finally, click on Accept.


Environmental data for the selected variable will be loaded and shown on the map. A scale will also be shown at the left side.Independently from that, you can work on MapMaker in the usual way (zooming, adding presence areas, editing maps..). Environmental data displayed doesn’t affect habitual MapMaker behavior.



If you load a distribution map or add presence data, they will be displayed over the environmental data. If you export a map to an image file when displaying environmental data on MapMaker, it also be visible on the resulting image.


Samples are displayed over the environmental data

Click on the button to export the current map view to an image file (JPG or BMP). For this example you can just accept default settings. As you’ll see, resulting image includes currently displayed environmental data.

There is another step-by-step tutorial about “How to create and edit a map downloading data from GBIF” where you can find how to add occurrence data from GBIF, for example.


You can hide or remove environmental data from the map by clicking on the corresponding button of the toolbar.To visualizer another variable, just repeat the previous steps: click on the button and select an environmental variable.


Use this button to remove environmental data from the MapMaker map.


Besides visualization, ModestR also haves features to clip environmental data. Let’s see it through an example. Please repeat the previously described steps to display an environmental on MapMaker.


Click on the button to add an environmental variable to the map.

In the dialog box that will be shown, check the wanted variable on the tree. For example, sstmean (if you are using Bio-Oracle data)


Let’s suppose you want to clip and export environmental data for a specific area you’ll directly select on the map using the Freehand tool.


Select the Freehand tool on the right tool panel.

Draw an arbitrary area on the map, taking care of including marine zones (Bio-Oracle environmental data we are using in this example only include marine areas)

Click with the right mouse button over the selected area and select Add as visual template.This option will convert the selection in a visual template (in

ModestR a visual template is a selection that is only used for visualization

purposes)


Once added the visual template that demarcates the wanted area, you just have to go to File/Export/Environmental data/For visual templates and select which environmental data you want to clip.


Go to File/Export/ Environmental data/For visual templates.

In the tree that is displayed, select the variables to be clipped. For this example, select the same variable that is displayed: sstmean.Then click on Accept.

For this example we’ll only select one variable, but in fact you can select several variables to be clipped according to the visual template.MapMaker will generate one new file for each one.


Clipped environmental data will be exported to the folder you select, in the previously mentioned ASCII format.


Select the folder where clipped data will be saved.Take into account that existing files with the same name will be overwritten!


You can open the resulting raster file with MapMaker: go to menu Layers/Raster templates/Load raster from ESRI ASC file and select the file generated in the previous step. The clipped raster will be shown.


Resulting clipped raster.


If you have environmental data for land areas, you can also use predefined visual templates to easily add a visual template and then clip data for a specific region, country, continent, etc.


You can add a predefined visual template using the Add visual template button

In the preselections tree, you can select a country, a whole continent, etc.Here we selected Africa.

The visual template is added to the map

In this example we are using environmental data for land areas (they are not included in Bio-Oracle dataset, but you may find some in other web sites)


Then, following the same steps previously described to clip environmental data using a visual template, you’ll obtain the corresponding clipped raster. This way ModestR makes very easy to obtain raster environmental data for specific areas.



Besides visual templates, you can also clip environmental data for a species presence areas. The steps area quite the same. You just have to go to File/Export/Environmental data/For presence areas and select which environmental data you want to clip.


Go to File/Export/ Environmental data/For presence areas and select which environmental data you want to clip.

Environmental data will be clipped to the presence areas of the current map.

In this example, we previously generated those presence areas from occurrences, by applying the alpha shape method to estimate EOO. This makes easy to obtain environmental data for the EOO of a specific species.


Environmental variables, once integrated in ModestR as previously described, can also be used to perform data cleaning basing on environmental conditions, al well as niche of occurrence estimation.


Data cleaning and niche of occurrence estimation should use environmental variables previously integrated in ModestR.Those features will be explained in other tutorials.You can also find information in the ModestR user’s manual available in the ModestRwebsite.


Moreover, in DataManager you can perform quite all those operations (map image exportation, environmental data clipping, data cleaning, niche of occurrence…) in a batch mode, for any rank of species (a class, an order…) in a single step!


While in MapMaker you can perform an operation on a single map, in DataManageryou can easily apply it to all maps of a group (a class, an order…) in a single step.

For example, you can export all maps of a whole class as images (JPG) , including in them environmental data.Or generate clipped environmental data for each one of a whole set of species in a single step.


It was theStep by step tutorial:

Integrating and using environmental data in ModestR

Thank you for your interest.

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how to integrate and use environmental data in modestr

Environment

environmental data files

modestr doesnt

modestr v2

different data

clipped environmental

environmental data collections

uses of environmental

data exportation