Creating and working with environmental layers in ModestR

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

Step by step tutorial: Creating environmental layers in Modest

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

What do you need for this tutorial:

1. ModestR v3.1 or higher

2. Environmental data already integrated in ModestR (if you have not done that yet, tutorial “How to

integrate and use environmental data in ModestR” can help you doing that; available in ModestR web site)

3. Internet connection4. About 45 minutes

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


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

http://www.ipez.es/ModestR



We’ll describe how to create an environmental layer in ModestR, integrating several environmental

variables in a single space. Environmental layers can be used to estimate distribution of a species, to

visualize its niche, and to compare environmental conditions of different areas, among other things.

Follow the next steps!



The first step is running ModestR and going to menu Mapping/Niche of occurrence/Create new environmental layer.


Go to menu Mapping/Niche of occurrence/Create new environmental layer


The first step to create an environmental layer is selecting the environmental variables that will be part of it. In some way, an environmental layer represents way of visualizing and working with multiple environmental dimensions in a simpler way.


Environmental data is notprovided with ModestR. Itshould be the user who addsthose data.For details of how to integrateenvironmental data in ModestR,see the step-by-step tutorial“How to integrate and useenvironmental data in ModestR”or the ModestR user’s manual,in the Modestr website.

For this example we are selecting some terrestrial variables such as altitude or temperature. You must select at least two variables, but an environmental layer may typically involve 4 or more variables.You should use variables that mostly cover the same geographic area.Then click on Continue button.


In the next step, Variance Inflation Factor can be optionally calculated, in order to detect collinearities between variables,and, eventually, delete variables that can be redundant. This step is optional, and you can just skip and continue.


For this example we’ll neither calculate VIF nor delete variables.A value that already appears is the minimal relative % of coverage of each variable regarding the other ones. If one variable has a low value (e.g.< 50%) this usually indicates that there are many missing values for the geographic areas where the other variables do have values. An extreme case would be if you selected terrestrial and marine variables, that will not have the same geographic coverage, then they should not be used in the same environmental layer.

Click on Continue button.


In the next step, the polar coordinates system that will constitute the environmental layer is depicted. Each variable is an axe of this polar coordinates system. In this step you may optionally change the order of the axes, but you mostly accept the default order and continue to the next step.


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.

You can optionally select variables in the list and change their position using those buttons.



In the next step, the environmental layer is generated and shown both on the map and in the polar coordinates system.


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). A color scale is assigned the polar coordinates system, and used to visualize the correspondence with the geographic areas.



Finally, the new environmental layer can be optionally saved to be used later. A report can also be exported.


Enter a name and a description for the new layer and click on Save layer to save it.You can optionally export a report of the environmental layer, that contains several files such as the polar data map, the X and Y rastersand other ones.


Now we will load this new layer in MapMaker, to be able to use it immediately after.


Click on Load layer to load it in MapMaker.MapMaker will then automatically use this layer for any subsequent operation that requires an environmental layer.You can change the currently loaded environmental layer going to menu Mapping/Niche of occurrence/Load environmental layer.Currently loaded layer (if any) is shown in the bottom status bar.


Now we’ll see some things that can be done using an environmental layer. Such as showing the environmental conditions of a geographic area within the whole layer. For this example, we’ll use ModestR predefined selections.


The first step is selecting the target area. In this example, we’ll use predefined selections that are already integrated in ModestR

Go to menu Layers/Visual templates/Add visual template


A dialog box shows the collection of predefined selections integrated in ModestR. To add a predefined selection to the map, just select it in the tree or in the active map.


For this example, we’re adding some basins of Africa. To do that, we’ll open the “World Basins” node in the tree and next the “Basins of Africa”. Then we’ll select some of them.

The active map shows the selected areas. It also allows going into an area or selecting it using the right mouse button.

Click on Close to continue


Selections (called visual templates in ModestR) added to the map will appear by default as semitransparent shapes.


You can place the mouse over any selection to see its name


Now we can calculate the environmental conditions of the areas corresponding to those selections, according to the environmental layer previously built.


Go to menu Mapping/Niche of occurrence/Polar data maps for visual templates


If no environmental layer is currently loaded, a dialog box will be shown to select a previously stored layer. If you alreadyloaded a layer, this one will be automatically used.


Currently loaded layer (if any) is shown in the bottom status bar.If a layer is currently loaded, it will automatically be used, and this dialog box will not be shown.You can change the currently loaded environmental layer going to menu Mapping/Niche of occurrence/Load environmental layer.

Select the layer to be used and click on the Accept button.


Next, a dialog with the whole data map of the current environmental layer will be show. In this dialog you can select one of the selections previously added to the map.


By default, the data map of the whole environmental layer is shown

Select one of the selections previously added to the map to see its specific data map

Clicking on the Export button, a report including this type of graph, as well as other data, is exported for each area of the left list, to a folder.


MapMaker will show the parts of the whole environmental layer corresponding to the environmental conditions present in the selected area. This provide an insight of the diversity of the environmental conditions in this area, and its relationship with the whole environmental conditions.


Select one of the selections previously added to the map to see its specific data map

In the data map displayed only the conditions present in the selected area are shown.This can provide an overview of the kind of environmental conditions present in this area, regarding its place within the polar coordinates system.The gray background represents the whole environmental layer, allowing to see the selected area within the whole map.


Selecting different areas and showing their maps can provide an insight of their global differences regarding their environmental conditions. As an environmental layer is a compound of several variables, it provides a more global overview thant comparing the values of each variable one by one for each area.


Select another selection to see its specific data map.

The data map displayed clearly shows that there are environmental differences between this area and the previous one.This provides a simple and intuitive way of visualizing and understanding environmental differences between several areas.


Besides data corresponding to a specific region, the density of its environmental conditions can also be displayed. This can provide an overview of which conditions are more frequent in this region, and can be useful to compare several regions.


In the right tabbed panel, select the Region density map.

In the graph displayed the conditions present in the selected area are shown in the form of a density graph. Zones with a warmer color (green, yellow, red) indicate more frequent conditions than zones with colder colors (blue).



The same data, but projected to the corresponding geographic area, can be displayed by clicking on the Show button

Clicking on the Show button, the corresponding data for the selected area (either from the density map or from the data map) will be shown in the world map as raster data. Now close the dialog box to go back to the main map. Then go to menu Layers/raster templates/Clear raster templates to clear the map.


Now we’ll see another utility of environmental layers: estimate the potencial niche of a species. That is what is called “niche of occurrence” in ModestR.


The first step will be to add occurrences of a species to the map. We can download them from GBIF, for example.To do that, go to menu File/Import/Samples from online GBIF database.Then write “Ursus arctos” in the species name, for example, and click on the Accept button.


The “Niche of occurrence” can be calculated from occurrence data, such as those downloaded from GBIF or imported from CSV files.


Once data downloaded from GBIF, you have to select habitats to be accepted for this species. For this example, we’ll select “Land”

Then click on the Accept button.



Now data is added to the map. Samples that fall outside of the habitats selected for the species will appear in another color (by default black)

The “Niche of occurrence” feature works by looking for environment similarities to infer the areas favorable to a species. To do that, it uses an environmental layer, to measure the distance between the environmental conditions where the species already has confirmed presences, and the other conditions that appear in the layer.



Once occurrence data added to the map, we can do a density map using the “niche of occurrence” approach.

Go to Mapping/Niche of occurrence/Density map


If no environmental layer is currently loaded, a list will appear to let you to select one. If any was already loaded, it will be used.


If no environmental layer is currently loaded, a list will appear to let you to select one.

If a layer is already loaded, (which is shown in the bottom status bar) MapMaker will automatically use this layer.

You can change the currently loaded environmental layer going to menu Mapping/Niche of occurrence/Load environmental layer.


Density map uses a kernel density approach to determine the environmental areas with higher density of a species in the polar coordinates system of an environmental layer.


Several parameters can be adjusted, but most of the times, default options are OK (as usual in ModestR! )

Just click on the Apply button.


Therefore, environmental areas (not geographic!) where the species is already present will have more density, and then environmental areas nearest those ones, which will have a high density, can be considered also favorable to the species.


Polar density map show the environmental areas with higher density of the species in the environmental layer. Areas with higher density will be considered favorable to the species. They form the “niche of occurrence” of the species.

Click on the Close button to go back, to the map.


The geographic niche of occurrence is just a projection of the areas with higher density in the environmental layer into the geographic space.


The same density information is shown in the map, but, obviously, translated to the geographic space. The geographic areas that have the environmental conditions with higher density of the species in the environmental layer will appear here highlighted.


Besides density, we can calculate and add the niche of occurrence as presence areas to the map.


Go to menu Layers/raster templates/Clear raster templatesto clear the map.

Go to Mapping/Niche of occurrence/Distribution map


The areas added are those with higher density of the species in the environmental layer.


Several parameters can be adjusted, but most of the times, default options are OK (as usual in ModestR! )

Select Add area option to add the presence areas to the map.

Then click on the Apply button.


This is an example of the result. Of course, results depend from the species, and, particularly from the variables used to build the environmental layer. More information in the ModestR user manual available at www.ipez.es/ModestR


The geographic areas that have the environmental conditions with higher density of the species in the environmental layer are added to the map.


http://www.ipez.es/MODESTR/

It was theStep by step tutorial:

Creating environmental layers in Modest

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



Science

Creating and working with environmental layers in ModestR