Model Mapper for Predicted Species Density Online Help

Table of Contents

• Quick Start
• Density Models Panel
  • Select species / model
  • Filter by species group or protected status
  • Tools available in species card
  • Drawing options & legend
  • Histogram & Statistics
• Map Interaction with Density Layer
  • Analyzing with Region of Interest
  • Compare Two Density Layers
  • Export Data, Map, Chart & Summary
• Advanced Use
  • Managing Layers
  • Mapping Options
  • OBIS-SEAMAP Layer
  • Metric for Aggregated Summary
• FAQs

1. Go to the Model Mapper (see the above URL).
   
2. The species are listed in the right-side Density Model Panel. Click one of the species / guild to display the density layer on the map.
3. Move your cursor over the density layer to display the density value at that location..
4. To see the statistics and explore the model layer with a histogram, click (Stats & Histogram icon).
5. To see the legend or change the symbology, click (Drawing Options & Legend icon).

The Density Models Panel shows available models / species. Each species is presented as a card with a species illustration and a thumbnail of the density layer. The card also provides tools to explore the species.

The Panel can be collapsed by clicking the up arrow icon at the upper right.

Select species / model

Click anywhere above the tool buttons within the species card to select the model / species. The selected card is highlighted in orange and its density layer is overlaid on the map. When you click the already selected card, the species / model is deselected.

You can choose multiple species by clicking the species cards. This results in an Aggregated Summary placed on the top of the Panel. The Aggregated Summary merges the selected species' density layers and calculates the total density (adding up the densities of the selected species). The aggregated density is displayed on the map.

A species may have monthly (January through December) or seasonal (Spring through Winter) periods of the prediction. In such a case, the period selection dropdown and buttons appear below the thumbnail. You can click [Prev] or [Next] button to move the period back and forth or choose a particular period from the dropdown. Either way, the density layer on the map will be updated accordingly.

Filter by species group or protected status

You can filter the species by species group or protected status. To do so, click at the upper left of the Panel.

By default, "All species" is selected. You can click one of the groups to list up the species in that group.

"ESA/IUCN-listed species" lists the species with the status of endangered or vulnerable in either Endangered Species Act or IUCN Red list. The protected statuses are also flagged in the species card (e.g. "E" or "EN" = the endangered status).

Species groups vary by project. See the table below regarding which groups are included in projects.

The Drawing Options & Legend section provides several options to change how the density layer is visualized on the map. This section also shows the legend of the current density layer.

Layer Type

When the density layer is generated, supplementary layers such as CV, standard error are also produced. You can investigate these supplementary layers by choosing such a layer from the dropdown. What supplementary layers are available depends on the projects.

• DUKE_EC, DUKE_GOM: Density, CV, Standard error, 5 percent CI, 95 percent CI
• DUKE_ARCTIC, NOAA_GOM, NOAA_CCE, NUWC_EC: Density, CV
• NOAA_PACGOA: Density

Symbology

The symbology defines how to render the density layer. DUKE_EC, DUKE_GOM, DUKE_ARCTIC and NUWC_EC have pre-defined symbologies and each species gets assigned the most appropriate one as a default symbology. For the other projects, each species has its own symbology. In addition, there are symbologies that statistically define breaks.

You can choose one of the color ramps from the Color Ramp dropdown to change the color scheme of the density layer. Looking at the color ramp samples in the table to the right, the colors toward the left are applied to the lower density values and those toward the right are applied to the higher density values.

One of the essential features of the Model Mapper is to draw an interactive histogram that gives you non-spatial representation of the model output. The histogram calculates frequency of cells over binned density values of the model output.

Above the histogram is the summary statistics of the layer. If the species has monthly or seasonal density estimates, you can compare them in a tabular format. To do so, you move forward or backward of the period by clicking [Prev] or [Next] button below the thumbnail or choose a particular month or season from the dropdown. When the statistics table has multiple periods (e.g. January, February, March etc), you can also click a row of the period to change the density layer of the map to that period.

The x-axis of the histogram is the value of the density. The values are split into bins whose size is automatically determined based on the value range and the number of bins which is 20 by default. The y-axis on the left is the frequency or the count of cells within each bin. Below the histogram is the table showing the statistics of the density.

Clickable bins allow you to filter the density layer based on the density range. When one of the bins is selected, it's highligted in red and the statistics table shows the stats within the selected bin, the range below the bin and the range above the bin.

There is also a slider below the histogram where you can define a range of the density by moving the two dots. This is useful if you are interested in a particular density range rather than auto-calculated bins.

In the PRO edition, if you want to set a range with particular values (e.g. density within 10.0 to 20.0), choosing the appropriate slider increment helps you move the two dots to such exact values. For example, if you choose "10" from the Slider Increment options, the dot on the slider steps over to 0, 10, 20, 30,... If you choose "0.1", the dot moves to 0, 0.1, 0.2,... The available options depend on the density range of the species. For example, for the Atlantic spotted dolphin in the US EC, there are "Auto", "0.1", "1" and "10". The North Atlantic right whale gets "Auto", "0.01", "0.1" and "1".

Supplementary charts

Supplementary charts are available to turn on or off. In the STD edition, only the mean density is available and turned on by default. You can't turn it off.

Upon selecting the species, its density layer is mapped with the default symbology. You can move the mouse cursor over the density layer and you will see the popup that follows the mouse move, showing the density range of the location that corresponds to the symbology class / break.

If you want to know the exact density, you can identify the cell by cliking on the density layer. The Identify popup shows the location of the click (usually longitude and latitude but can vary depending on the projection) and the density of the species in the period chosen. If the Aggregated Summary is mapped, the density of each species that contributes to the Aggregated Summary is also shown.

The identify popup also has the Snapshot tool icon. By clicking it, a close-up image of the density layer is shown within the popup. If the Aggregated Summary is mapped, you can see the close-up images for all species in the Aggregated Summary so you can visually compare the densities of the species.

To analyze the density or species distribution within a particular area (region of interest or ROI), you can draw a rectangular or circular region or a polygon on the map to define your ROI.

To do so, click and choose the type of the ROI (Rectangle, Polygon or Circle). Right after you chose the ROI type, the popup disappears and the mouse cursor changes to a drawing mode. How to draw a ROI varies depending on the ROI type. You can draw multiple ROIs.

• Rectangle: Press the mouse at the location of one of the four corners and drag the mouse to the opposite corner and release the mouse.
• Polygon: Click the mouse at the location of the first vertex of the polygon. Move the mouse to the next vertex and click. Continue this and at the last vertex, instead of a single click, double click the mouse to finish the drawing.
• Circle: Click the mouse at the center location of the circle. Move the mouse as far as the radius of the circle and click again to finish the drawing.

After finishing the ROI drawing, click the histogram icon. The density statistics are calculated usinig the cells within the ROI(s) and the histogram is drawn based on these data. Please be patient as the calculation may take a minute or so. As described above, you can play around with the interactive histogram. When you select a bin or define a range of the density, the map gets updated to show only the cells within that density range inside the ROI(s).

You can modify the shape of the ROI. To do so, click it on the map. Then, the square or bounding box of the ROI appears with movable dots along the lines. You can drag and drop the movable dots to change the shape. Once done, click the outside of the ROI (on an empty space of the map). If the ROI actually is changed, the statistics and histogram will be refreshed automatically.

To delete the ROI, click the ROI. Then Identify popup opens up with "Delete ROI" button available. Just click the button and the ROI is removed from the map and the statistics and histogram are refreshed automatically.

You can also upload a polygon as a ROI. Currently, ESRI shapefile is supported.

To do so, click and choose the ""Upload a shapefile" (the last icon within the popup). Choose a shapefile. As a shapefile consists of multiple files, they have to be zipped. Then, click [UPLOAD] button.

Optionally, you can add a buffer around the polygon you are going to upload. Enter the buffer size in the box and choose the unit. You can modify or delete the polygon once the shapefile is uploaded and added to the map in the same way as for the ROI you draw using the drawing tools.

Notes

• The maximum size of the zipfile allowed is 2MB.
• The projection of the shapefile should be WGS84 or Web Mercator. Other projections may work but not guaranteed.

There is a feature that allows you to compare two density layers side by side. This is useful to compare the density layers of two species or two months of the same species (e.g. January and July).

To use this feature, click and a popup shows up. Choose "Two maps side by side". Then, the second map is brought up to the right. A click anywhere on the right-side map or a circle placed above the zoom buttons makes the right-side map active. When activated, the circle above the zoom buttons turns green.

The Density Models Panel always works for the active map. When the right-side map is open and active (the circle above the zoom buttons is green), a click on the species card in the Density Models Panel displays its density layer on the right-side map.

"Sync both maps" option is very useful to synchronize the two maps for panning, zooming and identifying the density. When you click the density layer on the left-side map to identify the density value, the Identify popup opens not only on the left side but also on the right side, showing the density of the left and right side maps at the exactly same location.

You can choose the basemap or turn on / off additional layers using the Layers popup. In addition to the pre-defined layers, you can also overlay external resources served through ArcGIS Servers.

Click to open up the Layers popup. The Layers popup has three tabs: Basemaps / Pre-defined Layers / External Services

Basemaps

There are many basemaps. Simply choose the one you want to see.

In addition to the pre-defined layers, you can also overlay layers from external services served through ArcGIS Servers. The URL of the external resource is needed. It should look like:

https://coast.noaa.gov/arcgis/rest/services/MarineCadastre/BoundariesAndRegions/MapServer/
(Boundaries and Regions resource by NOAA)

To overlay an external layer, follow the steps below.

1. Open the Layers popup by clicking .
2. If this is the first time to access the service, enter the URL of the external service into the textbox and click "+" button. The information of the service and available layers will be displayed.
3. If you have used the services before, they should be listed. Click the title of the service.
4. Turn on one of the layers to display on the map.
5. You can change the opacity of the layer by entering value from 0.0 to 1.0 into the box next to the service title. 1 is opaque and 0 is completely transparent.
6. You can select multiple layers and change the order of the layers by dragging and dropping the two-line icon at the left of the service title.

In the PRO edition, you can control how the map behaves and renders the layers. Click to open the Mapping Options popup.

There are two ways to explore the OBIS-SEAMAP sightings along with the density layer.

Overlaying on density layer

You can display the OBIS-SEAMAP sightings on top of the model layer. Click and the OBIS-SEAMAP data will be visualized. By default, it's a gridded summary at a certain resolution. The summarizing resolution (grid size) changes according to the zoom level. To see the legend, click the down arrow at the right of the icon, which opens up the OBIS-SEAMAP Options & Legend Panel.

There are viewing options in the the OBIS-SEAMAP Options & Legend Panel. The legend is also shown in thie panel.

• Rectangular gridded summary: The OBIS-SEAMAP sightings are aggregated by rectangular grids at a certain resolution.
• Hexagonal gridded summary: The OBIS-SEAMAP sightings are aggregated by hexagonal grids at a certain resolution.
• Points: Individual sightings in the OBIS-SEAMAP database are mapped.
• Filter by month or season: If the species has monthly or seasonal density layers, the OBIS-SEAMAP data are filtered with the same period as for the density layer. You can turn this option off to see all the sightings of the species. This option is not applied to the species with annual density prediction. For the aggregated summary, the period of each species is reflected.
• Filter by year: If you are interested in more recent sightings or those within a certain range of years, you can specify the years and turn this option on.
• Data within U.S. EEZs: The OBIS-SEAMAP sightings are initially filtered within U.S. EEZs. however, you can turn this option off so you can see the sightings outsite the U.S. waters.