Appendix C — Shiny Apps User Guide (retired)

Step-by-step walkthrough of the retired Scores and Species Shiny applications

ImportantRetired

The Scores and Species Shiny apps this guide walks through were retired in October 2026 when the Atlas became the project’s application; their URLs now redirect to the Atlas. The screenshots below were captured on 2026-06-05; the apps changed after that until their retirement, so they may differ in detail from the last build. They are kept as a record. For the current app see the Atlas user guide.

This guide walked through the two interactive Shiny applications — Scores (app.marinesensitivity.org/{ver}/scores/) and Species (app.marinesensitivity.org/{ver}/species/) — one control at a time. Each numbered step below mirrors a step in that app’s built-in Take a Tour (About → Take a Tour in either app), with the relevant control highlighted on the screenshot.

For a feature-by-feature reference instead, see the Scores and Species pages.

TipHow this guide was generated

The steps, captions, and highlighted screenshots were generated directly from the apps’ in-app tours (the Conductor$new()$step(...) chains in each app.R) by libs/apps-guide-regenerate.R, which wrote figures/apps-guide/steps.json. The apps are retired and unreachable, so that script can no longer run and this page is frozen at the last capture.

C.1 Scores app

C.1.1 1. Study Area

Pick a region to focus on. ‘Full study area’ shows all US federal waters from the Aleutians to the Caribbean and out to the Pacific Island Territories. The other choices zoom into a single subregion.

Pick a region to focus on. 'Full study area' shows all US federal waters from the Aleutians to the Caribbean and out to the Pacific Island Territories. The other choices zoom into a single subregion.
Figure C.1: Study Area

C.1.2 2. Spatial Units

Toggle between fine-grained raster cells (0.05°) and aggregated BOEM Program Area polygons. Cell mode lets you click any pixel; Program Area mode shows pre-aggregated zone scores.

Toggle between fine-grained raster cells (0.05°) and aggregated BOEM Program Area polygons. Cell mode lets you click any pixel; Program Area mode shows pre-aggregated zone scores.
Figure C.2: Spatial Units

C.1.3 3. Layer Selection

Choose which sensitivity metric to display — composite score, individual species categories (bird, fish, mammal, etc.), or primary productivity. Note that some cells (Atlantic, Gulf of America, Hawaii, Puerto Rico, Pacific Islands) have scores but lie outside any v6 BOEM Program Area; they appear dimmed under a ‘Cells outside Program Areas’ overlay.

Choose which sensitivity metric to display — composite score, individual species categories (bird, fish, mammal, etc.), or primary productivity. Note that some cells (Atlantic, Gulf of America, Hawaii, Puerto Rico, Pacific Islands) have scores but lie outside any v6 BOEM Program Area; they appear dimmed under a 'Cells outside Program Areas' overlay.
Figure C.3: Layer Selection

C.1.4 4. Map tab

The Map tab is where you explore scores spatially — click cells or click Program Areas to see their scores.

The Map tab is where you explore scores spatially — click cells or click Program Areas to see their scores.
Figure C.4: Map tab

C.1.5 5. Layers control

Toggle individual map layers on and off — program area outlines, ecoregion outlines, raster cells, and the gray ‘Cells outside Program Areas’ overlay.

Toggle individual map layers on and off — program area outlines, ecoregion outlines, raster cells, and the gray 'Cells outside Program Areas' overlay.
Figure C.5: Layers control

C.1.6 6. Go to location

Search for a place name and the map will fly there — useful for jumping to a specific Program Area, port, or feature.

Search for a place name and the map will fly there — useful for jumping to a specific Program Area, port, or feature.
Figure C.6: Go to location

C.1.7 7. Full screen

Expand the map to fill the entire window.

Expand the map to fill the entire window.
Figure C.7: Full screen

C.1.8 8. Zoom in / out

Zoom and reset the view. You can also use the mouse wheel, pinch gesture, or double-click.

Zoom and reset the view. You can also use the mouse wheel, pinch gesture, or double-click.
Figure C.8: Zoom in / out

C.1.9 9. Plot of Scores tab

Switch here to see the flower plot of aggregated sensitivity scores for the current selection, broken out by species category. Petal length = score (0–100); center number = weighted mean. Defaults to ‘All USA’ until you click a cell or click a Program Area.

Switch here to see the flower plot of aggregated sensitivity scores for the current selection, broken out by species category. Petal length = score (0–100); center number = weighted mean. Defaults to 'All USA' until you click a cell or click a Program Area.
Figure C.9: Plot of Scores tab

C.1.10 10. Table of Species tab

A sortable, downloadable table of every species in the currently selected area, with extinction-risk codes, areas, and per-category contributions.

A sortable, downloadable table of every species in the currently selected area, with extinction-risk codes, areas, and per-category contributions.
Figure C.10: Table of Species tab

C.1.11 11. Report tab

Generate a sensitivity report for one or more custom areas. Build up a list of labeled areas by drawing a polygon on the map (using the polygon tool) and/or by selecting a Program Area, then clicking ‘Add’ for each. Set a title, data version, and output format (HTML, Word, or PDF), then click ‘Generate report’.

Generate a sensitivity report for one or more custom areas. Build up a list of labeled areas by drawing a polygon on the map (using the polygon tool) and/or by selecting a Program Area, then clicking 'Add' for each. Set a title, data version, and output format (HTML, Word, or PDF), then click 'Generate report'.
Figure C.11: Report tab

C.2 Species app

C.2.1 1. Select a Species

Search by common or scientific name. Results are grouped by category (bird, fish, mammal, etc.).

Search by common or scientific name. Results are grouped by category (bird, fish, mammal, etc.).
Figure C.12: Select a Species

C.2.2 2. Mask Selection

Choose whether to overlay BOEM Program Area or Ecoregion boundaries on the map.

Choose whether to overlay BOEM Program Area or Ecoregion boundaries on the map.
Figure C.13: Mask Selection

C.2.3 3. Layer Selector

The colored bar shows which model layer is displayed. Green means the final Merged Model; orange means you are viewing a single input. Click the pills to switch layers.

The colored bar shows which model layer is displayed. Green means the final Merged Model; orange means you are viewing a single input. Click the pills to switch layers.
Figure C.14: Layer Selector

C.2.4 4. Species Map

The map shows the species distribution model. Cell values range from 1 (low sensitivity) to 100 (high sensitivity). Click cells for details.

The map shows the species distribution model. Cell values range from 1 (low sensitivity) to 100 (high sensitivity). Click cells for details.
Figure C.15: Species Map

C.2.5 5. Species Info

Open the sidebar to see ESA listing, IUCN status, MMPA/MBTA flags, and extinction risk score for the selected species.

Open the sidebar to see ESA listing, IUCN status, MMPA/MBTA flags, and extinction risk score for the selected species.
Figure C.16: Species Info