Controls

Several departures after the selected time can be evaluated for walk + transit.

Map

Biodiversity Access Score

Transit Access Score

Biodiversity Access Index

Closest Greenspace

Closest RSF Program

Biodiversity Access Index Profile

This spider plot summarizes biodiversity access across mobility, biodiversity, observation intensity, environmental quality, and equity context.

Summary Data

Biodiversity & Socioeconomic Summary

GBIF Records by Institution

Biodiversity & Transit Metrics by Mode

Bivariate Isochrone Plot: Biodiversity vs Environmental Justice

Each point is a generated isochrone. Higher x-values indicate more unique species reachable. Higher y-values indicate lower environmental justice burden. Point size reflects greenspace cover.

Compare two locations side by side

Place two points (click a map or search an address), pick one transport mode and travel time for each, then press Compare. The spider plots and difference table summarise how biodiversity access differs between the two.

Point A

Click the map or search an address to place Point A.

Point B

Click the map or search an address to place Point B.

BAI Spider — Point A vs Point B

Both points on one axis: Point A vs Point B . Each spoke is scored 0–100 against the citywide distribution.

Difference (Point B − Point A)

Point B minus Point A for each metric. Greenspace is reported by name, so its row shows the gap in distance to the nearest greenspace.

Filters

Data Summary

Observations vs. Species Richness

This plot displays the relationship between the number of observations and species richness.

Partner Community Organizations

Community Organizations Data

Exploring equitable access to urban biodiversity across San Francisco

About This Tool

The SF Biodiversity Access Decision Support Tool is an interactive web application developed by the Reimagining San Francisco (RSF) Data Working Group to investigate how equitably San Francisco residents can reach urban biodiversity depending on their transportation options and socioeconomic context.

Users select any location in San Francisco — by clicking the map or geocoding an address — choose one or more transport modes and travel-time thresholds, and the app generates isochrones (reachable-area polygons). Within each isochrone the app computes biodiversity, greenspace, transit, socioeconomic, environmental quality, and equity metrics, and synthesises them into the Biodiversity Access Index (BAI) .

Team
  • Diego Ellis Soto
  • Avery Hill
  • Lizzy Edson
  • Álvaro Casanova
  • Christopher J. Schell
  • Carl Boettiger
  • Rebecca Johnson
Institutions
  • UC Berkeley — ESPM
  • California Academy of Sciences

Contact

diego.ellissoto@berkeley.edu

Reimagining San Francisco

Reimagining San Francisco is an initiative integrating ecological, social, and technological dimensions to shape a sustainable future for the Bay Area. The RSF Data Working Group co-develops frameworks that bring together multiple sources of socio-ecological biodiversity information for decision-support.

California Academy of Sciences
Source Code

diego-ellis-soto/SF_biodiv_access_shiny

The full source code, setup scripts, and data pipeline are publicly available on GitHub.

Why Biodiversity Access Matters

Access to urban biodiversity is deeply unequal. Legacies of redlining, disinvestment, and car-centric planning have concentrated green, biodiverse spaces in wealthier neighbourhoods, while lower-income and environmental-justice communities often face longer travel distances and fewer transit options to reach them.

Areas with higher biodiversity support essential ecosystem services — pollinators, carbon sequestration, urban heat mitigation — and provide documented cultural, recreational, and mental health benefits to local residents.

Cities are complex socio-ecological systems shaped by ongoing human pressures and historical decisions. The RSF initiative integrates multiple facets of biodiversity with variables used by city planners, public health practitioners, and equity advocates to support a more integrative, justice-oriented lens for urban sustainability.

This tool is designed to make those inequities visible, quantifiable, and actionable — surfacing where the gaps are largest and where investment could make the greatest difference.

How to Use

  1. Go to the Isochrone Explorer tab in the left sidebar.
  2. Pick a location.
    • Click on Map: click anywhere in SF; a red marker confirms selection.
    • Address (Geocode): type a street address in the search box.
  3. Select transport modes. Driving, Walking, Cycling, and Driving with Traffic use Mapbox. Transit and Walk + Transit use the SF Muni GTFS timetable. Extra sliders appear for departure hour and first/last-mile walking budgets.
  4. Choose time budgets — 5, 10, and/or 15 minutes.
  5. Click Generate Isochrones. Shaded polygons appear for each mode × time combination. Click a polygon for a summary popup.
  1. Toggle map layers (top-right layer control) to overlay income, species richness, greenspace, CalEnviroScreen, EJ communities, transit routes, and NDVI.
  2. Explore the panels below the map:
    • Score boxes: biodiversity access percentile, transit density, and BAI.
    • Closest Greenspace: nearest OSM green area, distance, and % greenspace cover.
    • Spider / Radar Plot: 7-axis BAI profile comparing all isochrones.
    • Summary Table: full per-isochrone metrics.
    • Metric Plots: species, population, GBIF institutions, and transit by mode.
  3. GBIF Summaries tab — filter records by class or family; explore richness vs. sampling effort.
  4. Community Science tab — map and table of RSF partner organisations.
  5. Click Clear to reset the map for a new query.

Map Layers

All layers are toggled in the map's layer-control panel (top-right). The default base map is CartoDB Positron; you can switch to Street or Satellite.

Layer Description Source
Income Median household income per census block group ACS 5-yr
Greenspace OSM parks, gardens, and public green areas OpenStreetMap
Greenspace Distance Raster showing distance (m) to the nearest greenspace pixel Derived from OSM
RSF Program Projects Partner project polygons from the Reimagining SF Initiative RSF Initiative
RSF Program Distance Raster showing distance (m) to the nearest RSF program polygon RSF Initiative
Hotspots (KnowBR) Block groups with anomalously high species richness relative to sampling effort KnowBR / GBIF
Coldspots (KnowBR) Block groups with anomalously low species richness relative to sampling effort KnowBR / GBIF
Species Richness Unique GBIF species per census block group GBIF
Data Availability Total GBIF occurrence records per block group GBIF
CalEnviroScreen (CI Score) Cumulative environmental and health burden by census tract OEHHA
SF EJ Communities SF Environment Dept. environmental justice community burden scores SF Environment
Transit Routes All SF Muni routes from GTFS shapes, coloured by official SFMTA route colour SFMTA GTFS
Transit Stops All SF Muni stops with AM peak headway and departure frequency SFMTA GTFS
Isochrones Generated travel-time polygons (one per mode × time combination) Mapbox / gtfsrouter
NDVI Raster Sentinel-2 NDVI cropped and masked to the isochrone union Sentinel-2

Transportation Modes

Six modes are supported across two routing engines. Walk + Transit is an approximation combining a Mapbox first-mile walk, GTFS stop-to-stop reachability (SF Muni), and a last-mile walk buffer — not a full door-to-door multimodal isochrone.

Mode Engine Data Source Notes
Driving Mapbox OSM road network Free-flow speed
Walking Mapbox Pedestrian network Pedestrian paths and crossings
Cycling Mapbox Bicycle network Dedicated cycle lanes where available
Driving with Traffic Mapbox Traffic-aware road network Real-time + historical congestion
Transit (GTFS) gtfsrouter SF Muni GTFS Timetable-based stop-to-stop reachability from nearest stop
+ Walk + Transit Mapbox + gtfsrouter Pedestrian + SF Muni GTFS First-mile walk → Muni ride → last-mile walk within one total time budget

Biodiversity Access Index (BAI) & Spider Plot

The Biodiversity Access Index (BAI) is a composite indicator benchmarked against citywide empirical distributions (ECDFs across all SF census block groups). Each dimension is scaled 0–1, where 1 means the isochrone ranks at the top of the city-wide distribution for that metric.

# BAI Dimension Variable What it measures Direction
1 Mobility Access Transit_Access_Score Muni stops per km² within the isochrone Higher = better
2 Route Access Unique_Muni_Routes Distinct Muni route IDs crossing the isochrone Higher = better
3 Biodiversity Potential GBIF_Species Unique GBIF species recorded within the isochrone Higher = better
4 Sampling Density SamplingDensity_km2 GBIF occurrence records per km² — proxy for community science coverage Higher = better
5 Environmental Quality MeanNDVI Mean Sentinel-2 NDVI within the isochrone Higher = better
6 Greenspace Cover Greenspace_percent % of isochrone area covered by OSM greenspace polygons Higher = better
7 Equity Context SF_EJ_Score (inverted) Lower EJ burden → more favourable access context Lower burden = better

The BAI is the unweighted mean of all seven standardised components:

BAI = mean(
  Mobility_Access, Route_Access,
  Biodiversity_Potential, Sampling_Density,
  Environmental_Quality, Greenspace_Cover,
  Equity_Context
)
Prototype / Work in Progress: Variable weighting, spatial units, and benchmark distributions should be refined through stakeholder co-development before the BAI is used as a policy-grade score.

Data Sources & Cyberinfrastructure

Dataset Source Format Use in App
GBIF occurrences Global Biodiversity Information Facility Parquet Species richness, sampling density, taxonomic breakdowns
ACS / Census US Census Bureau (tidycensus) .Rdata Population and median income per census block group
NDVI raster Sentinel-2 (pre-processed) GeoTIFF Vegetation quality within isochrones
OSM Greenspace OpenStreetMap GeoPackage Greenspace cover %, distance raster, map layer
SF Muni GTFS SFMTA CSV / ZIP Transit isochrones, stop density, route access, headways
CalEnviroScreen 4.0 OEHHA File GDB Cumulative environmental burden scores
SF EJ Communities SF Environment Dept. Shapefile Environmental justice burden and equity context
Hotspots / Coldspots KnowBR analysis on GBIF Shapefile Under- and over-observed biodiversity areas
RSF Program Projects RSF Initiative GeoPackage Partner project areas overlay
Remote Data Hosting

Greenspace, CBG, hotspots, NDVI, and GBIF data are hosted on HuggingFace (boettiger-lab/sf_biodiv_access) . The cloud deployment streams these via GDAL's /vsicurl/ virtual filesystem — no large files need to be bundled in the Docker image.

GBIF Queries via DuckDB

GBIF occurrence records (~3M rows for SF) are stored as a local .parquet file and queried on-the-fly using DuckDB with the spatial extension. SQL ST_Intersects filters records to the isochrone without loading the full dataset into memory.

Open Source

Full source code, data pipeline scripts, and setup instructions are available at:
github.com/diego-ellis-soto/SF_biodiv_access_shiny

Status & Roadmap

Current Status

This tool is a decision-support prototype co-developed with the RSF Data Working Group. The BAI should be treated as an exploratory indicator; variable weights and reference distributions are subject to revision through ongoing stakeholder engagement.

Planned Additions
  • Impervious surface coverage layer
  • National Walkability Index integration
  • CDC Social Vulnerability Index
  • NatureServe biodiversity and rarity maps
  • Frequency-weighted multimodal transit accessibility score
  • Pre-cached transit isochrones for faster querying
  • Stakeholder-driven BAI dimension weighting
  • Historical and comparative isochrone analysis