SF Biodiversity Access Tool

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. Each point is scored independently against its own matching mode × time reference before the spider plot and difference table are shown.

Download Comparer HTML report card

Point A

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

Mode:

Time (min):

Point B

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

Mode:

Time (min):

Biodiversity Access Profile — Point A vs Point B

Point A vs Point B Farther outward = higher / more favourable percentile

Each point is ranked independently against the SF reference matching its own selected mode and travel time. The chart compares relative citywide standing, while the difference table below pairs the raw values with their citywide percentiles.

ACCESS
Transit access · Muni route access

BIODIVERSITY EVIDENCE
Species richness · GBIF sampling density

GREEN ENVIRONMENT
Vegetation NDVI · Greenspace cover

EQUITY CONTEXT
SF EJ context · outward = lower burden

Difference (Point B − Point A)

Point B minus Point A for each metric. Percentile differences are percentile-point differences after each point has been independently benchmarked against its own matching mode × time reference. Raw values are also retained.

Green Corridor Planner

Draw a proposed street corridor, habitat patch, pocket park, or other green intervention. The planner compares it with mapped existing San Francisco greenspace, identifies potential habitat links, and estimates nearby population and equity context.

Screening tool: Connectivity is based on a user-selected distance rule. It does not yet model species-specific movement, road barriers, vegetation quality, land ownership, or project feasibility.

Scenario Controls

Scenario name:

Uses existing San Francisco greenspace: Your proposal is checked against 3,899 mapped OSM greenspace polygons loaded for the city.

1. Draw the intervention
Use the line tool on the map for a street corridor or the polygon tool for a park, garden, or habitat patch.

For a line, choose the total planted width:

This setting affects line drawings only. Polygon drawings already have an area and ignore this control.

2. Choose the connection rule

When should two habitat patches count as connected?

This is a structural planning threshold, not a species-specific movement distance. The 500 m and 1,000 m options are broad exploratory screens and may connect many urban patches.

3. View the result

Export this scenario
The report card is a self-contained HTML file. Open it in a browser and choose Print → Save as PDF if needed. Download Corridor HTML report card

Show population-estimate area (purple, optional)

Assumed walking time:

This purple area is used only to estimate nearby population and equity context. It is not habitat and does not affect connectivity.

Map colors

Green = existing mapped greenspace

Active analysis isochrone = the only access area used for scenario BAI

Blue = your proposed intervention

Orange = existing greenspaces reached

Purple = optional population-estimate area

Corridor Scenario Map

What This Proposal Connects

Existing Greenspaces Reached

These are existing mapped greenspaces within the selected connection rule. They are highlighted in orange and numbered on the map.

Potentially Reached Residents

Connectivity results are available now. To compare the proposal with the Biodiversity Access Index, first generate isochrones in the Isochrone Explorer, then use Evaluate a green intervention within these isochrones .

Planned Conservation Action — BAI Before vs After

ACCESS
Transit access · Muni route access

BIODIVERSITY EVIDENCE
Species richness · GBIF sampling density

GREEN ENVIRONMENT
Vegetation NDVI · Greenspace cover

EQUITY CONTEXT
SF EJ context · outward = lower burden

Connectivity is displayed alongside the BAI as a separate structural-connectivity outcome; it is not inserted as an eighth BAI axis.

Detailed BAI Change — Selected Isochrone

Detailed standardized BAI dimensions for the selected Explorer isochrone (0–100 scale).

Green Investment & Displacement Context

Context screen — not a green-gentrification risk score. This tab places greenspace access and SF environmental-justice context side by side. The current app does not contain the housing-market variables needed to estimate displacement risk.

Use this view to identify places where a greening opportunity overlaps with greater environmental-justice burden, and therefore where community governance and anti-displacement safeguards may deserve explicit consideration. Do not interpret the plot as evidence that a proposed greening action will cause displacement.

Download Context HTML report card

Selected Isochrone Context

Greenspace Access Gap × EJ Burden Context

Each point is one independently scored isochrone. Farther right means a larger relative greenspace-access gap; farther up means greater EJ burden context. The 50/50 guide lines are descriptive visual references, not validated risk thresholds.

What Is Still Needed for Displacement-Risk Screening?

A defensible displacement or green-gentrification screen should add housing and tenure indicators rather than infer risk from EJ or income alone.

Renter share / tenure
Rent burden
Eviction notices or displacement events
Recent rent and home-value change
Subsidized / permanently affordable housing
Housing production and loss
An established displacement-vulnerability classification

Current interpretation: equity-sensitive greening context, not predicted displacement.

NGO / Grant Reporting Language

Exploring equitable access to urban biodiversity across San Francisco

Green Corridor Scenario Planner

The corridor workflow links three questions: where habitat is fragmented, where a proposed corridor or stepping-stone intervention could be placed, and how ecological connectivity and equitable human access change under that scenario.

Conceptual framework showing a fragmented baseline landscape, a proposed green corridor, and ecological and human-access outcomes.

Conceptual values shown in the figure are illustrative; the app reports results calculated from the user's drawing and selected thresholds.

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

Go to the Isochrone Explorer tab in the left sidebar.
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.
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.
Choose time budgets — 5, 10, and/or 15 minutes.
Click Generate Isochrones. Shaded polygons appear for each mode × time combination. Click a polygon for a summary popup.

Toggle map layers (top-right layer control) to overlay income, species richness, greenspace, CalEnviroScreen, EJ communities, transit routes, and NDVI.
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: independently benchmarked per-isochrone profiles; mode × time combinations are never averaged or pooled.
- Summary Table: full per-isochrone metrics.
- Metric Plots: species, population, GBIF institutions, and transit by mode.
Green Corridor Planner tab — draw a corridor or habitat patch, identify existing greenspaces reached, and compare the proposal with Explorer isochrones.
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 calculated separately for each generated isochrone. Where a comparable Step-5 reference metric exists, the raw value is converted to a percentile using only the precomputed 100 m SF origins with the same transportation mode and same travel-time budget . Walking 10-minute results are therefore compared only with Walking 10-minute references; different modes and travel times are never pooled. The validated reference contains 24,182 SF 100 m origin cells in each supported mode × time group. For each metric, the percentile uses all finite comparable values from that full matching citywide group. Raw scored metrics use the same explicit 100 m grid support as Step 5: a cell contributes when its projected centroid falls within that one isochrone.

Reference rule: one user isochrone → one matching mode × time reference distribution. If no comparable precomputed reference exists (for example transit, walk + transit, or driving with traffic), the app reports the raw metric and an N/A percentile rather than borrowing a different benchmark.

#	BAI Dimension	Variable	What it measures	Direction
1	Mobility Access	`Transit_Access_Score`	Muni stops per km² across the isochrone's 100 m grid support	Higher = better
2	Route Access	`Unique_Muni_Routes`	Distinct Muni route IDs intersecting the selected 100 m support cells	Higher = better
3	Biodiversity Potential	`GBIF_Species`	Unique GBIF species assigned to selected 100 m support cells	Higher = better
4	Sampling Density	`SamplingDensity_km2`	GBIF records per km² across the selected 100 m support cells — proxy for observation coverage	Higher = better
5	Environmental Quality	`MeanNDVI`	Area-weighted mean of 100 m cell NDVI values selected by the isochrone	Higher = better
6	Greenspace Cover	`Greenspace_percent`	OSM greenspace area as % of the selected 100 m grid-support area	Higher = better
7	Equity Context	`SF_EJ_Score (inverted)`	Lower EJ burden → more favourable access context	Lower burden = better

The displayed isochrone-benchmarked BAI is calculated only when all seven percentile-standardised dimensions are available for that single isochrone. Unsupported dimensions remain missing and are not replaced with census-block-group benchmarks. The score box reports how many comparable reference dimensions are available; an incomplete seven-axis profile returns BAI = N/A rather than silently changing the denominator.

For each isochrone i:
  percentile(metric_i) = rank within SAME mode × SAME time reference
  BAI_i = mean(all 7 percentile-standardised dimensions for isochrone i)
  if any required axis is unavailable: BAI_i = N/A

No averaging or union across different isochrones occurs.

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

Controls

Map

Biodiversity Access Score

Transit Access Score

Isochrone-Benchmarked Biodiversity Access Index

Closest Greenspace

Closest RSF Program

Citywide Biodiversity Access Profile — BAI Dimensions

Data Confidence / Observation Coverage

BAI Dimensions — Raw Values + Citywide Percentiles

Summary Data

Biodiversity & Transit Metrics by Mode