so it begins :seedling:

.github/workflows/deploy.yml

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+name: Sync to Hugging Face hub
+on:
+  push:
+    branches: [main]
+
+  # to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  sync-to-hub:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          lfs: true
+      - name: Push to hub
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: git push -f https://cboettig:$HF_TOKEN@huggingface.co/spaces/boettiger-lab/biodiversity-justice main

Dockerfile

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+FROM rocker/geospatial:latest
+
+WORKDIR /code
+
+RUN install2.r --error \
+    bsicons \
+    bslib \
+    duckdbfs \
+    fontawesome \
+    gt \
+    markdown \
+    shiny \
+    shinychat \
+    tidyverse
+
+RUN installGithub.r cboettig/mapgl tidyverse/ellmer
+
+COPY . .
+
+CMD ["R", "--quiet", "-e", "shiny::runApp(host='0.0.0.0', port=7860)"]

LICENSE

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+BSD 2-Clause License
+
+Copyright (c) 2024, Boettiger Lab, UC Berkeley
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1 +1,14 @@
-# biodiversity-justice
+---
+title: Biodiversity Justice
+emoji: 📚
+colorFrom: blue
+colorTo: green
+sdk: docker
+pinned: false
+license: bsd-2-clause
+---
+
+# Demo Shiny App with Maplibre + open LLM interface
+
+:hugs: Shiny App on Huggingface: <https://huggingface.co/spaces/boettiger-lab/geo-llm-r>
+

app.R

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+library(shiny)
+library(bslib)
+library(htmltools)
+library(markdown)
+library(fontawesome)
+library(bsicons)
+library(gt)
+library(glue)
+library(ggplot2)
+
+library(mapgl)
+library(dplyr)
+library(duckdbfs)
+
+duckdbfs::load_spatial()
+
+css <- HTML("<link rel='stylesheet' type='text/css' href='https://demos.creative-tim.com/material-dashboard/assets/css/material-dashboard.min.css?v=3.2.0'>")
+
+
+# Define the UI
+ui <- page_sidebar(
+  fillable = FALSE, # do not squeeze to vertical screen space
+  tags$head(css),
+  titlePanel("Demo App"),
+
+"This is a proof-of-principle for a simple chat-driven interface to dynamically explore geospatial data. 
+ ",
+
+
+  card(
+    layout_columns(
+    textInput("chat",
+      label = NULL,
+      "Which counties in California have the highest average social vulnerability?",
+      width = "100%"),
+    div(
+    actionButton("user_msg", "", icon = icon("paper-plane"),
+                 class = "btn-primary btn-sm align-bottom"),
+    class = "align-text-bottom"),
+    col_widths = c(11, 1)),
+    fill = FALSE
+  ),
+  layout_columns(
+    card(maplibreOutput("map")),
+    card(includeMarkdown("## Plot"),
+         plotOutput("chart1"),
+         plotOutput("chart2"),
+         ),
+    col_widths = c(8, 4),
+    row_heights = c("600px"),
+    max_height = "700px"
+  ),
+
+
+  gt_output("table"),
+
+  card(fill = TRUE,
+    card_header(fa("robot")),
+ 
+    accordion(
+      open = FALSE,
+      accordion_panel(
+        title = "show sql",
+        icon = fa("terminal"),
+        verbatimTextOutput("sql_code"),
+      ),
+      accordion_panel(
+        title = "explain",
+        icon = fa("user", prefer_type="solid"),
+        textOutput("explanation"),
+      )
+    ),
+
+    card(
+      card_header("Errata"),
+      markdown(
+"
+#### Credits
+
+Developed by Carl Boettiger, UC Berkeley, 2025.  BSD License.
+
+Data from the US Census and CDC's [Social Vulnerability Index](https://www.atsdr.cdc.gov/place-health/php/svi/index.html)
+
+#### Technical details
+
+The app is written entirely in R using shiny. The app will translate natural language queries in SQL code using
+a small open-weights language model. The SQL code is executed using the duckdb backend against cloud-native
+geoparquet snapshot of the Social Vulnerability Index hosted on Source Cooperative. Summary chart data are also
+computed in duckdb by streaming, providing responsive updates while needing minimal RAM or disk storage despite
+the large size of the data sources. 
+
+The map is rendered and updated using MapLibre with PMTiles, which provides responsive rendering for large feature sets.
+The PMTiles layer is also hosted on Source cooperative where it can be streamed efficiently.
+")
+    )
+
+  ),
+
+  sidebar = sidebar(
+
+    input_switch("redlines", "Redlined Areas", value = FALSE),
+    input_switch("svi", "Social Vulnerability", value = TRUE),
+    input_switch("richness", "Biodiversity Richness", value = FALSE),
+    input_switch("rsr", "Biodiversity Range Size Rarity", value = FALSE),
+
+    card(
+      card_header(bs_icon("github"), "Source code:"),
+      a(href = "https://github.com/boettiger-lab/geo-llm-r",
+        "https://github.com/boettiger-lab/geo-llm-r"))
+  ),
+
+  theme = bs_theme(version = "5")
+)
+
+
+
+
+repo <- "https://data.source.coop/cboettig/social-vulnerability"
+pmtiles <- glue("{repo}/svi2020_us_tract.pmtiles")
+parquet <- glue("{repo}/svi2020_us_tract.parquet")
+svi <- open_dataset(parquet, tblname = "svi") |>
+  filter(RPL_THEMES > 0)
+
+
+con <- duckdbfs::cached_connection()
+schema <- DBI::dbGetQuery(con, "PRAGMA table_info(svi)")
+
+system_prompt = glue::glue('
+You are a helpful agent who always replies strictly in JSON-formatted text.
+Your task is to translate the users question into a SQL query that will be run
+against the "svi" table in a duckdb database. The duckdb database has a
+spatial extension which understands PostGIS operations as well. 
+Include semantically meaningful columns like COUNTY and STATE name.
+
+In the data, each row represents an individual census tract. If asked for 
+county or state level statistics, be sure to aggregate across all the tracts
+in that county or state. 
+
+The table schema is <schema>
+
+The column called "RPL_THEMES" corresponds to the overall "Social vulnerability index" number. 
+
+Format your answer as follows:
+
+{
+"query": "your raw SQL response goes here",
+"explanation": "your explanation of the query"
+}
+', .open = "<", .close = ">")
+
+chat <- ellmer::chat_vllm(
+  base_url = "https://llm.nrp-nautilus.io/",
+  model = "llama3",
+  api_key = Sys.getenv("NRP_API_KEY"),
+  system_prompt = system_prompt,
+  api_args = list(temperature = 0)
+)
+
+# helper utilities
+# faster/more scalable to pass maplibre the ids to refilter pmtiles,
+# than to pass it the full geospatial/sf object
+filter_column <- function(full_data, filtered_data, id_col = "FIPS") {
+  if (nrow(filtered_data) < 1) return(NULL)
+  values <- full_data |>
+    inner_join(filtered_data, copy = TRUE) |>
+    pull(id_col)
+  # maplibre syntax for the filter of PMTiles  
+  list("in", list("get", id_col), list("literal", values))
+}
+
+chart1_data <- svi |>
+  group_by(COUNTY) |>
+  summarise(mean_svi = mean(RPL_THEMES)) |>
+  collect()
+
+chart1 <- chart1_data |>
+  ggplot(aes(mean_svi)) + geom_density(fill="darkred") +
+  ggtitle("County-level vulnerability nation-wide")
+
+
+# Define the server
+server <- function(input, output, session) {
+  data <- reactiveValues(df = tibble())
+  output$chart1 <- renderPlot(chart1)
+
+  observeEvent(input$user_msg, {
+    stream <- chat$chat(input$chat)
+
+    # optional, remember previous discussion
+    #chat_append("chat", stream)
+
+    # Parse response
+    response <- jsonlite::fromJSON(stream)
+    output$sql_code <- renderText(stringr::str_wrap(response$query, width = 60))
+    output$explanation <- renderText(response$explanation)
+
+    # Actually execute the SQL query generated:
+    df <- DBI::dbGetQuery(con, response$query)
+
+    # don't display shape column in render
+    df <- df |> select(-any_of("Shape"))
+    output$table <- render_gt(df, height = 300)
+
+
+    y_axis <- colnames(df)[!colnames(df) %in% colnames(svi)] 
+    chart2 <- df |> 
+      rename(social_vulnerability = y_axis) |>
+      ggplot(aes(social_vulnerability)) +
+      geom_density(fill = "darkred")  +
+      xlim(c(0, 1)) +
+      ggtitle("Vulnerability of selected areas")
+
+    output$chart2 <- renderPlot(chart2)
+
+    # We need to somehow trigger this df to update the map.
+    data$df <- df
+
+  })
+
+
+
+  output$map <- renderMaplibre({
+
+    m <- maplibre(center = c(-92.9, 41.3), zoom = 3, height = "400")
+    if (input$redlines) {
+      m <- m |>
+        add_fill_layer(
+          id = "redlines",
+          source = list(type = "vector",
+                        url = paste0("pmtiles://", "https://data.source.coop/cboettig/us-boundaries/mappinginequality.pmtiles")),
+          source_layer = "mappinginequality",
+          fill_color = list("get", "fill")
+        )
+    }
+    if (input$richness) {
+      m <- m |>
+        add_raster_source(id = "richness",
+                          tiles = "https://data.source.coop/cboettig/mobi/tiles/red/species-richness-all/{z}/{x}/{y}.png",
+                          maxzoom = 11
+                          ) |>
+        add_raster_layer(id = "richness-layer",
+                         source = "richness")
+
+    }
+
+     if (input$rsr) {
+      m <- m |>
+        add_raster_source(id = "rsr",
+                          tiles = "https://data.source.coop/cboettig/mobi/tiles/green/range-size-rarity-all/{z}/{x}/{y}.png",
+                          maxzoom = 11
+                          ) |>
+        add_raster_layer(id = "richness-layer",
+                         source = "rsr")
+
+    }
+    if (input$svi) {
+      m <- m |>
+        add_fill_layer(
+          id = "svi_layer",
+          source = list(type = "vector",
+                        url = paste0("pmtiles://", pmtiles)),
+          source_layer = "SVI2000_US_tract",
+          filter = filter_column(svi, data$df, "FIPS"),
+          fill_opacity = 0.5,
+          fill_color = interpolate(column = "RPL_THEMES",
+                                  values = c(0, 1),
+                                  stops = c("lightpink", "darkred"),
+                                  na_color = "lightgrey")
+        )
+    }
+  m})
+
+
+
+}
+
+# Run the app
+shinyApp(ui = ui, server = server)