overture-based location

app.R

@@ -1,102 +1,70 @@
+library(shinybusy)
 library(shiny)
 library(bslib)
-library(shinybusy)
+library(colourpicker)
 
-source("utils.R")
-source("inat-ranges.R")
-public_endpoint <- Sys.getenv("AWS_PUBLIC_ENDPOINT", Sys.getenv("AWS_S3_ENDPOINT"))
+library(mapgl)
+library(sf)
+library(dplyr)
+library(duckdbfs)
+library(overture)
 
-# intialize data
-load_h3()
-load_spatial()
-duckdbfs::duckdb_secrets()
-inat <- open_dataset("s3://public-inat/hex")
-taxa <- open_dataset(glue("s3://public-inat/taxonomy/taxa.parquet"),
-                     recursive = FALSE) |> rename(taxon_id = id)
-cache <- tempfile(fileext = ".json")
 
+source("utils.R")
+source("inat-ranges.R")
 
-# I/O limited, we can have many more processes than CPU threads
-con <- duckdbfs::cached_connection()
-DBI::dbExecute(con, "SET threads = 128;")
 
-###### User interface ######
 ui <- page_sidebar(
-  title = "iNaturalist Rangemaps",
-  markdown("Visualize species richness from [iNaturalist Range map datasets](https://www.inaturalist.org/pages/range_maps).
-  Pan & zoom the map over the desired area and hit 'map richness', or draw the desired area with the draw tool.
-  Filter by specific taxonomic ranks or view all 100,293 mapped species. 
-  Note that larger areas will be slower to compute. (Area selections that overlap the antimerdian may create visual artefacts).
-  "),
   shinybusy::add_busy_spinner(),
+
+  title = "iNaturalist Species Ranges",
   sidebar = sidebar(
-    card(
-    markdown("Filter by taxonomic group or toggle off to see all species."),
-    input_switch("filter", "filter taxa:", value = TRUE),
-    varSelectInput("rank", NULL, taxa, selected = "class"),
-    textInput("taxon", NULL, "Aves")
-    ),
-    actionButton("get_features", "Map richness")
+    textInput("location", "Location", "California"),
+    varSelectInput("rank", NULL, taxa, selected = "scientificName"),
+    textInput("taxon", NULL, "Canis lupus"),
   ),
   card(
-    maplibreOutput("map"),
+    full_screen = TRUE,
+    maplibreOutput("map")
   )
 )
 
-###### Server ######
 server <- function(input, output, session) {
-# observeEvent(input$map_bbox, { }) # We can react to any zoom/pan on the map
+  # output$map <- renderMaplibre({overture:::map(gdf)})
 
-  output$map <- renderMaplibre({
+  observeEvent(input$taxon, {
+    aoi <- get_division(input$location)
 
-    # Hacky -- we sidecar the metadata here
-    if(file.exists(cache)) {
+    message("Computing richness...")
+
+    meta <- richness(inat, aoi, input$rank, input$taxon)
+    jsonlite::write_json(meta, cache, auto_unbox = TRUE)
+
+    message(paste("rendering", meta$url))
+
+    # session$reload()
+  }) |>
+    debounce(millis = 600)
+
+  output$map <- renderMaplibre({
+    if (file.exists(cache)) {
       meta <- jsonlite::read_json(cache)
       print(meta$url)
     } else {
-      meta <- list(X = -110,
-                   Y = 37,
-                   zoom = 4,
-                   url = paste0("https://",
-                                public_endpoint,
-                                "/public-data/inat-tmp-ranges.h3j"))
+      meta <- list(
+        X = -110,
+        Y = 37,
+        zoom = 4,
+        url = paste0(
+          "https://",
+          public_endpoint,
+          "/public-data/inat-tmp-ranges.h3j"
+        )
+      )
     }
-   
     m <- richness_map(meta)
     m
-
   })
-
-  observeEvent(input$get_features, {
-    # Use the bbox as the focal area unless user has selected a focal area
-    drawn_features <- get_drawn_features(mapboxgl_proxy("map"))
-
-    if(nrow(drawn_features) > 0) {
-      aoi <- drawn_features
-    } else if (!is.null(input$map_bbox)){
-      aoi <- sf::st_bbox(unlist(input$map_bbox), crs = 4326)
-    } else {
-      aoi <- spData::us_states
-    }
-
-    rank <- taxon <- NULL
-    if (input$filter) {
-      rank <- input$rank
-      taxon <- input$taxon
-    }
-
-    message("Computing richness...")
-    meta <- richness(inat, aoi, rank, taxon, zoom = input$map_zoom)
-    jsonlite::write_json(meta, cache, auto_unbox = TRUE)
-    message(paste("rendering", meta$url))
-    session$reload()
-
-
-
-  })
-
-
-
 }
 
-shinyApp(ui, server)
+shinyApp(ui, server)

inat-ranges.R

@@ -4,11 +4,44 @@ library(mapgl)
 library(glue)
 
 
-# Also requires get_h3_aoi() from utils.R
+public_endpoint <- Sys.getenv(
+  "AWS_PUBLIC_ENDPOINT",
+  Sys.getenv("AWS_S3_ENDPOINT")
+)
+# intialize data
+
+duckdbfs::duckdb_secrets()
+inat <- open_dataset("s3://public-inat/hex")
+taxa <- open_dataset(
+  glue("s3://public-inat/taxonomy/taxa.parquet"),
+  recursive = FALSE
+)
+
+sci <- duckdbfs::open_dataset(
+  "s3://public-inat/taxonomy/taxa.parquet",
+  recursive = FALSE
+)
+common <- duckdbfs::open_dataset(
+  "s3://public-inat/taxonomy/vernacular/VerqnacularNames-english.csv",
+  format = "csv",
+  recursive = FALSE
+) |>
+  select(id, vernacularName)
+
+taxa <- left_join(sci, common, by = "id") |>
+  rename(taxon_id = id)
+
+common_names <- taxa |> pull(vernacularName)
+
+cache <- tempfile(fileext = ".json")
 
-richness <- function(inat, aoi, rank = NULL, taxon = NULL, zoom = 3) {
 
-  public_endpoint <- Sys.getenv("AWS_PUBLIC_ENDPOINT", Sys.getenv("AWS_S3_ENDPOINT"))
+# Also requires get_h3_aoi() from utils.R
+richness <- function(inat, aoi, rank = NULL, taxon = NULL, zoom = 3) {
+  public_endpoint <- Sys.getenv(
+    "AWS_PUBLIC_ENDPOINT",
+    Sys.getenv("AWS_S3_ENDPOINT")
+  )
   hash <- digest::digest(list(aoi, rank, taxon))
   s3 <- paste0("s3://public-data/cache/inat/", hash, ".h3j")
 
@@ -16,49 +49,49 @@ richness <- function(inat, aoi, rank = NULL, taxon = NULL, zoom = 3) {
 
   # filter
   if (!is.null(rank) && !is.null(taxon)) {
-    taxa <- open_dataset(glue("s3://public-inat/taxonomy/taxa.parquet"),
-           recursive = FALSE)
-    inat <- taxa |> 
+    taxa <- open_dataset(
+      glue("s3://public-inat/taxonomy/taxa.parquet"),
+      recursive = FALSE
+    )
+    inat <- taxa |>
       rename(taxon_id = id) |>
-      filter(.data[[rank]] == taxon) |> 
+      filter(.data[[rank]] == taxon) |>
       select(taxon_id) |>
       inner_join(inat, by = "taxon_id")
   }
 
-  h3_aoi  <- get_h3_aoi(aoi, precision = 4) |> select(h3id)
+  h3_aoi <- get_h3_aoi(aoi, precision = 4) |> select(h3id)
 
   clock <- bench::bench_time({
-  inat |> 
-    rename(h3id = h4) |>
-    inner_join(h3_aoi, by = "h3id") |>
-    distinct(taxon_id, h3id) |> 
-    group_by(h3id) |>
-    summarise(n = n()) |>
-    mutate(height = n / max(n)) |> 
-    duckdbfs::to_h3j(s3)
-  #  write_dataset("s3://public-data/inat-tmp-ranges.parquet")
+    inat |>
+      rename(h3id = h4) |>
+      inner_join(h3_aoi, by = "h3id") |>
+      distinct(taxon_id, h3id) |>
+      group_by(h3id) |>
+      summarise(n = n()) |>
+      mutate(height = n / max(n)) |>
+      duckdbfs::to_h3j(s3)
+    #  write_dataset("s3://public-data/inat-tmp-ranges.parquet")
   })
 
-
   center <- c(st_coordinates(st_centroid(st_as_sfc(st_bbox(aoi)))))
   url <- gsub("s3://", glue("https://{public_endpoint}/"), s3)
 
-  meta <- list(X = center[1], 
-               Y = center[2],
-               zoom = zoom, 
-               url = url, 
-               time = clock[[2]])
+  meta <- list(
+    X = center[1],
+    Y = center[2],
+    zoom = zoom,
+    url = url,
+    time = clock[[2]]
+  )
   return(meta)
 }
 
 richness_map <- function(meta) {
-
-  m <- 
+  m <-
     maplibre(center = c(meta$X, meta$Y), zoom = meta$zoom) |>
     add_draw_control() |>
-    add_h3j_source("h3j_source",
-                  url = meta$url
-    ) |>
+    add_h3j_source("h3j_source", url = meta$url) |>
     add_fill_extrusion_layer(
       id = "h3j_layer",
       source = "h3j_source",
@@ -69,7 +102,8 @@ richness_map <- function(meta) {
         list("linear"),
         list("zoom"),
         0,
-        0, 1,
+        0,
+        1,
         list("*", 100000, list("get", "height"))
       ),
       fill_extrusion_opacity = 0.7

old-app.R

@@ -0,0 +1,108 @@
+library(shiny)
+library(bslib)
+library(shinybusy)
+
+source("utils.R")
+source("inat-ranges.R")
+public_endpoint <- Sys.getenv(
+  "AWS_PUBLIC_ENDPOINT",
+  Sys.getenv("AWS_S3_ENDPOINT")
+)
+
+# intialize data
+load_h3()
+load_spatial()
+duckdbfs::duckdb_secrets()
+inat <- open_dataset("s3://public-inat/hex")
+taxa <- open_dataset(
+  glue("s3://public-inat/taxonomy/taxa.parquet"),
+  recursive = FALSE
+) |>
+  rename(taxon_id = id)
+cache <- tempfile(fileext = ".json")
+
+
+# I/O limited, we can have many more processes than CPU threads
+con <- duckdbfs::cached_connection()
+DBI::dbExecute(con, "SET threads = 128;")
+
+###### User interface ######
+ui <- page_sidebar(
+  title = "iNaturalist Rangemaps",
+  markdown(
+    "Visualize species richness from [iNaturalist Range map datasets](https://www.inaturalist.org/pages/range_maps).
+  Pan & zoom the map over the desired area and hit 'map richness', or draw the desired area with the draw tool.
+  Filter by specific taxonomic ranks or view all 100,293 mapped species. 
+  Note that larger areas will be slower to compute. (Area selections that overlap the antimerdian may create visual artefacts).
+  "
+  ),
+  shinybusy::add_busy_spinner(),
+  sidebar = sidebar(
+    card(
+      markdown("Filter by taxonomic group or toggle off to see all species."),
+      input_switch("filter", "filter taxa:", value = TRUE),
+      varSelectInput("rank", NULL, taxa, selected = "class"),
+      textInput("taxon", NULL, "Aves"),
+      textInput("aoi", "Location", "California"),
+    ),
+    actionButton("get_features", "Map richness")
+  ),
+  card(
+    maplibreOutput("map"),
+  )
+)
+
+###### Server ######
+server <- function(input, output, session) {
+  # observeEvent(input$map_bbox, { }) # We can react to any zoom/pan on the map
+
+  output$map <- renderMaplibre({
+    # Hacky -- we sidecar the metadata here
+    # Cache at the URL level instead?
+    if (file.exists(cache)) {
+      meta <- jsonlite::read_json(cache)
+      print(meta$url)
+    } else {
+      meta <- list(
+        X = -110,
+        Y = 37,
+        zoom = 4,
+        url = paste0(
+          "https://",
+          public_endpoint,
+          "/public-data/inat-tmp-ranges.h3j"
+        )
+      )
+    }
+
+    m <- richness_map(meta)
+    m
+  })
+
+  observeEvent(input$get_features, {
+    # Use the bbox as the focal area unless user has selected a focal area
+    drawn_features <- get_drawn_features(mapboxgl_proxy("map"))
+
+    if (nrow(drawn_features) > 0) {
+      aoi <- drawn_features
+    } else if (!is.null(input$map_bbox)) {
+      aoi <- sf::st_bbox(unlist(input$map_bbox), crs = 4326)
+    } else {
+      aoi <- spData::us_states
+    }
+
+    rank <- taxon <- NULL
+    if (input$filter) {
+      rank <- input$rank
+      taxon <- input$taxon
+    }
+
+    message("Computing richness...")
+    meta <- richness(inat, aoi, rank, taxon, zoom = input$map_zoom)
+    jsonlite::write_json(meta, cache, auto_unbox = TRUE)
+    message(paste("rendering", meta$url))
+    session$reload()
+  })
+}
+
+shinyApp(ui, server)