:butterfly:

app.R

@@ -49,12 +49,15 @@ server <- function(input, output, session) {
     if(file.exists(cache)) {
       meta <- jsonlite::read_json(cache)
     } else {
-      meta <- list(center = c(-110, 37), zoom=4)
+      meta <- list(center = c(-110, 37),
+                   zoom = 4,
+                   url = paste0("https://minio.carlboettiger.info/",
+                                "public-data/inat-tmp-ranges.h3j"))
     }
 
     m <- maplibre(center = meta$center, zoom = meta$zoom) |>
       add_draw_control()
-    richness_map(m)
+    richness_map(m, url = meta$url)
 
   })
 
@@ -70,19 +73,18 @@ server <- function(input, output, session) {
       aoi <- spData::us_states
     }
 
+    rank <- taxon <- NULL
     if (input$filter) {
-      inat <- taxa |> 
-      filter(.data[[input$rank]] == input$taxon) |> 
-      select(taxon_id) |>
-      inner_join(inat, by = "taxon_id")
+      rank <- input$rank
+      taxon <- input$taxon
     }
 
     message("Computing richness...")
-    clock <- richness(inat, aoi)
+    url <- richness(inat, aoi, rank, taxon)
 
     center <- st_coordinates(st_centroid(st_as_sfc(st_bbox(aoi))))
     zoom <- input$map_zoom
-    jsonlite::write_json(list(center = c(center), zoom = zoom), cache)
+    jsonlite::write_json(list(center = c(center), zoom = zoom, url = url), cache)
 
     session$reload()
 

inat-ranges.R

@@ -4,7 +4,22 @@ library(mapgl)
 
 # Also requires get_h3_aoi() from utils.R
 
-richness <- function(inat, aoi) {
+richness <- function(inat, aoi, rank = NULL, taxon = NULL) {
+
+  taxa <- open_dataset("https://minio.carlboettiger.info/public-inat/taxonomy/taxa.csv", format = "csv", recursive = FALSE)
+
+  hash <- digest::digest(list(aoi, rank, taxon))
+  s3 <- paste0("s3://public-data/cache/inat/", hash, ".h3j")
+
+  # check if hash exists
+
+  # filter
+  if (!is.null(rank) && !is.null(taxon)) {
+    inat <- taxa |> 
+      filter(.data[[rank]] == taxon) |> 
+      select(taxon_id) |>
+      inner_join(inat, by = "taxon_id")
+  }
 
   h3_aoi  <- get_h3_aoi(aoi, precision = 4) |> select(h3id)
 
@@ -16,17 +31,17 @@ richness <- function(inat, aoi) {
     group_by(h3id) |>
     summarise(n = n()) |>
     mutate(height = n / max(n)) |> 
-    duckdbfs::to_h3j("s3://public-data/inat-tmp-ranges.h3j")
+    duckdbfs::to_h3j(s3)
   #  write_dataset("s3://public-data/inat-tmp-ranges.parquet")
   })
 
-  return(clock)
+  url <- gsub("s3://", "https://minio.carlboettiger.info/", s3)
+  return(url)
 }
 
 richness_map <- function(
   m = maplibre(),
-  url = "https://minio.carlboettiger.info/public-data/inat-tmp-ranges.h3j",
-  aoi = NULL
+  url = "https://minio.carlboettiger.info/public-data/inat-tmp-ranges.h3j"
   ) {
   
   m <- m |>
@@ -49,10 +64,6 @@ richness_map <- function(
       ),
       fill_extrusion_opacity = 0.7
     )
-  if(!is.null(aoi)) {
-    # center <- st_coordinates(st_centroid(st_as_sfc(st_bbox(aoi))))
-   # m <- m |> set_view(center = center, zoom = 3)
-  }
 
   return(m)
 }

test.R

@@ -15,12 +15,20 @@ duckdbfs::duckdb_secrets()
 inat <- open_dataset("s3://public-inat/hex")
 
 aoi <- spData::us_states
-
-taxa <- open_dataset("https://minio.carlboettiger.info/public-inat/taxonomy/taxa.csv", format = "csv", recursive = FALSE)
+aoi <- spData::world
 
 # publish richness at the aoi (bbox or poly)
 richness(inat, aoi)
-richness_map()
+m <- richness_map()
+
+library(htmlwidgets)
+htmlwidgets::saveWidget(m, "total-richness.html")
+
+
+# publish richness at the aoi (bbox or poly)
+richness(inat, aoi, rank = "class", taxon = "Aves")
+m <- richness_map()
+htmlwidgets::saveWidget(m, "aves-richness.html")