inat-ranges/test.R at main · boettiger-lab/inat-ranges · GitHub

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source("utils.R")
source("inat-ranges.R")

url <- "https://s3-west.nrp-nautilus.io/public-data/cache/inat/f0108ef86feababffeab3d2be6f09373.h3j"
#url <-  "https://minio.carlboettiger.info/public-data/cache/inat/4fd3323845ee860b39609783566b2212.h3j"

url <- "https://minio.carlboettiger.info/public-data/cache/inat/f0108ef86feababffeab3d2be6f09373.h3j"

#x <- jsonlite::read_json(url)

m = maplibre(center = c(-110, 37), zoom = 3) |>
  add_draw_control() |>
  add_h3j_source("h3j_source", url = url) |>
  add_fill_extrusion_layer(
    id = "h3j_layer",
    source = "h3j_source",
    tooltip = "n",
    fill_extrusion_color = viridis_pal("height"),
    fill_extrusion_height = list(
      "interpolate",
      list("linear"),
      list("zoom"),
      0,
      0,
      1,
      list("*", 100000, list("get", "height"))
    ),
    fill_extrusion_opacity = 0.7
  )


htmlwidgets::saveWidget(m, "test2.html")


## Illustrate/test core app functionality without shiny
library(dplyr)
library(duckdbfs)
library(ggplot2)
library(mapgl)
library(glue)
library(jsonlite)
load_h3()
load_spatial()

source("utils.R")
source("inat-ranges.R")


duckdbfs::duckdb_secrets()
inat <- open_dataset("s3://public-inat/hex")

aoi <- spData::us_states
aoi <- spData::world

# publish richness at the aoi (bbox or poly)
meta <- richness(inat, aoi)
m <- richness_map(meta)
m
library(htmlwidgets)
htmlwidgets::saveWidget(m, "total-richness.html")


# publish richness at the aoi (bbox or poly)
meta <- richness(inat, aoi, rank = "class", taxon = "Aves")
m <- richness_map(meta)
htmlwidgets::saveWidget(m, "aves-richness.html")

# publish richness at the aoi (bbox or poly)
meta <- richness(inat, aoi, rank = "class", taxon = "Mammalia")
m <- richness_map(meta)
htmlwidgets::saveWidget(m, "mammals-richness.html")


## UGH can't deal with antimeridian
# dropme <- antimeridian_hexes(3)
# dropme <- antimeridian_hexes(4) |> rename(h4 = h3id)
# inat |> anti_join(dropme) |> write_dataset("s3://public-inat/ranges.parquet")
# inat <- open_dataset("s3://public-inat/ranges.parquet", recursive = FALSE)

# mutate(h3 = h3_cell_to_parent(h4, 3L))

m <- maplibre(center = c(-110.5, 34.8), zoom = 4) |> add_draw_control()
richness_map(
  m,
  "https://minio.carlboettiger.info/public-data/inat-tmp-ranges.h3j"
)


install.packages(
  'spDataLarge',
  repos = 'https://nowosad.github.io/drat/',
  type = 'source'
)


library(htmlwidgets)
htmlwidgets::saveWidget(m, "example.html")


amphib = open_dataset(
  "s3://public-inat/polygon/Amphibia.parquet",
  recursive = FALSE
)

gdf <- amphib |>
  filter(name == "Ambystoma californiense") |>
  to_sf(crs = 4326)

maplibre(center = c(-122.5, 37.8), zoom = 4) |>
  add_source(id = "gdf", gdf) |>
  add_layer(
    "gdf-layer",
    type = "fill",
    source = "gdf",
    paint = list(
      "fill-color" = "darkgreen",
      "fill-opacity" = .9
    )
  )


# Access SVI
#svi = open_dataset("https://minio.carlboettiger.info/public-social-vulnerability/2022/SVI2022_US_tract.parquet")
#tracts = open_dataset("https://minio.carlboettiger.info/public-social-vulnerability/2022-tracts-h3-z5.parquet") # Access CalEnviroScreen
# ces = open_dataset("https://minio.carlboettiger.info/public-calenviroscreen/ces_2021.parquet", format="parquet")

# Filter GBIF to our area-of-interest (h-index) and species of interest

ca <- tracts |>
  filter(STATE == "California") |>
  mutate(h4 = h3_cell_to_parent(h5, 4L)) |>
  mutate(h4 = tolower(as.character(h4)))

out <- ca |>
  inner_join(inat, by = "h4") |>
  count(STATE, COUNTY, FIPS, h5)


#  mutate(height = n / max(n)) |>

url = "https://minio.carlboettiger.info/public-data/cache/inat/cec4b3087f0b6c41ecc384da2521f97c.h3j"
maplibre() |>
  add_draw_control() |>
  add_h3j_source("h3j_source", url = url) |>
  add_fill_extrusion_layer(
    id = "h3j_layer",
    source = "h3j_source",
    tooltip = "n",
    fill_extrusion_color = viridis_pal("height"),
    fill_extrusion_height = list(
      "interpolate",
      list("linear"),
      list("zoom"),
      0,
      0,
      1,
      list("*", 100000, list("get", "height"))
    ),
    fill_extrusion_opacity = 0.7
  )