| # setup | |
| require(shinyjs) | |
| library(shiny) | |
| library(shinydashboard) | |
| library(leaflet) | |
| library(mapboxapi) | |
| library(tidyverse) | |
| library(tidycensus) | |
| library(sf) | |
| library(DT) | |
| library(RColorBrewer) | |
| library(terra) | |
| library(data.table) | |
| library(mapview) | |
| library(sjPlot) | |
| library(sjlabelled) | |
| library(bslib) | |
| library(shinycssloaders) | |
| # ------------------------------------------------ | |
| # 1) API Keys | |
| # ------------------------------------------------ | |
| mapbox_token <- "pk.eyJ1Ijoia3dhbGtlcnRjdSIsImEiOiJjbHc3NmI0cDMxYzhyMmt0OXBiYnltMjVtIn0.Thtu6WqIhOfin6AykskM2g" | |
| # mb_access_token(mapbox_token, install = FALSE) | |
| # ------------------------------------------------ | |
| # 2) Load Data | |
| # ------------------------------------------------ | |
| # -- Greenspace | |
| getwd() | |
| osm_greenspace <- st_read("/vsicurl/https://huggingface.co/datasets/boettiger-lab/sf_biodiv_access/resolve/main/greenspaces_osm_nad83.shp", quiet = TRUE) %>% | |
| st_transform(4326) | |
| if (!"name" %in% names(osm_greenspace)) { | |
| osm_greenspace$name <- "Unnamed Greenspace" | |
| } | |
| # -- NDVI Raster | |
| ndvi <- terra::rast("/vsicurl/https://huggingface.co/datasets/boettiger-lab/sf_biodiv_access/resolve/main/SF_EastBay_NDVI_Sentinel_10.tif") | |
| # -- GBIF data | |
| # Load what is basically inter_gbif !!!!! | |
| # load("data/sf_gbif.Rdata") # => sf_gbif | |
| download.file('https://huggingface.co/datasets/boettiger-lab/sf_biodiv_access/resolve/main/gbif_census_ndvi_anno.Rdata', '/tmp/gbif_census_ndvi_anno.Rdata') | |
| load('/tmp/gbif_census_ndvi_anno.Rdata') | |
| vect_gbif <- vect(sf_gbif) | |
| # -- Precomputed CBG data | |
| download.file('https://huggingface.co/datasets/boettiger-lab/sf_biodiv_access/resolve/main/cbg_vect_sf.Rdata', '/tmp/cbg_vect_sf.Rdata') | |
| load('/tmp/cbg_vect_sf.Rdata') | |
| if (!"unique_species" %in% names(cbg_vect_sf)) { | |
| cbg_vect_sf$unique_species <- cbg_vect_sf$n_species | |
| } | |
| if (!"n_observations" %in% names(cbg_vect_sf)) { | |
| cbg_vect_sf$n_observations <- cbg_vect_sf$n | |
| } | |
| if (!"median_inc" %in% names(cbg_vect_sf)) { | |
| cbg_vect_sf$median_inc <- cbg_vect_sf$medincE | |
| } | |
| if (!"ndvi_mean" %in% names(cbg_vect_sf)) { | |
| cbg_vect_sf$ndvi_mean <- cbg_vect_sf$ndvi_sentinel | |
| } | |
| # -- Hotspots/Coldspots | |
| biodiv_hotspots <- st_read("/vsicurl/https://huggingface.co/datasets/boettiger-lab/sf_biodiv_access/resolve/main/hotspots.shp", quiet = TRUE) %>% st_transform(4326) | |
| biodiv_coldspots <- st_read("/vsicurl/https://huggingface.co/datasets/boettiger-lab/sf_biodiv_access/resolve/main/coldspots.shp", quiet = TRUE) %>% st_transform(4326) | |
| # | |
| # # Community Organizations shapefile | |
| # # For now simulate | |
| # | |
| # # Define San Francisco bounding box coordinates | |
| # sf_bbox <- st_bbox(c( | |
| # xmin = -122.5247, # Western longitude | |
| # ymin = 37.7045, # Southern latitude | |
| # xmax = -122.3569, # Eastern longitude | |
| # ymax = 37.8334 # Northern latitude | |
| # ), crs = st_crs(4326)) # WGS84 CRS | |
| # | |
| # # Convert bounding box to polygon | |
| # sf_boundary <- st_as_sfc(sf_bbox) %>% st_make_valid() | |
| # | |
| # # Transform boundary to projected CRS for accurate buffering (EPSG:3310) | |
| # sf_boundary_proj <- st_transform(sf_boundary, 3310) | |
| # | |
| # # Set seed for reproducibility | |
| # set.seed(123) | |
| # | |
| # # Simulate 20 random points within San Francisco boundary | |
| # community_points <- st_sample(sf_boundary_proj, size = 20, type = "random") | |
| # | |
| # # Convert to sf object with POINT geometry and assign unique names | |
| # community_points_sf <- st_sf( | |
| # NAME = paste("Community Org", 1:20), | |
| # geometry = community_points | |
| # ) | |
| # # Select first 3 points to buffer | |
| # buffered_points_sf <- community_points_sf[1:3, ] %>% | |
| # st_buffer(dist = 100) # Buffer distance in meters | |
| # | |
| # # Update the NAME column to indicate buffered areas | |
| # buffered_points_sf$NAME <- paste(buffered_points_sf$NAME, "Area") | |
| # community_points_sf <- st_transform(community_points_sf, 4326) | |
| # buffered_points_sf <- st_transform(buffered_points_sf, 4326) | |
| # | |
| # # Combine points and polygons into one sf object | |
| # community_orgs <- bind_rows( | |
| # community_points_sf, | |
| # buffered_points_sf | |
| # ) | |
| # | |
| # # View the combined dataset | |
| # print(community_orgs) | |
| # | |
| # community_points_only <- community_orgs %>% filter(st_geometry_type(geometry) == "POINT") | |
| # community_polygons_only <- community_orgs %>% filter(st_geometry_type(geometry) == "POLYGON") | |
| # | |