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global.R
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global.R
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# Attach packages
library(shiny)
library(tidyverse)
library(kableExtra)
library(shinythemes)
library(here)
library(janitor)
# library(paletteer)
library(raster)
library(sf)
library(tmap)
library(leaflet)
library(ggplot2)
library(shinyWidgets)
# Read in data
## read in national parks boundaries
nps <- read_sf(dsn = here("data", "National_Park_Service__Park_Unit_Boundaries"),
layer = "National_Park_Service__Park_Unit_Boundaries", crs = 4326) %>%
clean_names()
nps_ca <- nps %>%
filter(state == "CA")
nps_ca_five <- nps_ca %>%
filter(unit_name %in% c("Death Valley National Park", "Joshua Tree National Park", "Yosemite National Park", "Channel Islands National Park", "Sequoia National Park")) %>%
dplyr::select(unit_name) %>%
mutate(lat1 = c(36.2 , 33.3, 37.5, 33.5, 35.6),
lat2 = c(36.8 , 34.5, 38.2, 34.3, 37.4),
long1 = c(-119 , -120.6, -120, -116.7, -118.1),
long2 = c(-118.2 , -119, -119.1, -115, -116.2))
#plot(nps_ca_five)
# Read in park data
# Channel islands
channel_islands <- read_csv(here::here("data", "Animals", "channel_islands.csv")) %>%
dplyr::select(latitude, longitude, common_name, iconic_taxon_name) %>%
mutate(iconic_taxon_name = as.character(iconic_taxon_name)) %>%
filter(!iconic_taxon_name %in% c("Actinopterygii", "Animalia")) %>%
mutate(park = "Channel Islands National Park")
channel_islands_sf <- st_as_sf(channel_islands,
coords = c("longitude", "latitude"),
crs = 4326)
# Death Valley
death_valley <- read_csv(here::here("data", "Animals", "death_valley.csv")) %>%
dplyr::select(latitude, longitude, common_name, iconic_taxon_name) %>%
filter(!iconic_taxon_name == "Animalia") %>%
mutate(park = "Death Valley National Park")
death_valley_sf <- st_as_sf(death_valley,
coords = c("longitude", "latitude"),
crs = 4326)
# Joshua Tree
joshua_tree <- read_csv(here::here("data", "Animals", "joshua_tree.csv")) %>%
dplyr::select(latitude, longitude, common_name, iconic_taxon_name) %>%
filter(!iconic_taxon_name %in% c("Animalia", "Plantae")) %>%
mutate(park = "Joshua Tree National Park")
joshua_tree_sf <- st_as_sf(joshua_tree,
coords = c("longitude", "latitude"),
crs = 4326)
# Yosemite
yosemite <- read.csv(here("data", "Animals", "yosemite.csv")) %>%
clean_names()
yosemite_clean <- yosemite %>%
dplyr::select(longitude, latitude, common_name, iconic_taxon_name) %>%
mutate(iconic_taxon_name = as.character(iconic_taxon_name)) %>%
filter(iconic_taxon_name != "Animalia") %>%
mutate(park = "Yosemite National Park")
yosemite_sf <- st_as_sf(yosemite_clean, coords = c("longitude", "latitude"),
crs = 4326)
# Sequoia
sequoia <- read.csv(here("data", "Animals", "sequoia.csv")) %>%
clean_names()
sequoia_clean <- sequoia %>%
dplyr::select(longitude, latitude, common_name, iconic_taxon_name) %>%
mutate(iconic_taxon_name = as.character(iconic_taxon_name)) %>%
mutate(park = "Sequoia National Park")
sequoia_sf <- st_as_sf(sequoia_clean, coords = c("longitude", "latitude"),
crs = 4326)
# join species observations data
animal <- rbind(channel_islands_sf, death_valley_sf, yosemite_sf, sequoia_sf, joshua_tree_sf)
# ONLY keep *animal points* inside the polygons
park_animals <- st_join(animal, nps_ca_five, left = FALSE) %>%
filter(!common_name %in% c("Birds", "Mammals", "Reptiles", "Snakes", "Amphibians", "NA", "Lizards", "Ensatina",
"Frogs and Toads", "Rodents", "Tree Squirrels", "Typical Squirrels", "Canines", "Squamates"))
# change island fox to santa cruz island fox
park_animals$common_name[park_animals$common_name == "Island Fox"] <- "Santa Cruz Island Fox"
# change western side-blotched lizard to common side-blotched lizard
park_animals$common_name[park_animals$common_name == "Western Side-blotched Lizard"] <- "Common Side-blotched Lizard"
# change western sagebrush lizard to common sagebrush lizard
park_animals$common_name[park_animals$common_name == "Western Sagebrush Lizard"] <- "Common Sagebrush Lizard"
taxon_to_common <- data.frame(iconic_taxon_name = unique(park_animals$iconic_taxon_name),
common_taxon = c("Birds", "Mammals", "Reptiles", "Amphibians"))
park_animals <- park_animals %>%
full_join(taxon_to_common)
# Also get the lat & long for the animal observations, lon - X, lat - Y
park_animals_coords <- data.frame(park_animals,
sf::st_coordinates(park_animals))