In dbca-wa/etlTurtleNesting: Data ETL of Turtle Nesting Census Data from ODK Central to WAStD

knitr::opts_chunk$set(echo = TRUE)
library(wastdr)
library(etlTurtleNesting)
library(ruODK)
library(dplyr)
library(janitor)
library(reactable)
library(sf)

x <- readRDS(here::here("inst/data/wastd_data_pth.rds"))

sw <- geojsonsf::geojson_sf(here::here("inst/data/seawall.geojson")) %>%
  dplyr::transmute(subsite = name)

x$tracks <- x$tracks %>%
  wastdr::filter_realspecies() %>%
  dplyr::filter(season > 2018, site_name == "Port Hedland Cemetery Beach") %>%
  sf::st_as_sf(coords = c("longitude", "latitude"), crs = 4326, remove = FALSE) %>%
  sf::st_join(sw) %>%
  wastdr::sf_as_tbl()

x$animals <- x$animals %>%
  wastdr::filter_realspecies() %>%
  dplyr::filter(
    taxon == "Cheloniidae",
    season > 2018,
    site_name == "Port Hedland Cemetery Beach"
  ) %>%
  sf::st_as_sf(
    coords = c("longitude", "latitude"),
    crs = 4326,
    remove = FALSE
  ) %>%
  sf::st_join(sw) %>%
  wastdr::sf_as_tbl()

x$nest_excavations <- x$nest_excavations %>%
  wastdr::filter_realspecies() %>%
  dplyr::filter(
    season > 2018,
    encounter_site_name == "Port Hedland Cemetery Beach"
  ) %>%
  sf::st_as_sf(
    coords = c("encounter_longitude", "encounter_latitude"),
    crs = 4326,
    remove = FALSE
  ) %>%
  sf::st_join(sw) %>%
  wastdr::sf_as_tbl()

x_reh <- x
x_reh$tracks <- x_reh$tracks %>%
  dplyr::filter(subsite == "rehab")
x_reh$animals <- x_reh$animals %>%
  dplyr::filter(subsite == "rehab")
x_reh$nest_excavations <- x_reh$nest_excavations %>%
  dplyr::filter(subsite == "rehab")

x_sea <- x
x_sea$tracks <- x_sea$tracks %>%
  dplyr::filter(subsite == "seawall")
x_sea$animals <- x_sea$animals %>%
  dplyr::filter(subsite == "seawall")
x_sea$nest_excavations <- x_sea$nest_excavations %>%
  dplyr::filter(subsite == "seawall")


rt <- . %>%
  janitor::clean_names() %>%
  reactable::reactable(
    filterable = TRUE,
    sortable = TRUE,
    searchable = TRUE,
    defaultColDef = reactable::colDef(html = TRUE)
  )

Data

Data was extracted from WAStD on r x$downloaded_on AWST.

Location

The above areas "rehab" (Rehabilitation Zone) and "seawall" (Seawall footprint) were digitised from visual interpretation of the maps above and extended to the waterline.

wastdr::leaflet_basemap() %>%
  leaflet::addPolygons(data = sw, label = ~subsite) %>%
  leaflet::setView(118.615, -20.306, 18)

Overview

Tagged turtles

x$animals %>%
  wastdr::map_mwi(sites = x$sites, cluster = TRUE) %>%
  leaflet::addPolygons(data = sw, label = ~subsite) %>%
  leaflet::setView(118.615, -20.306, 15)

Tracks Cemetery Beach

x$tracks %>%
  wastdr::map_tracks(sites = x$sites, cluster = TRUE) %>%
  leaflet::addPolygons(data = sw, label = ~subsite) %>%
  leaflet::setView(118.615, -20.306, 15)

Tracks rehab

A visual check whether the data was correctly clipped to the subsites rehab and seawall.

x_reh$tracks %>%
  wastdr::map_tracks(cluster = TRUE) %>%
  leaflet::addPolygons(data = sw, label = ~subsite) %>%
  leaflet::setView(118.615, -20.306, 15)

Tracks seawall

x_sea$tracks %>%
  wastdr::map_tracks(cluster = TRUE) %>%
  leaflet::addPolygons(data = sw, label = ~subsite) %>%
  leaflet::setView(118.615, -20.306, 15)

Nesting effort

Cemetery Beach (total)

x %>%
  wastdr::total_emergences_per_site_season_species() %>%
  rt()

Rehab

x_reh %>%
  wastdr::total_emergences_per_site_season_species() %>%
  rt()

Seawall

x_sea %>%
  wastdr::total_emergences_per_site_season_species() %>%
  rt()

Nesting Success

Cemetery Beach (total)

x %>% wastdr::nesting_success_per_area_season_species() %>% rt()

Rehab

x_reh %>% wastdr::nesting_success_per_area_season_species() %>% rt()

Seawall

x_sea %>% wastdr::nesting_success_per_area_season_species() %>% rt()

Hatching and Emergence Success

Cemetery Beach (total)

x$nest_excavations %>% wastdr::hatching_emergence_success_area() %>% rt()

Rehab

x_reh$nest_excavations %>% wastdr::hatching_emergence_success_area() %>% rt()

Seawall

x_sea$nest_excavations %>% wastdr::hatching_emergence_success_area() %>% rt()

dbca-wa/etlTurtleNesting documentation built on Nov. 18, 2022, 8:03 a.m.