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

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
options(rmarkdown.html_vignette.check_title = FALSE)
library(tidyverse)
library(wastdr)
library(sparkline)
library(ggplot2)
library(gt)
library(reactable)
library(sf)

if(require(mapview)) mapview::mapviewOptions(
  fgb = FALSE,
  basemaps = c("Esri.WorldImagery", 
               "Esri.WorldShadedRelief", 
               "OpenTopoMap",
               "OpenStreetMap"),
  layers.control.pos = "topright")

# -----------------------------------------------------------------------------#
# Helpers
# 
# Rendered tables: gt
# Interactive tables: reactable
rt <- . %>% 
  reactable::reactable(
    ., 
    filterable = T, 
    sortable = T, 
    searchable = T,
    defaultColDef = reactable::colDef(html = TRUE)
  )

# -----------------------------------------------------------------------------#
# Data export
# 
zipfn <- wastdr::urlize(params$area_name)
fn <- here::here(params$export_dir, zipfn)
if (!fs::file_exists(fn)) {
  "Creating dir {fn}" %>% glue::glue() %>% wastdr::wastdr_msg_info()
  fs::dir_create(fn, recurse = TRUE)
}

# Data labels
pn <- params$area_name
pf <- params$prefix
ld <- fn

# -----------------------------------------------------------------------------#
# WAStD data: load snapshot from ETL
# 
drake::loadd("wastd_data")

x <- wastd_data %>%
  wastdr::filter_wastd_turtledata(area_name = params$area_name)

x %>% wastdr::export_wastd_turtledata(outdir = fn, filename = zipfn)

saveRDS(x, file = here::here(params$wastd_filepath), compress="xz")

# -----------------------------------------------------------------------------#
# WAMTRAM direct database export
species_lookup <- tibble::tribble(
  ~ species_code, ~ species,
  "HK", "eretmochelys-imbricata",
  "FB", "natator-depressus",
  "LB", "dermochelys-coriacea", 
  "GN", "chelonia-mydas"
)

w2db <- readRDS(here::here(params$w2_rds_filepath)) 

w2tags <- w2db$enc %>% 
  dplyr::filter(grepl("TH", place_code)) %>% 
  dplyr::left_join(species_lookup, by="species_code") %>%
  wastdr::add_dates(date_col = "observation_datetime_utc", parse_date = FALSE)

# -----------------------------------------------------------------------------#
# Sites and options
sites0 <- geojsonsf::geojson_sf(here::here("data/areas.geojson"))
sites1 <- geojsonsf::geojson_sf(here::here("data/areas1.geojson"))
sites2 <- geojsonsf::geojson_sf(here::here("data/areas2.geojson"))
sites3 <- geojsonsf::geojson_sf(here::here("data/areas3.geojson"))

x <- readRDS(here::here(params$wastd_filepath))
w2db <- readRDS(here::here(params$w2_rds_filepath))

Option 1

tracks_sites1 <- 
  x$tracks %>% 
  dplyr::select(
    latitude, longitude, when, calendar_date_awst, season,
    leaflet_title, nest_age, nest_type, species
  ) %>% 
  sf::st_as_sf(coords = c("longitude", "latitude"), crs=4326) %>% 
  sf::st_join(sites1)

tag_sites1 <-
  w2tags %>% 
  sf::st_as_sf(coords = c("longitude", "latitude"), crs=4326) %>% 
  sf::st_join(sites1)

sites1_thv <- sites1 %>% 
  dplyr::filter(grepl("Thevenard", name))

mapview::mapview(
  list(sites1_thv, tag_sites1, tracks_sites1),
  layer.name=c("Sites Option 1", "Tags", "Tracks"),
  zcol=c("name", "season", "season"),
  alpha = c(0.2, 1, 1))

tracks_sites1_tally <- 
  tracks_sites1 %>% 
  wastdr::sf_as_tbl() %>% 
  dplyr::group_by(name, species, season) %>% 
  dplyr::tally(name = "tracks") %>% 
  dplyr::ungroup()

tag_sites1_tally <- 
  tag_sites1 %>% 
    wastdr::sf_as_tbl() %>% 
  dplyr::group_by(name, species, season) %>% 
  dplyr::tally(name = "tags") %>% 
  dplyr::ungroup()

tally_sites1 <-
  tracks_sites1_tally %>% 
  dplyr::full_join(tag_sites1_tally, by=c("name", "species", "season")) %>% 
  dplyr::arrange(name, -season, species)

tally_sites1 %>% rt

Option 2

tracks_sites2 <- 
  x$tracks %>% 
  dplyr::select(
    latitude, longitude, when, calendar_date_awst, season,
    leaflet_title, nest_age, nest_type, species
  ) %>% 
  sf::st_as_sf(coords = c("longitude", "latitude"), crs=4326) %>% 
  sf::st_join(sites2)

tag_sites2 <-
  w2tags %>% 
  sf::st_as_sf(coords = c("longitude", "latitude"), crs=4326) %>% 
  sf::st_join(sites2)

sites2_thv <- sites2 %>% 
  dplyr::filter(grepl("Thevenard", name))

mapview::mapview(
  list(sites2_thv, tag_sites2, tracks_sites2),
  layer.name=c("Sites Option 2", "Tags", "Tracks"),
  zcol=c("name", "season", "season"),
  alpha = c(0.2, 1, 1))

tracks_sites2_tally <- 
  tracks_sites2 %>% 
  wastdr::sf_as_tbl() %>% 
  dplyr::group_by(name, species, season) %>% 
  dplyr::tally(name = "tracks") %>% 
  dplyr::ungroup()

tag_sites2_tally <- 
  tag_sites2 %>% 
    wastdr::sf_as_tbl() %>% 
  dplyr::group_by(name, species, season) %>% 
  dplyr::tally(name = "tags") %>% 
  dplyr::ungroup()

tally_sites2 <-
  tracks_sites2_tally %>% 
  dplyr::full_join(tag_sites2_tally, by=c("name", "species", "season")) %>% 
  dplyr::arrange(name, -season, species)

tally_sites2 %>% rt

Option 3

tracks_sites3 <- 
  x$tracks %>% 
  dplyr::select(
    latitude, longitude, when, calendar_date_awst, season,
    leaflet_title, nest_age, nest_type, species
  ) %>% 
  sf::st_as_sf(coords = c("longitude", "latitude"), crs=4326) %>% 
  sf::st_join(sites3)

tag_sites3 <-
  w2tags %>% 
  sf::st_as_sf(coords = c("longitude", "latitude"), crs=4326) %>% 
  sf::st_join(sites3)

sites3_thv <- sites3 %>% 
  dplyr::filter(grepl("Thevenard", name))

mapview::mapview(
  list(sites3_thv, tag_sites3, tracks_sites3),
  layer.name=c("Sites Option 3", "Tags", "Tracks"),
  zcol=c("name", "season", "season"),
  alpha = c(0.2, 1, 1))

tracks_sites3_tally <- 
  tracks_sites3 %>% 
  wastdr::sf_as_tbl() %>% 
  dplyr::group_by(name, species, season) %>% 
  dplyr::tally(name = "tracks") %>% 
  dplyr::ungroup()

tag_sites3_tally <- 
  tag_sites3 %>% 
    wastdr::sf_as_tbl() %>% 
  dplyr::group_by(name, species, season) %>% 
  dplyr::tally(name = "tags") %>% 
  dplyr::ungroup()

tally_sites3 <-
  tracks_sites3_tally %>% 
  dplyr::full_join(tag_sites3_tally, by=c("name", "species", "season")) %>% 
  dplyr::arrange(name, -season, species)

tally_sites3 %>% rt

Tracks

x$tracks %>% 
  wastdr::filter_wastd_season(2020) %>% 
  wastdr::filter_realspecies() %>% 
  wastdr::map_tracks()

library(leaflet.extras)
x$tracks %>% 
  wastdr::filter_wastd_season(2020) %>% 
  wastdr::filter_realspecies() %>% 
  dplyr::filter(species=="natator-depressus") %>% 
  leaflet() %>%
  leaflet::addProviderTiles("Esri.WorldImagery", group = "Aerial") %>%
  leaflet::addProviderTiles("OpenStreetMap.Mapnik", group = "Place names") %>%
  addHeatmap(
    lng = ~longitude, lat = ~latitude, #intensity = ~mag,
    blur = 20, max = 0.05, radius = 15
  )

Comparison

Missed and morning FB tracks 2020-21 seasons

summary1 <- tally_sites1 %>% 
  dplyr::rename(tracks1=tracks) %>% 
  dplyr::select(-tags) %>% 
  dplyr::filter(species=="natator-depressus", season==2020)

summary2 <- tally_sites2 %>% 
  dplyr::rename(tracks2=tracks) %>% 
  dplyr::select(-tags) %>% 
  dplyr::filter(species=="natator-depressus", season==2020)

summary3 <- tally_sites3 %>% 
  dplyr::rename(tracks3=tracks) %>% 
  dplyr::select(-tags) %>% 
  dplyr::filter(species=="natator-depressus", season==2020)

comp <- 
  summary1 %>% 
  dplyr::left_join(summary2, by=c("name", "species", "season")) %>% 
  dplyr::left_join(summary3, by=c("name", "species", "season")) %>% 
  dplyr::mutate(
    diff31 = tracks3 - tracks1,
    diff21 = tracks2 - tracks1,
    diff32 = tracks3 - tracks2,
    pct31 = round(100 * diff31 / tracks3, 0),
    pct32 = round(100 * diff32 / tracks3, 0),
    pct21 = round(100 * diff21 / tracks3, 0)
  )

comp %>% gt::gt()

Missed and morning FB tracks all seasons

tracks_sites1_tally_all <- 
  tracks_sites1 %>% 
  wastdr::sf_as_tbl() %>% 
  dplyr::filter(species=="natator-depressus") %>% 
  dplyr::group_by(name, species) %>% 
  dplyr::tally(name = "tracks1") %>% 
  dplyr::ungroup()

tracks_sites2_tally_all <- 
  tracks_sites2 %>% 
  wastdr::sf_as_tbl() %>% 
  dplyr::filter(species=="natator-depressus") %>% 
  dplyr::group_by(name, species) %>% 
  dplyr::tally(name = "tracks2") %>% 
  dplyr::ungroup()

tracks_sites3_tally_all <- 
  tracks_sites3 %>% 
  wastdr::sf_as_tbl() %>% 
  dplyr::filter(species=="natator-depressus") %>% 
  dplyr::group_by(name, species) %>% 
  dplyr::tally(name = "tracks3") %>% 
  dplyr::ungroup()

compa <- 
  tracks_sites1_tally_all %>% 
  dplyr::left_join(tracks_sites2_tally_all, by=c("name", "species")) %>% 
  dplyr::left_join(tracks_sites3_tally_all, by=c("name", "species")) %>% 
  dplyr::mutate(
    diff31 = tracks3 - tracks1,
    diff21 = tracks2 - tracks1,
    diff32 = tracks3 - tracks2,
    pct31 = round(100 * diff31 / tracks3, 0),
    pct32 = round(100 * diff32 / tracks3, 0),
    pct21 = round(100 * diff21 / tracks3, 0)
  )


compa %>% gt::gt()

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