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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(etlTurtleNesting)
library(wastdr)
library(dplyr)
library(gt)
library(ggplot2)
library(leaflet)
library(leaflet.minicharts)

Data

w2 = readRDS(here::here(params$w2_path))

The data analysed here is a snapshot of the turtle tagging database retrieved on r w2$downloaded_on. We exclude data captured at Thevenard and Delambre Island 2021 for now.

Morphometrics

We show number of observations (n), min, max, mean, sd, and median for morphometric measurements of type CCL (curved carapace length), CCL Notch (CCL entered into wrong field), CCW (curved carapace width) for nesting female Flatback turtles by rookery.

Caveats: The dataset could contain incorrect data, mainly with decimal point errors. The data contain live sightings (daytime in-water captures), night taggings of nesting turtles, stranded injured or dead turtles, as well as juvenile animals.

Morphometrics table

morph <- w2$obs_measurements %>% 
  dplyr::left_join(w2$enc, by="observation_id") %>% 
  dplyr::filter(species_code=="FB", nesting=="Y", sex=="F") 

morph_stats <- morph %>% 
  dplyr::group_by(
    location_code,
    measurement_type_code
  ) %>% 
  dplyr::summarise(
    n = dplyr::n(),
    min = min(measurement_value),
    max = max(measurement_value),
    mean = mean(measurement_value),
    sd = sd(measurement_value),
    median = median(measurement_value),
    .groups = "keep"
  ) %>% 
  dplyr::ungroup() %>%
  dplyr::filter(n>100) %>% 
  dplyr::arrange(measurement_type_code, location_code)

morph_stats %>% 
  gt::gt() %>% 
  gt::tab_header(title="Flatback Morphometrics") %>% 
  gt::cols_label(
    location_code = "Rookery",
    measurement_type_code = "Measurement"
  )

Morphometrics histogram

We show selected morphometrics (CCL, CCL NOTCH, CCW) for the three most sampled rookeries, Barrow (BW), Dampier Archipelago (DA), Mundabullangana (MN), and Port Hedland (PH).

morph %>% 
  dplyr::filter(
    measurement_type_code %in% c("CCL", "CCL NOTCH", "CCW"),
    location_code %in% c("BW", "DA", "MN", "PH")
    ) %>% 
  dplyr::mutate(
    morphometric = measurement_type_code, 
    measurement = measurement_value) %>% 
  ggplot(aes(x=measurement, fill=morphometric)) +
  ggplot2::labs(
    title="Morphometric measurements of nesting female Flatback turtles",
    subtitle=paste0(
      "Locations: Barrow (BW), Dampier Archipelago (DA), Mundabunllangana (MN), Port Hedland (PH)\n",
      "Measurements: Curved Carapace Length (CCL / CCL NOTCH) and Width (CCW)"),
    x="Measurement [mm]",
    y="Number of turtles"
    ) +
  ggplot2::xlim(c(600, 1000)) +
  geom_histogram(binwidth=5, colour="black") +
  facet_wrap("location_code", ncol=1) +
  theme_classic()

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