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

knitr::opts_chunk$set(echo = TRUE)
library(wastdr)

drake::loadd("wastd_data")

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

Data was accessed on r wastd_data$downloaded_on.

We filter AnimalEncounters to those with turtles in calendar years 2016-18 and split them by live and dead turtles. We exclude tagged turtles (which can also record damages/injuries).

ani <- wastd_data$animals %>% 
  dplyr::mutate(calendar_year = datetime %>% lubridate::year()) %>% 
  dplyr::filter(calendar_year>=2016, calendar_year<=2018) %>%  
  dplyr::filter(taxon=="Cheloniidae")

ani_dead <- ani %>% filter_dead()
ani_alive <- ani %>% filter_alive() %>% dplyr::filter(health!="na")

dmg <- wastd_data$turtle_dmg %>% 
  dplyr::filter(calendar_year>=2016, calendar_year<=2018)
morph <- wastd_data$turtle_morph %>% 
  dplyr::filter(calendar_year>=2016, calendar_year<=2018)

Exports

Both alive and dead turtles are exported to CSV and RDS (to open in R), plus damages and morphometrics for combined dead and alive animals.

dest <- "inst/reports/strandings_2016_2018"

ani_alive %>% saveRDS(here::here(dest, "alive.rds"))
ani_alive %>% readr::write_csv(here::here(dest, "alive.csv"))

ani_dead %>% saveRDS(here::here(dest, "dead.rds"))
ani_dead %>% readr::write_csv(here::here(dest, "dead.csv"))

dmg %>% saveRDS(here::here(dest, "dmg.rds"))
dmg %>% readr::write_csv(here::here(dest, "dmg.csv"))

morph %>% saveRDS(here::here(dest, "morph.rds"))
morph %>% readr::write_csv(here::here(dest, "morph.csv"))

Strandings

This map provides a quick overview of stranding locations.

ani_dead %>% map_mwi()

The following table previews the contents of the CSV "ani_dead.csv".

ani_dead %>% rt()

Rescues / non-mortalities

This map provides a quick overview of rescue/non-mortalities locations.

ani_alive %>% map_mwi()

The following table previews the contents of the CSV "ani_alive.csv".

ani_alive %>% rt()

Damages (dead and alive)

dmg %>% rt

Morphometrics (dead and alive)

morph %>% rt

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