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

library(flexdashboard)
library(drake)
library(gt)
library(reactable)
library(wastdr)

wastd_data <- drake::readd("wastd_data")

# helpers > move to wastdr
filter_calendar_year_2021 <- . %>% 
  dplyr::mutate(calendar_year = datetime %>% lubridate::year()) %>% 
  dplyr::filter(calendar_year==2021)

# surveys ---------------------------------------------------------------------#
surveys <- wastd_data$surveys %>% 
  dplyr::mutate(datetime = start_time) %>% 
  filter_calendar_year_2021() %>% 
  # wastdr::filter_wastd_season(2020) %>% 
  wastdr::filter_realsurveys()

svy_stats <- surveys %>% 
  wastdr::survey_season_stats()

# tracks ----------------------------------------------------------------------#  
tracks <- wastd_data$tracks %>% 
  # wastdr::filter_wastd_season(2020) %>% 
  filter_calendar_year_2021() %>% 
  wastdr::filter_realspecies()

no_tracks <- tracks %>% nrow()

# animals ---------------------------------------------------------------------#
turtles <- wastd_data$animals %>% 
  # wastdr::filter_wastd_season(2020) %>% 
  filter_calendar_year_2021() %>% 
  dplyr::filter(taxon == "Cheloniidae") %>% 
  wastdr::filter_realspecies()

# AnimalEncounters with alive turtles in cal year 2021 excluding training records
turtles_tagged <- turtles %>% 
  filter_alive() %>% 
  dplyr::filter(encounter_type == "tagging")

no_turtles_tagged <- turtles_tagged %>% nrow()

animal_enc_types_area <- turtles %>% 
  dplyr::group_by(encounter_type, area_name, species) %>% 
  dplyr::tally() %>% 
  dplyr::ungroup() %>% 
  tidyr::spread(encounter_type, n)

animal_enc_types <- turtles %>% 
  dplyr::group_by(encounter_type, species) %>% 
  dplyr::tally() %>% 
  dplyr::ungroup() %>% 
  tidyr::spread(encounter_type, n)

Column {data-width=600}

Map

turtles_tagged %>% 
  map_mwi(sites=wastd_data$sites, cluster=TRUE, split_species=TRUE)

Column {data-width=400}

Surveys {.value-box}

# Stats go per season == FY, filter by cal year gets two rows needing to sum
flexdashboard::valueBox(
  sum(svy_stats$number_surveys), caption = "Surveys", icon="fa-pencil")

Survey hours {.value-box}

flexdashboard::valueBox(
  sum(svy_stats$hours_surveyed), caption = "Survey hours", icon="fa-hourglass-half")

Turtles Tagged {.value-box}

flexdashboard::valueBox(
  no_turtles_tagged, caption = "Turtles Tagged", icon="fa-eye")

Turtle Tracks {.value-box}

flexdashboard::valueBox(
  no_tracks, caption = "Turtle Tracks", icon="fa-shoe-prints")

Animal handling

All of WA

animal_enc_types %>% 
  dplyr::mutate(
    species=stringr::str_to_sentence(species) %>% stringr::str_replace("-"," ")
  ) %>% 
  janitor::clean_names(case="title") %>% 
  gt::gt()

DBCA core programs: Thevenard, Delambre, Eco Beach, Roebuck Bay

animal_enc_types_area %>% 
  dplyr::filter(
    area_name %in% c(
      "Delambre Island",
      "Thevenard Island",
      "Eco Beach",
      "Roebuck Bay"
    )
  ) %>% 
  dplyr::mutate(
    species=stringr::str_to_sentence(species) %>% stringr::str_replace("-"," ")
  ) %>% 
  janitor::clean_names(case="title") %>% 
  reactable::reactable(filterable = TRUE)

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