old/ATBR_filters.R

In Vin985/gblincoln: Lincoln estimates for the GameBirds database

library(tidyverse)
library(RMark)
library(stringr)
library(geosphere)
library(rworldmap)
library(rnaturalearth)
library(sf)
library(xlsx)

root <- getwd()

ATBRBAND <-
  read.csv("../data/ATBR_allbandings.csv", stringsAsFactors = FALSE)
names(ATBRBAND) <-
  str_replace_all(names(ATBRBAND), c(" " = "." , "," = ""))
table(ATBRBAND$B.Year, useNA = "always")
ATBRBAND$TAGE[ATBRBAND$Age == 1] <- "AHY"
ATBRBAND$TAGE[ATBRBAND$Age == 5] <- "AHY"
ATBRBAND$TAGE[ATBRBAND$Age == 6] <- "AHY"
ATBRBAND$TAGE[ATBRBAND$Age == 7] <- "AHY"
ATBRBAND$TAGE[ATBRBAND$Age == 8] <- "AHY"
ATBRBAND$TAGE[ATBRBAND$Age == 2] <- "HY"
ATBRBAND$TAGE[ATBRBAND$Age == 3] <- "HY"
ATBRBAND$TAGE[ATBRBAND$Age == 4] <- "HY"
ATBRBAND$TAGE[ATBRBAND$Age == 0] <- NA
ATBRBAND$TSEX[ATBRBAND$Sex == 4] <- "MALE"
ATBRBAND$TSEX[ATBRBAND$Sex == 5] <- "FEMALE"



ATBRBAND1 <- ATBRBAND %>%
  filter(Status == 3) %>% # normal, wild birds
  filter(Add.Info %in% c(00, 01, 07, 08, 25, 18),  #00 (normal), 01 (color band), 07 (double bands), 08 (temp marker-paint or dye), 25 (geolocators), 18 (blood sampled)
         Sex %in% c(4, 5)) %>%
  filter(TAGE == 'AHY') %>%
  rename(LOC = Location_lu..STATE_NAME)

ATBRBAND2 <- ATBRBAND1 %>%
  filter(!is.na(TAGE)) %>%
  filter(LOC %in% c("Nunavut")) %>%
  filter(B.Month > 6) %>%
  filter(B.Month < 9) %>%
  select(
    -Sex..VSEX,
    -B.Coordinate.Precision,
    -Band.Size,
    -How_aged..How.Aged.Description,
    -How.Sexed,
    -How.Aged,
    -Age..VAGE,-AI..VAI,
    -coord_precision..LOCATION_ACCURACY_DESC,
    -DayCode..Day.Span,
    -How_sexed..How.Sexed.Description,-Location_lu..COUNTRY_NAME,
    -Month..VMonth,
    -Permits..Permittee,
    -Region..Flyway,
    -Status..VStatus,
    -Region..State,
    -Object_Name,
    -MARPLOT.Layer.Name,
    -MARPLOT.Map.Name,
    -symbol,
    -color,
    -idmarplot,
    -Species.Game.Birds..Species
  )

head(ATBRBAND2)

ATBRBANDsum <- ATBRBAND2 %>%
  filter(B.Year %in% 2000:2019) %>%
  group_by(B.Year) %>%
  summarise(total = sum(Count.of.Birds))
ATBRBANDsum