molt_dates_locs_summary_stats.R

# Summary stats for molt dates and locations
# code started 2022-02-25 by AS
library(tidyverse)


molt_locs <-data.table::fread("data/molt_locs500_2022-02-15.csv")

# summarize molt dates of birds that are included in molt locs table
molt_locs%>%
  filter(doy<86)%>%
  group_by(season)%>%
  summarise(mean_doy  = mean(doy), 
            min_doy = min(doy), 
            max_doy = max(doy), 
            se_doy = sd(doy)/sqrt(n()))

molt_locs%>%
  filter(doy<86)%>%
  group_by(season,bird_id)%>%
  summarise(n=n()/500)%>%
  summary()


# Table with molt and arrival dates estimated from GDR data
molt_tab <-
  read_csv("data/gdr_molt_dates_v2022-02-11.csv")%>%
  mutate(mstart_doy = as.numeric(format(start_molt,"%j")), mend_doy = as.numeric(format(end_molt,"%j")))

# summarise length of molt and SE
molt_tab %>%
  summarise(mean_dur = mean(molt_dur),
    min_dur = min(molt_dur, na.rm = TRUE), 
            max_dur = max(molt_dur, na.rm = TRUE),
            SE_dur = sd(molt_dur)/sqrt(n()))


# summarise start of molt dates
molt_tab %>%
  summarise(mean_start = mean(mstart_doy),
            min_start = min(mstart_doy, na.rm = TRUE), 
            max_start = max(mstart_doy, na.rm = TRUE),
            SE_start = sd(mstart_doy)/sqrt(n()))
                          


# table with info on deployed individuals
gdr_depl <- read_csv("data\croz_royds_gdr_depl_all_v2021-08-27.csv")


# individuals with molt dates that don't have locations
molt_locs_ids <-molt_locs%>%
  group_by(season,bird_id)%>%
  tally()%>%
  select(season,bird_id)

missing_locs <- anti_join(molt_tab,molt_locs_ids) %>%
  left_join(gdr_depl)


summary(missing_locs)

filter(molt_locs, bird_id==3698)

# confirm birds missing from locs500 table
locs500 <- data.table::fread("data/gdr_locs_final_500_all_yr_v2021-06-03.csv")

# summarise date of first locations for each bird
first_loc_dates <- locs500%>%
  filter(inserted==FALSE)%>%
  group_by(season,bird_fn)%>%
  summarise(first_loc=min(time1))%>%
  mutate(first_loc_doy = as.numeric(format(first_loc,"%j")))
summary(first_loc_dates)


missing_locs_date <- missing_locs%>%
  left_join(first_loc_dates)%>%
  mutate(molt_off = first_loc_doy-mend_doy)

# number of birds from each colony with molts dates
molt_tab%>%
  group_by(br_col)%>%
  tally()