In pratikunterwegs/holeybirds: Link bird moult with movement.

Wing gap index change over study period

Load libraries

# libs for data
library(data.table)
library(glue)

library(ggplot2)
library(colorspace)

Load data

# read data
wgi <- fread("data/results/data_daily_rrv.csv")

# assign species name as ordered factor
wgi[, sp := factor(
  sp,
  levels = c("Pycnonotus", "Passer", "Acrocephalus", "Hirundo")
)]

WGI progression plot

# assign first and last day of tracking
wgi[, day := as.numeric(date - min(date), units = "days") + 1, by = "TAG"]

# remove days beyond 10
wgi <- wgi[day <= 10, ]

fig_wing_gap_progression <-
  ggplot(wgi) +
  geom_line(
    aes(
      day, rrv_calc,
      col = treat,
      group = TAG
    )
  ) +
  geom_point(
    aes(
      day, rrv_calc,
      group = TAG,
      col = treat
    )
  ) +
  facet_wrap(
    facets = vars(sp),
    scales = "fixed",
    labeller = labeller(
      sp = c(
        "Acrocephalus" = "Clamorous\nreed warbler",
        "Passer" = "House sparrow",
        "Pycnonotus" = "White-spectacled\nbulbul",
        "Hirundo" = "Barn swallow"
      )
    )
  ) +
  scale_x_continuous(
    breaks = seq(7)
  ) +
  scale_y_continuous(
    breaks = seq(0, 20, 5)
  ) +
  scale_colour_discrete_sequential(
    palette = "Batlow",
    l1 = 30, l2 = 60,
    breaks = c("NonMoulting", "Moulting", "Manipulated"),
    labels = c("Non-molting", "Molting", "Manipulated"),
    order = c(1, 2, 3)
  ) +
  coord_cartesian(
    xlim = c(NA, 7),
    ylim = c(0, 20)
  ) +
  theme_bw(
    base_size = 10
  ) +
  theme(
    legend.position = "top",
    strip.background = element_blank(),
    strip.text = element_text(
      face = "italic"
    ),
    legend.margin = margin(rep(0, 4))
  ) +
  labs(
    x = "Days since start of tracking",
    y = "Wing gap index",
    colour = NULL
  )

# save figure
ggsave(
  fig_wing_gap_progression,
  filename = "figures/fig_spm_01.png",
  width = 80, height = 100, units = "mm"
)