dataviz for GPS data and home range

gps_ctmm.R

# fig 1: plot GPS data with color coding for tracking time
# fig 2: estimate and plot home range (AKDE) with package ctmm

#------ fig 1

# pakages
library(ctmm)
library(viridis)
library(ggplot2)

# data
data(buffalo)

# single individual
buf <- buffalo[[1]]

# convert in data.frame
df <- as.data.frame(buf)

# create variable for time (for gradient)
df$time_num <- as.numeric(df$t - min(df$t))

# plot
ggplot(df, aes(x = x, y = y, color = time_num)) +
  #geom_point(size = 2, alpha = 0.9) +
  #geom_point(size = 1.8, alpha = 0.8) + 
  geom_point(size = 2.2, alpha = 0.95) + 
  scale_color_viridis(
    option = "plasma", # D ou magma
    begin = 0,
    end = 1,
    name = "Tracking time",
    breaks = range(df$time_num),
    labels = c("Start", "End"),
    guide = guide_colorbar(
      ticks = FALSE,
      title.position = "top",      
      title.hjust = 0.5            
    )
  ) +
  coord_equal() +
  theme_void() +
  theme(
    legend.position = "bottom",
    legend.title = element_text(size = 12, hjust = 0.5)
  ) + 
  geom_path(alpha = 0.4, linewidth = 0.4)

#------ fig 2

# package
library(ctmm)

# data
data(buffalo)
DATA <- buffalo[[1]]   

# initial guess
GUESS <- ctmm.guess(DATA, interactive = FALSE)

# select best model
FIT <- ctmm.select(DATA, GUESS, trace = FALSE)

# compute AKDE
UD <- akde(DATA, FIT)

# summary (area home range, etc.)
summary(UD)

# plot
plot(UD,
     col.level = "black",
     col.grid = NA,
     col.DF = "black",
     lwd = 2)
plot(DATA, col = "grey40", pch = 16, cex = 0.5, add = TRUE)