Plot species' activity patterns — mm_plot

This function visualizes species' activity patterns based on time-of-day data. It uses kernel density estimation to estimate activity density.

Usage

mm_plot_density(
  time,
  xscale = 24,
  xcenter = c("noon", "midnight"),
  n_grid = 128,
  kmax = 3,
  adjust = 1,
  rug = FALSE,
  linetype = 2,
  linecol = "gray10",
  linewidth = 1,
  rug_lentgh = 0.018,
  rug_color = "gray30",
  extend = "lightgrey",
  extend_alpha = 0.8,
  ...
)

Arguments

time: A numeric vector of time-of-day observations (in radians, 0 to \(2\pi\)).
xscale: A numeric value to scale the x-axis. Default is 24 for representing time in hours.
xcenter: A string indicating the center of the x-axis. Options are "noon" (default) or "midnight".
n_grid: An integer specifying the number of grid points for density estimation. Default is 128.
kmax: An integer indicating the maximum number of modes allowed in the activity pattern. Default is 3.
adjust: A numeric value to adjust the bandwidth of the kernel density estimation. Default is 1.
rug: A logical value indicating whether to include a rug plot of the observations. Default is FALSE.
linetype: A numeric specifying the line types. Default is c(1, 2).
linecol: A string specifying the colors of the density lines for species A and B. Default is c("gray10", "gray0").
linewidth: A numeric value specifying the line widths for species A and B density lines. Default is c(1, 1).
rug_lentgh: A numeric value specifying the length of the rug ticks. Default is 0.018 (in normalized plot coordinates).
rug_color: A string specifying the color of the rug ticks. Default is "gray30".
extend: A string specifying the color of the extended area beyond the activity period. Default is "lightgrey".
extend_alpha: A numeric value (0 to 1) for the transparency of the extended area. Default is 0.8.
...: Additional arguments passed to the geom_rug function.

Value

A ggplot object representing the activity density curves of the species.

Examples


 # Generate random data for two species
 set.seed(42)
 A <- runif(100, 0, 2 * pi)

 # Plot overlap with default settings
 mm_plot_density(A)
#> Error in mm_plot_density(A): object 'A' not found
 # Customize plot with specific colors and line types
 mm_plot_density(A, linecol = "gray10", linewidth = 0.8,
                 xcenter = "midnight", rug = TRUE,
                 rug_color = 'red', extend_alpha = 0)
#> Error in mm_plot_density(A, linecol = "gray10", linewidth = 0.8, xcenter = "midnight",     rug = TRUE, rug_color = "red", extend_alpha = 0): object 'A' not found