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Coordinated singing graphs

Source: R/plot_coordination.R
plot_coordination.Rd

plot_coordination creates graphs of coordinated singing and highlights the signals that overlap in time. The signals are represented by polygons of different colors.

Usage

plot_coordination(
  X = NULL,
  only.coor = FALSE,
  ovlp = TRUE,
  xl = 1,
  res = 80,
  it = "jpeg",
  img = TRUE,
  tlim = NULL,
  pb = TRUE
)

Arguments

X

Data frame containing columns for singing event (sing.event), individual (indiv), and start and end time of signal (start and end).

only.coor

Logical. If TRUE only the segment in which both individuals are singing is included (solo singing is removed). Default is FALSE.

ovlp

Logical. If TRUE the vocalizations that overlap in time are highlighted. Default is TRUE.

xl

Numeric vector of length 1, a constant by which to scale spectrogram width. Default is 1.

res

Numeric argument of length 1. Controls image resolution. Default is 80.

it

A character vector of length 1 giving the image type to be used. Currently only "tiff" and "jpeg" are admitted. Default is "jpeg".

img

Logical argument. If FALSE, image files are not produced and the graphs are shown in the current graphic device. Default is TRUE.

tlim

Numeric vector of length 2 indicating the start and end time of the coordinated singing events to be displayed in the graphs.

pb

Logical argument to control progress bar and messages. Default is TRUE.

Value

The function returns a list of graphs, one for each singing event in the input data frame. The graphs can be plotted by simply calling the list. If 'img' is TRUE then the graphs are also saved in the working directory as files.

Details

This function provides visualization for coordination of acoustic signals. Signals are shown as polygon across a time axis. It also shows which signals overlap, the amount of overlap, and highlights the individual responsible for the overlap using a color code. The width of the polygons depicting the time of overlap.

References

Araya-Salas, M., & Smith-Vidaurre, G. (2017). warbleR: An R package to streamline analysis of animal acoustic signals. Methods in Ecology and Evolution, 8(2), 184-191.

Author

Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)

Examples

if (FALSE) { # \dontrun{
# load simulate singing events (see data documentation)
data(sim_coor_sing)

#' # make plot_coordination in graphic device format
cgs <- plot_coordination(X = sim_coor_sing, ovlp = TRUE, only.coor = FALSE, img = FALSE)

cgs
} # }