Skip to contents

Make a visualization of individual positions and calls during a time period specified by the user. The visualization can either show all individuals in the provided data or can zoom in on one individual and show its behavior in detail.

generate_movement_and_calls_visualization.Rd

[Experimental]

Usage

generate_movement_and_calls_visualization(
  xs = NULL,
  ys = NULL,
  timestamps = NULL,
  calls = NULL,
  start_time = NULL,
  end_time = NULL,
  time_step = 1,
  output_dir = NULL,
  ind_names = NULL,
  focus_ind = NULL,
  zoom_radius = 400,
  bg_color = "black",
  satellite_map = TRUE,
  utm_epsg = NULL,
  auto_zoom_tiles = TRUE,
  zoom_global = 15,
  zoom_focus = NULL,
  colors_inds = NULL,
  colors_calls = NULL,
  ind_point_size = 2,
  call_point_size = 1,
  pchs_inds = NULL,
  pchs_calls = NULL,
  tail_time = 10,
  call_persist_time = 10,
  show_legend_inds = TRUE,
  sort_legend_inds = NULL,
  show_legend_calls = FALSE,
  legend_loc = "topright",
  scalebar_size = 100,
  events = NULL,
  highlighted_radius = 1000
)

Arguments

xs

matrix of dimensions n_inds x n_times where xs[i,t] gives the x position (numeric) of individual i at time step t, positions in UTM format

ys

matrix of dimensions n_inds x n_times where ys[i,t] gives the y position (numeric) of individual i at time step t, positions in UTM format

timestamps

vector of timestamps (POSIXct), must have same dimensions as columns of xs and ys matrices

calls

data frame where first column ('ind_idx') specifies the index of the individual that gave the call, second column ('time_idx') specifies the time index at which the call was given, and third column ('call_type') specifies the type of call (character string)

start_time

time index at which to start the video

end_time

time index at which to end the video

time_step

time step to use (an image every time_step timesteps will be produced)

output_dir

directory in which to store the folder of outputted images

ind_names

vector of names of the individuals

focus_ind

name or index of a focal individual. This centers the frame on one individual instead of producing a broad overview. When using name, ind_names must be provided as well.

zoom_radius

meters around the focal individual (UTM)

bg_color

background color of the plot ("black", "white", etc.)

satellite_map

use a satellite map as the background (T or F)

utm_epsg

WGS 84 EPSG reference number to find the geographic location of the satellite map tile, use https://epsg.io to find the reference number

auto_zoom_tiles

choose satellite map zoom automatically when focusing on individual, determines satellite map resolution

zoom_global

zoom level for global tiles of the background satellite map, determines satellite map resolution

zoom_focus

optional explicit map zoom for focus tiles, determines satellite map resolution

colors_inds

vector of colors to use for each individual (length n_inds). Color indices must match the individual index in calls , xs and ys

colors_calls

vector of colors to use for each call type (alphabetical order by call_type)

ind_point_size

size of the individual points

call_point_size

size of the points for calls

pchs_inds

vector of plotting symbols for individuals

pchs_calls

vector of plotting symbols for calls

tail_time

number of previous time steps to plot as a "tail" which trails the point showing the current location

call_persist_time

number of previous time steps to still show the calls (they will shrink linearly over time in size)

show_legend_inds

whether to plot a legend showing the names of the individuals (T or F)

sort_legend_inds

vector to sort the legend showing the names of the individuals (vector containing the sort order by index)

show_legend_calls

whether to plot a legend showing the names of the call types (T or F)

legend_loc

location of the individual legend, either 'topleft' or 'topright'. Call legend will be opposite

scalebar_size

number of meters for the scalebar, set to 0 to deactivate

events

data frame with columns event_id, start_time_idx,end_time_idx,initiator

highlighted_radius

radius of the highlighted location (usually an epicenter from hyena whoop analysis)

Author

Ariana Strandburg-Peshkin (primary author)

Marius Faiß (secondary author)

NOT YET CODE REVIEWED