usagePlot: Plot usage, detections or sightings.

Description

usagePlot displays variation in effort (usage) over detectors as a bubble plot (circles with radius scaled so that area is proportional to effort).

sightingPlot displays spatial variation in the number of sightings at each detector as a bubble plot (circles with radius scaled so that area is proportional to either the average number per occasion or the total over occasions.

Usage

usagePlot(object, add = FALSE, occasions = NULL, col = "black", fill =
FALSE, scale = 2, metres = TRUE, rad = 5, ...)
sightingPlot(object, type = c("Detections", "Tu", "Tm", "Tn"), add = FALSE, 
occasions = "ALL", mean = TRUE, col = "black", fill = FALSE, scale = 2, 
metres = TRUE, dropunused = TRUE, title = type, legend = c(1, 2, 4, 8), 
px = 0.95, py = 0.95, ...)

Value

No value is returned by usagePlot.

sightingPlot invisibly returns a `traps' object with a covariate `f' holding the plotted values.

Arguments

object: traps object with usage attribute
add: logical; if FALSE plot.traps is called to create a base plot
occasions: integer number(s) of the occasion(s) for which effort is plotted, "ALL", or NULL
col: character or integer colour value
fill: logical; if TRUE the circle is filled with the line colour
scale: numeric value used to scale radius
metres: logical; if TRUE scale is a value in metres (see Details)
rad: numeric; radial displacement of symbol centre for each occasion from true detector location (metres)
...: other arguments passed to plot.traps
type: character to choose among sighting types and detections of marked animals
mean: logical; if TRUE then the plotted value is the average over occasions, otherwise the sum
dropunused: logical; if TRUE then detectors are omitted when they were unused on occasions
title: character
legend: numeric values for which legend circles will be drawn
px: legend x position as fraction of user coordinates
py: legend y position as fraction of user coordinates

Details

The behaviour of usagePlot is described first. By default (occasion = NULL) circles representing usage on each occasion are plotted around the detector location at distance rad, as in the petal plot of plot.capthist. Otherwise, the usage on a single specified occasion, or summed over occasions (length(occasion)>1, or occasion = "ALL"), is plotted as a circle centred at the detector location.

Package sp provides an alternative to usagePlot (see Examples).

sightingPlot may be used to display either detections of marked animals (whether or not occasions refers to sighting occasions) or any of the sighting attributes (unmarked sightings `Tu', marked, unidentified sightings `Tm', or other uncertain sightings `Tn').

If py is of length 2 then the values determine the vertical spread of symbols in the legend.

For both functions --

The metres argument switches between two methods. If metres = TRUE, the symbols function is used with inches = FALSE to plot circles with radius scaled in the units of object (i.e. metres; scale is then the radius in metres of the symbol for a detector with usage = 1.0). Otherwise, plotting uses points; this has the advantage of producing better filled circles, but a suitable value of scale must be found by trial and error.

Examples

Run this code


simgrid <- make.grid(nx = 10, ny = 10, detector = "proximity")
usage(simgrid) <- matrix(rep(1:10, 50), nrow = 100, ncol = 5)
usagePlot(simgrid, border = 20, scale = 1.5, fill = FALSE,
  metres = FALSE)

# It is hard to get the legend just right
# here is one attempt
legend (x = -50, y = 185, legend = c(1,2,5,10), pch = 1, pt.cex =
  c(1,2,5,10)^0.5 * 1.5, x.intersp = 3, y.intersp = 1.8, adj = 1,
  bty = "n", title = "Usage")

usagePlot(simgrid, occasion = NULL, border = 20, scale = 1.5, fill = FALSE,
  metres = FALSE)

if (FALSE) {
# bubble plot in package 'sp'
library(sp)
simgrid$usage <- usage(simgrid)[,1]  ## occasion 1
class(simgrid) <- "data.frame"
coordinates(simgrid) <- c("x","y")
bubble(simgrid)   
}