usagePlot: Plot usage, detections or sightings.

In secr: Spatially Explicit Capture-Recapture

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, ...)

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.

Value

No value is returned by usagePlot.

sightingPlot invisibly returns a ‘traps’ object with a covariate ‘f’ holding the plotted values.

See Also

usage, symbols, bubble, sightings

Examples

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)

## Not run: 
# 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)   

## End(Not run)

secr documentation built on Nov. 4, 2024, 9:06 a.m.