secr (version 3.0.1)

usagePlot:

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

Value

No value is returned by usagePlot.

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

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.

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)   
## ---------------------------------------------