secr (version 2.4.0)

plot.capthist: Plot Detection Histories

Description

Display a plot of detection (capture) histories over a map of the detectors.

Usage

## S3 method for class 'capthist':
plot(x, rad = 5,
    hidetraps = FALSE, tracks = FALSE,
    title = TRUE, subtitle = TRUE, add = FALSE, varycol = TRUE, 
    icolours = NULL, randcol = FALSE, 
    lab1cap = FALSE, laboffset = 4, ncap = FALSE, 
    splitocc = NULL, col2 = "green",
    type = "petal",
    cappar = list(cex = 1.3, pch = 16, col = "blue"), 
    trkpar = list(col = "blue", lwd = 1), 
    labpar = list(cex = 0.7, col = "black"), ...)

Arguments

x

an object of class capthist

rad

radial displacement of dot indicating each capture event from the detector location (used to separate overlapping points)

hidetraps

logical indicating whether trap locations should be displayed

tracks

logical indicating whether consecutive locations of individual animals should be joined by a line

title

logical or character string for title

subtitle

logical or character string for subtitle

add

logical for whether to add to existing plot

varycol

logical for whether to distinguish individuals by colour

icolours

vector of individual colours (when varycol = TRUE), or colour scale (non-petal plots)

randcol

logical to use random colours (varycol = TRUE)

lab1cap

logical for whether to label the first capture of each animal

laboffset

distance by which to offset labels from points

ncap

logical to display the number of detections per trap per occasion

splitocc

optional occasion from which second colour is to be used

col2

second colour (used with splitocc)

type

character string ("petal", "n.per.detector" or "n.per.cluster")

cappar

list of named graphical parameters for detections (passed to par)

trkpar

list of named graphical parameters for tracks (passed to par)

labpar

list of named graphical parameters for labels (passed to par)

...

arguments to be passed to plot.traps

Value

• For type = "petal", the number of detections in x. For type = "n.per.detector" or type = "n.per.cluster", a dataframe with data for a legend (see Examples).

Details

By default, a `petal' plot is generated in the style of Density (Efford 2007) using eqscplot from the MASS library. If type = "n.per.detector" or type = "n.per.cluster" the result is a colour-coded plot of the number of individuals at each unit, pooled over occasions. If title = FALSE no title is displayed; if title = TRUE, the session identifer is used for the title. If subtitle = FALSE no subtitle is displayed; if subtitle = TRUE, the subtitle gives the numbers of occasions, detections and individuals. If x is a multi-session capthist object then a separate plot is produced for each session. Use par(mfrow = c(nr, nc)) to allow a grid of plots to be displayed simultaneously (nr rows x nc columns). These arguments are used only for petal plots: rad, tracks, varycol, randcol, lab1cap, laboffset, ncap, splitocc, col2, trkpar, and labpar. If icolours = NULL and varycol = TRUE then a vector of colours is generated automatically as terrain.colors((nrow(x)+1) * 1.5). If there are too few values in icolours for the number of individuals then colours will be re-used.

References

Efford, M. G. (2007) Density 4.1: software for spatially explicit capture--recapture. Department of Zoology, University of Otago, Dunedin, New Zealand. http://www.otago.ac.nz/density

See Also

capthist

Examples

demotrap <- make.grid()
tempcapt <- sim.capthist(demotrap, 
    popn = list(D = 5, buffer = 50), 
    detectpar = list(g0 = 0.15, sigma = 30))
plot(tempcapt, border = 10, rad = 3, tracks = TRUE, 
    lab1cap = TRUE, laboffset = 2.5)


## type = n.per.cluster

## generate some captures
testregion <- data.frame(x = c(0,2000,2000,0),
    y = c(0,0,2000,2000))
popn <- sim.popn (D = 10, core = testregion, buffer = 0,
    model2D = "hills", details = list(hills = c(-2,3)))
t1 <- make.grid(nx = 1, ny = 1)
t1.100 <- make.systematic (cluster = t1, spacing = 100,
    region = testregion)
capt <- sim.capthist(t1.100, popn = popn, noccasions = 1)

## now plot captures ...
temp <- plot(capt, title = "Individuals per cluster",
    type = "n.per.cluster", hidetraps = FALSE,
    gridlines = FALSE, cappar = list(cex = 1.5))

## add legend; click on map to place top left corner
legend (locator(1), pch = 21, pt.bg = temp$colour,
    pt.cex = 1.3, legend = temp$legend, cex = 0.8)

## try varying individual colours - requires RColorBrewer
require(RColorBrewer)
plot(infraCH[[2]], icolours = brewer.pal(12, 'Set3'), tracks = T,
    bg = 'black', cappar = list(cex = 2), border = 10, rad = 2,
    gridlines=F)