plot.capthist {secr} | R Documentation

## 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",
        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)
`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`)
`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 `lines` if tracks are plotted

### Details

A plot is generated in the style of Density (Efford 2007) using `eqscplot` from the MASS library.

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 `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.

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).

### Value

The number of detections in `x`.

### Author(s)

Murray Efford murray.efford@otago.ac.nz

### 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)

[Package secr version 1.3.0 Index]