plot.mask {secr} | R Documentation

## Plot Habitat Mask

### Description

Plot a habitat mask either as points or as an `image` plot. Colours may be used to show the value of one mask covariate.

### Usage

    ## S3 method for class 'mask':
    plot(x, border = 20, add = F, covariate = NULL, axes = F,
        dots = T, col = "grey", ppoly = T, polycol = "red", ...)

### Arguments

`x` | `mask` object
`border` | width of blank display border (metres)
`add` | logical for adding mask points to an existing plot
`covariate` | name (as character string in quotes) or column number of a covariate to use for colouring
`axes` | logical for plotting axes
`dots` | logical for plotting mask points as dots, rather than as `image` plot
`col` | colour(s) to use for plotting
`ppoly` | logical for whether the bounding polygon should be plotted (applies only if mask type = 'polygon')
`polycol` | colour for outline of polygon (`ppoly` = TRUE)
`...` | other arguments passed to `eqscplot`

### Details

The argument `dots` selects between two distinct types of plot; see `image` for more on image plots. If using a `covariate` to colour points, the `col` argument should be a colour vector of length > 1; the default is `heat.colors(12)`.

### Author(s)

Murray Efford murray.efford@otago.ac.nz

### See Also

`colours`, `mask`

### Examples

    # simple

    temptrap <- make.grid()
    tempmask <- make.mask(temptrap)
    plot (tempmask)

    ## restrict to points over an arbitrary detection threshold,
    ## add covariate, plot image and overlay traps

    tempmask <- subset(tempmask, pdot(tempmask,temptrap)>0.001)

    covariates (tempmask) <- data.frame(circle =
        exp(-(tempmask$x^2 + tempmask$y^2)/10000) )

    plot (tempmask, covariate = 'circle', dots = FALSE, axes = TRUE,
        add = TRUE, col = terrain.colors(256))
    plot (temptrap, add = TRUE)

    ## add a legend

    par(cex = 0.9)
    covrange <- range(covariates(tempmask)$circle)
    step <- diff(covrange)/8
    colourlev <- terrain.colors(256)[seq(1,256,(256-1)/8)]
    zlev <- formatC(seq(covrange[1],covrange[2],step), format='f',
        digits=2, width=4)
    legend (x = 'topright', fill = colourlev, legend = zlev,
        y.intersp = 0.8, title = 'Covariate')

    title('Colour mask points with p.(X) > 0.001')
    mtext(side=3,line=-1, 'g0 = 0.2, sigma = 20, nocc = 5')

[Package secr version 1.3.0 Index]