secr (version 1.4.0)

plot.mask: 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", breaks = 12, ppoly = T, polycol = "red", \dots)

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 square pixels

breaks

number of levels to use when cutting continuous covariate for plotting

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. If using a covariate to colour points, the col argument should be a colour vector of length equal to the number of levels. Border lines around pixels are drawn in the current foreground colour (par('fg')). Set this to NA with par(fg=NA) to eliminate borders, but remember to reset it when you've finished.

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) )

par(fg='white')
plot (tempmask, covariate = 'circle', dots = FALSE, axes = TRUE, 
    add = TRUE, breaks = 8, col = terrain.colors(8))
par(fg='black')

plot (temptrap, add = TRUE)

## add a legend

par(cex = 0.9)
covrange <- range(covariates(tempmask)$circle)
step <- diff(covrange)/8
colourlev <- terrain.colors(9)
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')