| plot.mask {secr} | R Documentation |
Plot a habitat mask either as points or as an image plot. Colours may be used to show the value of one mask covariate.
## S3 method for class 'mask':
plot(x, border = 20, add = F, covariate = NULL, axes = F,
dots = T, col = "grey", ppoly = T, polycol = "red", ...)
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 |
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).
Murray Efford murray.efford@otago.ac.nz
# 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')