secr (version 5.0.0)

plot.mask: Plot Habitat Mask, Density or Resource Surface

Description

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

Usage

# S3 method for mask
plot(x, border = 20, add = FALSE, covariate = NULL, axes = FALSE,
    dots = TRUE, col = "grey", breaks = 10, meshcol = NA, ppoly = TRUE,
    polycol = "red", legend = TRUE, ...)
# S3 method for Dsurface
plot(x, covariate, group = NULL, plottype =
    "shaded", scale = 1, ...)
# S3 method for Rsurface
plot(x, covariate = "Resource", plottype =
    "shaded", scale = 1, ...)
spotHeight (object, prefix = NULL, dec = 2, point = FALSE, text = TRUE,
    sep = ", ",  session = 1, scale = 1, ...)

Value

If covariate is specified and plottype = "shaded" then

plot.mask invisibly returns a character vector of the intervals defined by `breaks' (useful for plotting a legend).

If plottype = "persp" then plot.mask invisibly returns a the perspective matrix that may be used to add to the plot with

trans3d.

spotHeight invisibly returns a dataframe of the extracted values and their coordinates.

Arguments

x, object

mask or Dsurface 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

col

colour(s) to use for plotting

breaks

an integer or a numeric vector -- see cut

meshcol

colour for pixel borders (NA for none)

ppoly

logical for whether the bounding polygon should be plotted (if `poly' specified)

polycol

colour for outline of polygon (ppoly = TRUE)

legend

logical; if TRUE a legend is plotted

...

other arguments passed to eqscplot (in the case of plot.mask), plot.mask (in the case of plot.Dsurface and plot.Rsurface), and points or text (in the case of spotHeight)

group

group for which plot required, if more than 1

plottype

character string c("dots", "shaded", "contour", "persp")

scale

numeric multiplier for density or other numeric covariate (see Dsurface)

prefix

character vector for name(s) of covariate(s) to retrieve

dec

number of decimal places for rounding density

point

logical for whether to plot point

text

logical for whether to place density label on plot

sep

character separator for elements if length(prefix)>1

session

session number or identifier

Details

The argument dots of plot.mask selects between two distinct types of plot (dots and shaded (coloured) pixels).

plot.Dsurface and plot.Rsurface offer contour and perspective plots in addition to the options in plot.mask. It may take some experimentation to get what you want - see contour and persp.

For plot.Dsurface the default value of `covariate' is `D' unless the Dsurface has a `parameter' attribute of `noneuc',

If using a covariate or Dsurface or Rsurface to colour dots or pixels, the col argument should be a colour vector of length equal to the number of levels (the default palette from 2.9.0 is terrain.colors, and this palette will also be used whenever there are too few levels in the palette provided; see Notes for more on palettes). Border lines around pixels are drawn in `meshcol'. Set this to NA to eliminate pixel borders.

If a covariate is specified in a call to plot.Dsurface then that covariate will be plotted instead of density. This is a handy way to contour a covariate (contouring is not available in plot.mask).

If `breaks' is an integer then the range of the covariate is divided into this number of equal intervals. Alternatively, `breaks' may be a vector of break points (length one more than the number of intervals). This gives more control and often `prettier'

spotHeight may be used to interrogate a plot produced with plot.Dsurface or plot.Rsurface, or by plot.mask if the mask has covariates. prefix defaults to `density.' for Dsurface objects and to `' (all covariates) for mask objects. The predicted density or covariate at the nearest point is returned when the user clicks on the plot. Multiple values may be displayed (e.g., prefix = c("lcl","ucl") if Dsurface includes confidence limits). Click outside the mask or hit the Esc key to end. spotHeight deals with one session at a time.

Legend plotting is enabled only when a covariate is specified. It uses legend when dots = TRUE and strip.legend otherwise.

See Also

colours, mask, Dsurface, rectangularMask, contour persp strip.legend

Examples

# simple

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

if (FALSE) {

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

tempmask <- subset(tempmask, pdot(tempmask, temptrap,
    noccasions = 5)>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, breaks = 8, col = terrain.colors(8), mesh = NA)
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 <- format(round(seq(covrange[1],covrange[2],step),2))
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")

## Waitarere possum density surface extrapolated across region

regionmask <- make.mask(traps(possumCH), buffer = 1000, spacing = 10,
    poly = possumremovalarea)
dts <- distancetotrap(regionmask, possumarea)
covariates(regionmask) <- data.frame(d.to.shore = dts)
shorePossums <- predictDsurface(possum.model.Ds, regionmask)

## plot as coloured pixels with white lines
colourlev <- terrain.colors(7)
plot(shorePossums, breaks = seq(0,3.5,0.5), plottype = "shaded",
    poly = FALSE, col = colourlev, mesh = NA)
plot(traps(possumCH), add = TRUE, detpar = list(col = "black"))
polygon(possumremovalarea)

## check some point densities
spotHeight(shorePossums, dec = 1, col = "black")

## add a legend
zlev <- format(seq(0,3,0.5), digits = 1)
legend (x = "topright", fill = colourlev, legend =
    paste(zlev,"--"), y.intersp = 1, title = "Density / ha")
}