| usagePlot {secr} | R Documentation |
usagePlot displays variation in effort (usage) over detectors as a
bubble plot (circles with radius scaled so that area is proportional to
effort).
sightingPlot displays spatial variation in the number of sightings at each detector as a
bubble plot (circles with radius scaled so that area is proportional to either the average number per occasion or the total over occasions.
usagePlot(object, add = FALSE, occasions = NULL, col = "black", fill =
FALSE, scale = 2, metres = TRUE, rad = 5, ...)
sightingPlot(object, type = c("Detections", "Tu", "Tm", "Tn"), add = FALSE,
occasions = "ALL", mean = TRUE, col = "black", fill = FALSE, scale = 2,
metres = TRUE, dropunused = TRUE, title = type, legend = c(1, 2, 4, 8),
px = 0.95, py = 0.95, ...)
object |
traps object with usage attribute |
add |
logical; if FALSE plot.traps is called to create a base plot |
occasions |
integer number(s) of the occasion(s) for which effort is plotted, "ALL", or NULL |
col |
character or integer colour value |
fill |
logical; if TRUE the circle is filled with the line colour |
scale |
numeric value used to scale radius |
metres |
logical; if TRUE scale is a value in metres (see Details) |
rad |
numeric; radial displacement of symbol centre for each occasion from true detector location (metres) |
... |
other arguments passed to plot.traps |
type |
character to choose among sighting types and detections of marked animals |
mean |
logical; if TRUE then the plotted value is the average over occasions, otherwise the sum |
dropunused |
logical; if TRUE then detectors are omitted when they were unused on |
title |
character |
legend |
numeric values for which legend circles will be drawn |
px |
legend x position as fraction of user coordinates |
py |
legend y position as fraction of user coordinates |
The behaviour of usagePlot is described first. By default (occasion = NULL) circles representing usage on each
occasion are plotted around the detector location at distance
rad, as in the petal plot of
plot.capthist. Otherwise, the usage on a single
specified occasion, or summed over occasions
(length(occasion)>1, or occasion = "ALL"), is plotted as
a circle centred at the detector location.
Package sp provides an alternative to usagePlot (see Examples).
sightingPlot may be used to display either detections of marked animals (whether or not occasions refers to sighting occasions) or any of the sighting attributes (unmarked sightings ‘Tu’, marked, unidentified sightings ‘Tm’, or other uncertain sightings ‘Tn’).
If py is of length 2 then the values determine the vertical spread of symbols in the legend.
For both functions –
The metres argument switches between two methods. If metres
= TRUE, the symbols function is used with inches = FALSE to plot
circles with radius scaled in the units of object (i.e. metres;
scale is then the radius in metres of the symbol for a detector
with usage = 1.0). Otherwise, plotting uses points; this has the
advantage of producing better filled circles, but a suitable value of
scale must be found by trial and error.
No value is returned by usagePlot.
sightingPlot invisibly returns a ‘traps’ object with a covariate ‘f’ holding the plotted values.
usage, symbols, bubble,
sightings
simgrid <- make.grid(nx = 10, ny = 10, detector = "proximity")
usage(simgrid) <- matrix(rep(1:10, 50), nrow = 100, ncol = 5)
usagePlot(simgrid, border = 20, scale = 1.5, fill = FALSE,
metres = FALSE)
# It is hard to get the legend just right
# here is one attempt
legend (x = -50, y = 185, legend = c(1,2,5,10), pch = 1, pt.cex =
c(1,2,5,10)^0.5 * 1.5, x.intersp = 3, y.intersp = 1.8, adj = 1,
bty = "n", title = "Usage")
usagePlot(simgrid, occasion = NULL, border = 20, scale = 1.5, fill = FALSE,
metres = FALSE)
## Not run:
# bubble plot in package 'sp'
library(sp)
simgrid$usage <- usage(simgrid)[,1] ## occasion 1
class(simgrid) <- "data.frame"
coordinates(simgrid) <- c("x","y")
bubble(simgrid)
## End(Not run)