plotACs: Plot activity centres from Bayesian SCR output

In mikemeredith/makeJAGSmask: Construct a Habitat Matrix for Use with SECR Analysis in JAGS or BUGS

Description

The function produces a plot of a large number of draws (default 3000) from the posterior distributions of the x and y coordinates of the activity centre (AC) for each animal.

The cloud of points represents what we know about the AC location for each animal. If we knew the AC location with certainty, there would only be one point (ie, the 3000 points would all be on top of each other). The most probable location for the AC is in the densest part of the cloud, and the extent of the cloud indicates the uncertainty about its location.

Note that the size of the cloud bears no relation to the extent of the animal's home range.

Usage

plotACs(which=NA, ACs, traps, Y, hab, howMany=3000, show.labels=TRUE,
    rad=50, link=TRUE, colors)

Arguments

which	The numbers of the ACs to plot; if NA, all captured animals' ACs will be plotted.
ACs	A 3D array of MCMC output, iterations x animals x 2, with the x and y coordinates of the activity centres. Typically this would be output from convertOutput. ACs for phantom animals should be converted to NA.
traps	An optional 2-column matrix or data frame with the coordinates of the traps.
Y	An optional detection history matrix, animals x traps, with Y[i,j] > 0 if animal i was caught in trap j, 0 otherwise. Row names are taken to be animal identifiers.
hab	Optional; either a SpatialPolygons* object or a 2-column matrix or data frame with the coordinates of the vertices of a polygon describing the extent of the available habitat.
howMany	The number of points to plot for each posterior distribution.
show.labels	If TRUE, animal identifiers are added to the plot.
rad	The jitter used to distance the points showing capture locations from the traps.
link	If TRUE, capture locations for each animal are linked by a line.
colors	A vector of colours to use to plot the different animals; default is to use palette().

Value

Returns invisibly the ACs plotted as a data frame with 3 columns, the animal ID in the first column and the x and y coordinates in the second and third.

Author(s)

Mike Meredith

Examples

data(simSCR)
str(simSCR$sims.list)

# Convert AC locations to the original units, remove phantoms:
AC <- convertOutput(simSCR$sims.list$S, simSCR$JAGSmask)
AC[simSCR$sims.list$w == 0] <- NA

# Default: plot the animals captured:
with(simSCR, plotACs(which=NA, AC=AC, traps=traps, Y=Y, hab=patchSP))

# Omit optional items, some information will not be displayed:
with(simSCR, plotACs(which=1:6, AC=AC))
with(simSCR, plotACs(which=1:6, AC=AC, traps=traps, hab=patchSP))
with(simSCR, plotACs(which=NA, AC=AC, Y=Y, hab=patchSP))

mikemeredith/makeJAGSmask documentation built on May 19, 2021, 1:10 a.m.