adehabitat (version 1.3)

NNCH: Nearest Neighbor Convex hull

Description

NNCH computes the home range of several animals using the nearest neighbor convex hull method (Getz and Wilmers, 2004). plot.NNCH gives a graphical display of the estimation. NNCH.area is used for home-range size estimation. neighNNCH is used to determine the optimum number of neighbors (plots the home-range size estimated to a given percentage level according to the number neighbors used for the estimation). getverticesNNCH is used to store the limits of the home ranges. plot.NNCHver displays the limits of the home ranges (but see the section "note"). NNCH.rast is used to convert the home range to raster.

Usage

NNCH(xy, id = NULL, k = 10, unin = c("m", "km"), unout = c("ha", "km2", "m2"))
plot.NNCH(x, which = names(x), add.points = TRUE, pch = 21,
          bgpts = "white", colpts = "black",
          cex = 0.7, add = FALSE, same4all = TRUE,
          border = NA, ...)
NNCH.area(x, percent = c(95,90,80,70,60,50,40,30,20,10))
neighNNCH(xy, id = NULL, rangek, percent = 95,
          unin = c("m", "km"), unout = c("ha", "km2", "m2"))
plot.ngNNCH(x, ...)
getverticesNNCH(x, percent = 95)
plot.NNCHver<-function(x, which = names(x),
                       colpol = NA,
                       colborder = rep("black", length(x)),
                       lwd = 2, add = FALSE, ...)
NNCH.rast(y, w)

Arguments

xy

a data frame containing the coordinates of the relocation of the monitored animals

id

a factor giving the identity of the animal for each relocation

k

the number of neighbors to take into account in the estimation

unin

the units of the relocations coordinates. Either "m" (default) for meters or "km" for kilometers

unout

the units of the output areas. Either "m2" for square meters, "km2" for square kilometers or "ha" for hectares (default)

x

an object of class "NNCH". For plot.NNCHver, an object of class NNCHver returned by the function getverticesNNCH. For plot.ngNNCH, an object of class ngNNCH re

which

a vector of character strings, indicating the names of the animals to be plotted

add.points

logical. TRUE if the relocations are to be plotted

pch

if add.points is TRUE, the size of the points to be used for the plot of the relocations (see par)

bgpts

if add.points is TRUE, the background color to be used for the plot of the relocations (see par)

colpts

if add.points is TRUE, the color of the points to be used for the plot of the relocations (see par)

cex

if add.points is TRUE, the size of the points to be used for the plot of the relocations (see par)

add

logical. Whether the home ranges should be displayed on a previous plot

border

The color of the border of the polygons. NA if a border is not required

same4all

logical. If TRUE, the plot displaying the home ranges has the same X and Y limits for all animals

...

additional arguments to be passed to the generic function plot

percent

for NNCH.area, a vector of percentage levels for home-range size estimation. For getverticesNNCH, one value giving the percentage level for the home range estimation.

colpol

a vector of the color for filling the polygon. The default, NA, is to leave polygons unfilled

colborder

a vector of the color to draw the border. The default. Use border = NA to omit borders

lwd

the border width, a positive number

w

an object of class asc or kasc

rangek

a vector giving several numbers of neighbors to test

Value

• NNCH returns a list of class NNCH. NNCH.area returns an object of class hrsize. neighNNCH returns a matrix of class ngNNCH. getverticesNNCH returns an object of class NNCHver. NNCH.rast returns a raster map of class asc or kasc.

Warning

These functions require the package gpclib.

References

Getz, W.M. & Wilmers, C.C. (2004). A local nearest-neighbor convex-hull construction of home ranges and utilization distributions. Ecography, in press.

See Also

plot.hrsize to display the home-range size according to the percentage level of the estimation.

Examples

## Can also be used to analyse a point pattern
## For example, locations of chamois in
## the Chartreuse mountains (French Alps)

data(chamois)
xy <- chamois$locs

## choice of the number of neighbors
## Warning: this command can be very long (more than two minutes)
u <- neighNNCH(xy, rangek = 5:30)
plot(u)

## 13 and 20 neighbours seem to be a good choice
## Estimates the home range levels
(aa <- NNCH(xy, k = 13))
plot(aa)

## plot of the home-range size
plot(NNCH.area(aa))

## gets the home range contour
cont <- getverticesNNCH(aa)
plot(cont)

## rasterizes these contours
sl <- getkasc(chamois$map, "Slope")
mm <- NNCH.rast(cont, sl)
image(mm)

## Note that two different sets of polygons can include
## the same percentage of relocation
aa[[1]]$area[97:105,]

## For example, the same percentage of relocations is
## included within the limits of the two home ranges
## (91.92 percent of the localisations) 
opar <- par(mfrow=c(1,2))
plot(aa[[1]]$polygons[[103]],
     poly.args = list(lwd = 2))
points(xy, pch = 16, cex = 0.5)

plot(aa[[1]]$polygons[[98]],
     poly.args = list(lwd = 2))
points(xy, pch=16, cex = 0.5)
par(opar)
## only the left-hand plot is considered as an
## home range estimation (the larger one)