The package adehabitat has been designed to allow the analysis of the space use by animals. This package is organised in four main parts: (i) management of raster maps, (ii) habitat selection/ecological niche analysis, (iii) home range estimation and (iv) analysis of animals trajectories. These four parts interact with each other to facilitate the analysis. Note that adehabitat strongly relies on the package ade4, which provides numerous functions for the analysis of multivariate data.
| Package: | adehabitat |
| Type: | Package |
| Version: | 1.8.3 |
| Date: | 2009-05-04 |
| License: | GPL version 2 or newer |
The four parts of the packages are described more in detail below:
Management of raster mapsHowever, it provides numerous
functions allowing to import and export raster maps from/to Geographic
information system, to compute buffers around points or lines, to
identify the value of environmental variables at given spatial
locations, to count the number of points of a pattern in each pixel of
a map, etc. Two basic object classes allow to manage ratser maps with
adehabitat: the class asc is intended to store basic raster
map (see help(import.asc)), whereas the class kasc is
intended to store multi-layer maps (all covering the same area with
the same resolution, see help(as.kasc)). For additional
information this part of the package, see the tutorial available in
the package. Type demo(rastermaps) for a demonstration of the
package capabilities. Note that the package sp also provides many
interesting functions to manage raster maps, and adehabitat provide
functions of conversion to the classes of the package (see
help(kasc2spixdf)).
Habitat selection/ecological niche analysismany methods have
been included in the package to render statistical methods allowing
the analysis of habitat selection available to wildlife
ecologists. Many of them are factor analyses of the niche or of the
habitat selection, but other methods are also available. They
include the selection ratios (see help(wi)), the Ecological
niche factor analysis (see help(enfa)), the Mahalanobis
distances (see help(mahasuhab)) and their factorial
decomposition (the MADIFA, see help(madifa)) or the algorithm
DOMAIN (see help(domain)). Other common methods, such as the
resource selection functions can also be used with the rest of the R
environment. Note that the package also include functions allowing
the analysis of habitat selection using radio-tracking data, such as
the compositional analysis (see help(compana)), the
eigenanalysis of selection ratios (see help(eisera)) or the
K-select analysis (see help(kselect)). An overview of these
methods is available by typing demo(nichehs).
home range estimationmany methods are available to estimate
the home range of animals relocated using radio-tracking data. Common
methods of estimation are available, such as the Minimum convex
polygon (see help(mcp)), the kernel estimation of the
utilization distribution (see help(kernelUD)), the cluster home
range (see help(clusthr)) or the nearest neighbour convex hull
(see help(NNCH)). Note that Paolo Cavallini has designed a
website dedicated to the analysis of space use by animals, which
contain a wiki page, a tutorial for the home range estimation using R
and adehabitat and a forum (URL:
http://www.faunalia.it/animov/index.php). Several methods of these
part of the package have been included following discussions that
arose on this forum (especially, the nearest neighbour convex hull and
the brownian bridge kernel). Type demo(homerange) for examples
of use of these functions.
The analysis of animals' trajectoriesThis part is the most recent
one in the package. A new class designed to store animals'
trajectories has been included in the package, the class
ltraj (see help(as.ltraj)). Two types of
trajectories can be handled with adehabitat: for trajectories of
type I, the time is not recorded for the relocations (e.g. the
sampling of the tracks of an animal in the snow). For trajectories
of type II, the time has been recorded during sampling
(e.g. radio-tracking, GPS, Argos monitoring). Many descriptive
parameters are automatically computed (relative or turning angles,
distance between successive relocations, mean squared
displacement). Many functions allow the management and analysis of
trajectories, through the analysis of these parameters (e.g. tests of
independence, see help(wawotest,indmove), first passage time,
see fpt). The rediscretisation of trajectories of type I is also
possible (help(redisltraj)). Many graphical functions are
available for the exploration of the trajectory properties
(plot,plotltr,sliwinltr), etc. A new partitioning algorithm
has been added (but it is still under research) to partition animals
trajectories into segment with homogeneous properties (see
modpartltraj). Further details can be found on
the help page of the function as.ltraj. For a demonstration,
type demo(managltraj) or demo(analysisltraj).
Calenge, C. (2006) The package adehabitat for the R software: a tool for the analysis of space and habitat use by animals. Ecological Modelling, 197, 516-519
# NOT RUN {
## For examples of use of mapping capabilities
demo(rastermaps)
## For examples of use of functions for
## habitat selection and niche analysis
demo(nichehs)
## For example of home range estimation
demo(homerange)
## For example of trajectory management and analysis
demo(managltraj)
demo(analysisltraj)
# }
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