# Analysis of habitat selection by animals

## Documentation for package ‘adehabitat’ version 1.8.12

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Code demos. Use demo() to run them.

## Help Pages

A B C D E F G H I J K L M N O P Q R S T V W misc

adehabitat-package | adehabitat: a Package for the Analysis of the Space Use by Animals

## -- A --

adehabitat | adehabitat: a Package for the Analysis of the Space Use by Animals
albatross | Argos Monitoring of Adult Albatross Movement
angles | Compute Turning Angles - Deprecated
ararea | Compute Areas and Perimeters of Objects of Class "area"
area | Objects of Class "area"
area2asc | Converts a Polygon to Raster
area2dxf | Exportation of Areas
area2spol | Conversion of maps from/to the package "sp"
as.area | Objects of Class "area"
as.asc | Arcview ASCII Raster File Importation And Exportation
as.kasc | Working with Several Raster Maps
as.ltraj | Working with Trajectories in 2D Space: the Class ltraj
as.sahrlocs | Exploratory Analysis of Habitat Selection
as.traj | Working with Trajects in 2D Space
asc | Arcview ASCII Raster File Importation And Exportation
asc2im | Conversion of Maps of Class 'asc' and 'im' (Package spatstat)
asc2spixdf | Conversion of maps from/to the package "sp"
ascgen | Creation of Raster Maps
attpol2area | Conversion of maps from/to the package "sp"

## -- B --

bauges | Census of chamois (Rupicapra rupicapra) in the Bauges mountains
bear | GPS monitoring of one brown bear
bestpartmod | Segmentation of a trajectory based on Markov models (STILL UNDER RESEARCH!!)
bighorn | Radio-Tracking of Bighorn Sheeps
bindltraj | Split Trajectories into Several Bursts
biv.plot | Bivariate Test
biv.test | Bivariate Test
buffer | Compute Buffers
buffer.ani | Compute Buffers
buffer.line | Compute Buffers
buffer.ltraj | Compute Buffers
burst | ID and Bursts of an Object of Class ltraj
burst<- | ID and Bursts of an Object of Class ltraj

## -- C --

c.ltraj | Combine Bursts of Relocations in Objects of Class "ltraj"
capreochiz | GPS Monitoring of one Roe Deer in Chize (France)
capreotf | GPS Monitoring of one Roe Deer in Trois-Fontaines (France)
chamois | Location of Chamois Groups in the Chartreuse Mountains
chi | The Chi Distribution
clusthr | Estimation of Home Range by Clustering
clusthr.area | Estimation of Home Range by Clustering
colasc | Creates a Vector of Colors for a Raster Map of Type 'factor'
compana | Compositional Analysis of Habitat Use
contour.asc | Displays a Color Image of a Matrix of Class 'asc'
convnum | Conversion from Factor to Numeric for Raster Map
count.points | Number of Points in Each Pixel of a Raster Map
count.points.id | Number of Points in Each Pixel of a Raster Map
cutltraj | Split Trajectories into Several Bursts

## -- D --

data2enfa | Ecological Niche Factor Analysis
dchi | The Chi Distribution
df2kasc | Conversion of Objects of Class kasc
df2traj | Working with Trajects in 2D Space
distfacmap | Compute distances to the different levels of a factor map
domain | Estimation of the Potential Distribution of a Species
dunnfa | Factorial Analysis of the Specialization in Habitat Selection Studies. Unpublished Work of James Dunn (University of Arkansas)

## -- E --

eisera | Eigenanalysis of Selection Ratios
enfa | Ecological Niche Factor Analysis
engen2008I | Measuring Habitat Selection Using the Method of Engen et al. (2008)
engen2008II | Measuring Habitat Selection Using the Method of Engen et al. (2008)
explore.kasc | Interactive Exploration of Maps of Class kasc (requires the package tkrplot)
export.asc | Arcview ASCII Raster File Importation And Exportation
Extract.ltraj | Extract or Replace Parts of an Object of Class ltraj
exwc | Kernel Smoothing in Space and Time of the Animals' Use of Space

## -- F --

findmaxasc | Find Local Maxima on a Map of Class 'asc'
fpt | Computation of the First Passage Time From Trajectories

## -- G --

gdltraj | Working with Trajectories: Specify a Time Period
getascattr | Copy the Attributes of an Object of Class 'asc' or 'kasc' to another Object
getburst | Working with Trajects in 2D Space
getcontour | Computes the Contour Polygon of a Raster Object
getkasc | Working with Several Raster Maps
getkascattr | Copy the Attributes of an Object of Class 'asc' or 'kasc' to another Object
getsahrlocs | Exploratory Analysis of Habitat Selection
getverticesclusthr | Estimation of Home Range by Clustering
getverticeshr | Estimation of Kernel Home-Range
getverticeshrk | Kernel Smoothing in Space and Time of the Animals' Use of Space
getverticeshrs | Kernel Smoothing in Space and Time of the Animals' Use of Space
getvolumeUD | Estimation of Kernel Home-Range
getvolumeUDk | Kernel Smoothing in Space and Time of the Animals' Use of Space
getvolumeUDs | Kernel Smoothing in Space and Time of the Animals' Use of Space
getXYcoords | Computes the X and Y Coordinates of the Pixels of a Raster Map
gnesfa | General Niche-Environment System Factor Analysis

## -- H --

hbrown | Estimates the value of h for a Brownian motion
hist.enfa | Ecological Niche Factor Analysis
hist.kasc | Histograms of Mapped Variables
hist.kselect | K-Select Analysis: a Method to Analyse the Habitat Selection by Animals
hist.ltraj | Histogram of the Descriptive Parameters of a Trajectory
hist.madifa | The MADIFA: a Factorial Decomposition of the Mahalanobis Distances
histniche | Histograms of the Ecological Niche
hr.rast | Rasterisation of Objects of Class 'area'
hseal | Argos Monitoring of Hooded Seal

## -- I --

ibex | GPS Monitoring of Four Ibex in the Belledonne Mountain
ibexraw | GPS Monitoring of Four Ibex in the Belledonne Mountain (irregular data)
id | ID and Bursts of an Object of Class ltraj
id<- | ID and Bursts of an Object of Class ltraj
im2asc | Conversion of Maps of Class 'asc' and 'im' (Package spatstat)
image.asc | Displays a Color Image of a Matrix of Class 'asc'
image.kasc | Working with Several Raster Maps
image.khr | Estimation of Kernel Home-Range
image.sahrlocs | Graphical Display of the Habitat Composition of the Home Ranges of Animals Monitored Using Radio-Tracking
import.asc | Arcview ASCII Raster File Importation And Exportation
indmove | Testing Independence in Regular Trajectory Parameters
indmove.detail | Testing Independence in Regular Trajectory Parameters
is.regular | Regular Trajectories
is.sd | Handling of Trajectories of the Same Duration

## -- J --

join.asc | Finds the Value of Mapped Variables at some Specified Locations (Spatial Join)
join.kasc | Finds the Value of Mapped Variables at some Specified Locations (Spatial Join)

## -- K --

kasc | Working with Several Raster Maps
kasc2df | Conversion of Objects of Class kasc
kasc2spixdf | Conversion of maps from/to the package "sp"
kernel.area | Estimation of Kernel Home-Range
kernelbb | Estimation of Kernel Brownian Bridge Home-Range
kernelkc | Kernel Smoothing in Space and Time of the Animals' Use of Space
kernelkcbase | Kernel Smoothing in Space and Time of the Animals' Use of Space
kerneloverlap | Spatial Interaction between Animals Monitored Using Radio-Tracking
kerneloverlaphr | Spatial Interaction between Animals Monitored Using Radio-Tracking
kernelUD | Estimation of Kernel Home-Range
kplot.kselect | K-Select Analysis: a Method to Analyse the Habitat Selection by Animals
kselect | K-Select Analysis: a Method to Analyse the Habitat Selection by Animals
kver | Handling of Objects of Class kver
kver.rast | Handling of Objects of Class kver
kver2shapefile | Handling of Objects of Class kver
kver2spol | Conversion of maps from/to the package "sp"

## -- L --

labcon | Labelling Connected Features
liker | Estimation of Kernel Brownian Bridge Home-Range
lowres | Reducing the Resolution of a Map
lowres.asc | Reducing the Resolution of a Map
lowres.kasc | Reducing the Resolution of a Map
ltraj | Working with Trajectories in 2D Space: the Class ltraj
ltraj2sldf | Conversion of maps from/to the package "sp"
ltraj2spdf | Conversion of maps from/to the package "sp"
ltraj2traj | Working with Trajectories in 2D Space: the Class ltraj
lynxjura | Monitoring of Lynx

## -- M --

madifa | The MADIFA: a Factorial Decomposition of the Mahalanobis Distances
mahasuhab | Habitat Suitability Mapping with Mahalanobis Distances.
managNAkasc | "Cleaning" Objects of Class 'kasc'
mapattr | Store Attributes of Maps of Class asc and kasc
mcp | Estimation of the Home Range Using the Minimum Convex Polygon Estimator
mcp.area | Estimation of the Home Range Using the Minimum Convex Polygon Estimator
mcp.rast | Converts a Polygon to Raster
meanfpt | Computation of the First Passage Time From Trajectories
mindistkeep | Detecting Absence of Movement in an Object of Class 'ltraj'
modpartltraj | Segmentation of a trajectory based on Markov models (STILL UNDER RESEARCH!!)
morphology | Morphology: Erosion or Dilatation of Features on a Raster Map
mouflon | GPS Monitoring of One Mouflon in the Caroux Mountain

## -- N --

niche.test | Monte-Carlo Test on Parameters of the Ecological Niche
NNCH | Nearest Neighbor Convex Hulls (LoCoH)
NNCH.a.area | LoCoH (NNCH): Home Range Area
NNCH.area | LoCoH (NNCH): Home Range Area
NNCH.asciigrid | LoCoH (NNCH): Useful Functions
NNCH.der.a.area | LoCoH (NNCH): Home Range Area
NNCH.der.k.area | LoCoH (NNCH): Home Range Area
NNCH.der.n.area | LoCoH (NNCH): Home Range Area
NNCH.der.r.area | LoCoH (NNCH): Home Range Area
NNCH.k.area | LoCoH (NNCH): Home Range Area
NNCH.n.area | LoCoH (NNCH): Home Range Area
NNCH.r.area | LoCoH (NNCH): Home Range Area
NNCH.select | LoCoH (NNCH): Useful Functions
NNCH.shapefile | LoCoH (NNCH): Useful Functions

## -- O --

offsetdate | Date Handling in an Object of Class 'ltraj'

## -- P --

partmod.ltraj | Segmentation of a trajectory based on Markov models (STILL UNDER RESEARCH!!)
pchi | The Chi Distribution
perarea | Compute Areas and Perimeters of Objects of Class "area"
persp.asc | Displays a Color Image of a Matrix of Class 'asc'
pheasant | Radio-Tracking of Pheasants
plot.area | Graphical Display of Objects of Class "area"
plot.asc | Displays a Color Image of a Matrix of Class 'asc'
plot.clusthr | Estimation of Home Range by Clustering
plot.fipati | Computation of the First Passage Time From Trajectories
plot.hrsize | Estimation of the Home Range Using the Minimum Convex Polygon Estimator
plot.kselect | K-Select Analysis: a Method to Analyse the Habitat Selection by Animals
plot.kver | Handling of Objects of Class kver
plot.ltraj | Graphical Display of an Object of Class "ltraj"
plot.madifa | The MADIFA: a Factorial Decomposition of the Mahalanobis Distances
plot.narea | LoCoH (NNCH): Home Range Area
plot.NNCH | LoCoH (NNCH): Useful Functions
plot.partltraj | Segmentation of a trajectory based on Markov models (STILL UNDER RESEARCH!!)
plot.sahrlocs | Exploratory Analysis of Habitat Selection
plot.traj | Working with Trajects in 2D Space
plot.wi | Computation of Selection Ratios for Habitat Selection Studies.
plotLSCV | Estimation of Kernel Home-Range
plotltr | Changes in Traject Parameters Over Time
plotNAltraj | Highlighting the Patterns in Missing Values in Trajects
porpoise | Argos monitoring of Porpoise Movements
predict.enfa | Habitat Suitability Maps Built from the ENFA
predict.madifa | The MADIFA: a Factorial Decomposition of the Mahalanobis Distances
print.asc | Arcview ASCII Raster File Importation And Exportation
print.clusthr | Estimation of Home Range by Clustering
print.compana | Compositional Analysis of Habitat Use
print.dataenfa | Ecological Niche Factor Analysis
print.dunnfa | Factorial Analysis of the Specialization in Habitat Selection Studies. Unpublished Work of James Dunn (University of Arkansas)
print.enfa | Ecological Niche Factor Analysis
print.engenetalI | Measuring Habitat Selection Using the Method of Engen et al. (2008)
print.engenetalII | Measuring Habitat Selection Using the Method of Engen et al. (2008)
print.esr | Eigenanalysis of Selection Ratios
print.gnesfa | General Niche-Environment System Factor Analysis
print.kasc | Working with Several Raster Maps
print.khr | Estimation of Kernel Home-Range
print.kselect | K-Select Analysis: a Method to Analyse the Habitat Selection by Animals
print.liker | Estimation of Kernel Brownian Bridge Home-Range
print.ltraj | Working with Trajectories in 2D Space: the Class ltraj
print.madifa | The MADIFA: a Factorial Decomposition of the Mahalanobis Distances
print.modpartltraj | Segmentation of a trajectory based on Markov models (STILL UNDER RESEARCH!!)
print.NNCH | LoCoH (NNCH): Useful Functions
print.partltraj | Segmentation of a trajectory based on Markov models (STILL UNDER RESEARCH!!)
print.plotsahr | Exploratory Analysis of Habitat Selection
print.rand.kselect | Test of the Third-Order Habitat Selection
print.sahrlocs | Exploratory Analysis of Habitat Selection
print.traj | Working with Trajects in 2D Space
print.wiI | Computation of Selection Ratios for Habitat Selection Studies.
print.wiII | Computation of Selection Ratios for Habitat Selection Studies.
print.wiIII | Computation of Selection Ratios for Habitat Selection Studies.
puech | Radio-Tracking Data of Wild Boar (2)
puechabon | Radio-Tracking Data of Wild Boar
puechcirc | Movements of wild boars tracked at Puechabon
puechdesIII | Habitat Selection by the Wild Boar at Puechabon

## -- Q --

qchi | The Chi Distribution
qqchi | Quantile-Quantile Plots for Trajectories of Class 'ltraj'
qqchi.default | Quantile-Quantile Plots for Trajectories of Class 'ltraj'
qqchi.ltraj | Quantile-Quantile Plots for Trajectories of Class 'ltraj'
qqnorm.ltraj | Quantile-Quantile Plots for Trajectories of Class 'ltraj'

## -- R --

rand.kselect | Test of the Third-Order Habitat Selection
randtest.enfa | Randomisation Test for the Ecological Niche Factor Analysis
rchi | The Chi Distribution
rec | Working with Trajectories in 2D Space: the Class ltraj
redisltraj | Rediscretization of a Trajectory With Regular Step Length
runsNAltraj | Highlighting the Patterns in Missing Values in Trajects
rupicabau | GPS Monitoring of One Chamois in the Bauges Mountains

## -- S --

s.madifa | The MADIFA: a Factorial Decomposition of the Mahalanobis Distances
sahrlocs | Exploratory Analysis of Habitat Selection
sahrlocs2kselect | Preparation of K-Select Analysis
sahrlocs2niche | OMI Analysis of Radio-Tracking Data
scatter.enfa | Scatter Plot of the Results of the ENFA
scatter.esr | Eigenanalysis of Selection Ratios
scatter.madifa | The MADIFA: a Factorial Decomposition of the Mahalanobis Distances
scatterniche | Display the Niche in the Ecological Space
schoener | Compute Schoener's ratio
schoener.rtest | Compute Schoener's ratio
sd2df | Handling of Trajectories of the Same Duration
set.limits | Define the Same Time Limits for several Bursts in a Regular Trajectory
setmask | Applies a Mask on Objects of Class 'asc' or 'kasc'
setNA | Place Missing Values in Objects of Class 'ltraj'
sett0 | Round the Timing of Collection of Relocations to Obtain Regular Trajectory
simm.bb | Brownian bridge motion
simm.brown | Simulate a Bivariate Brownian Motion
simm.crw | Simulation of a Correlated Random Walk
simm.levy | Simulates a Levy Walk
simm.mba | Simulation of an Arithmetic Brownian Motion
simm.mou | Simulation of a Bivariate Ornstein-Uhlenbeck Process
sliwinltr | Apply a Function on an Object of Class "ltraj", Using a Sliding Window
speed | Computes the Speed Between Successive Relocations of an Animal - Deprecated
spixdf2kasc | Conversion of maps from/to the package "sp"
spol2area | Conversion of maps from/to the package "sp"
squirrel | Radio-Tracking Data of Squirrels
squirreloc | Radio-tracking of squirrels
storemapattr | Store Attributes of Maps of Class asc and kasc
subsample | Subsample a Trajectory
subsetmap | Storing a Part of a Map
subsetmap.asc | Storing a Part of a Map
subsetmap.kasc | Storing a Part of a Map
summary.ltraj | Working with Trajectories in 2D Space: the Class ltraj
summary.NNCH | LoCoH (NNCH): Useful Functions
summary.traj | Working with Trajects in 2D Space
summaryNAltraj | Highlighting the Patterns in Missing Values in Trajects

## -- T --

teal | Teal (Anas crecca) Ring Recovery Dataset
testang.ltraj | Testing Independence in Regular Trajectory Parameters
testdist.ltraj | Testing Independence in Regular Trajectory Parameters
traj | Working with Trajects in 2D Space
traj2df | Working with Trajects in 2D Space
traj2ltraj | Working with Trajectories in 2D Space: the Class ltraj
traj2sldf | Conversion of maps from/to the package "sp"
traj2spdf | Conversion of maps from/to the package "sp"
trajdyn | Interactive Display of Objects of Class 'ltraj'
typeII2typeI | Change the Type of a Trajectory

## -- V --

vanoise | Habitat Use by Three Species of Galliformes in the Vanoise National Parc
varlogfpt | Computation of the First Passage Time From Trajectories

## -- W --

wawotest | Wald-Wolfowitz Test of Randomness
wawotest.default | Wald-Wolfowitz Test of Randomness
wawotest.ltraj | Wald-Wolfowitz Test of Randomness
whale | Argos Monitoring of Whale Movement
which.ltraj | Identify Relocations Fullfilling a Condition in an Object of Class "ltraj"
wi | Computation of Selection Ratios for Habitat Selection Studies.
widesI | Computation of Selection Ratios for Habitat Selection Studies.
widesII | Computation of Selection Ratios for Habitat Selection Studies.
widesIII | Computation of Selection Ratios for Habitat Selection Studies.
wiI | Computation of Selection Ratios for Habitat Selection Studies.
wiII | Computation of Selection Ratios for Habitat Selection Studies.
wiIII | Computation of Selection Ratios for Habitat Selection Studies.

## -- misc --

[.ltraj | Extract or Replace Parts of an Object of Class ltraj
[<-.ltraj | Extract or Replace Parts of an Object of Class ltraj