Analysis of Habitat Selection by Animals

Documentation for package ‘adehabitat’ version 1.8.18

DESCRIPTION file.
User guides, package vignettes and other documentation.
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
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
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

-- O --

offsetdate

Date Handling in an Object of Class 'ltraj'

-- P --

partmod.ltraj	Segmentation of a trajectory based on Markov models
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.partltraj	Segmentation of a trajectory based on Markov models
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
print.partltraj	Segmentation of a trajectory based on Markov models
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.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