Continuous-Time Movement Modeling

Documentation for package ‘ctmm’ version 1.2.0

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

Continuous-time movement modeling

-- A --

agde	Calculate a range distribution estimate
akde	Calculate an autocorrelated kernel density estimate
akde.list	Calculate an autocorrelated kernel density estimate
akde.telemetry	Calculate an autocorrelated kernel density estimate
annotate	Color telemetry objects by time
as.sf	Export ctmm data formats
as.telemetry	Import, coerce, summarize, and combine MoveBank data
as.telemetry.character	Import, coerce, summarize, and combine MoveBank data
as.telemetry.data.frame	Import, coerce, summarize, and combine MoveBank data
as.telemetry.Move	Import, coerce, summarize, and combine MoveBank data

-- B --

bandwidth	Calculate the optimal bandwidth matrix of movement data
buffalo	African buffalo GPS dataset from Kruger National Park, South Africa.

-- C --

cde	Encounter statistics
cleave	Spatial selection methods for telemetry objects.
cluster	Clustering of movement-model parameters
coati	Coatis on Barro Colorado Island, Panama.
color	Color telemetry objects by time
compass	Projection
correlogram	Calculate model fit residuals and assess their autocorrelation
ctmm	Specify, fit, and select continuous-time movement models
ctmm-FAQ	ctmm FAQ
ctmm-faq	ctmm FAQ
ctmm.boot	Parametric bootstrap continuous-time movement models
ctmm.fit	Specify, fit, and select continuous-time movement models
ctmm.guess	Visually fit a movement model to a variogram
ctmm.loglike	Specify, fit, and select continuous-time movement models
ctmm.select	Specify, fit, and select continuous-time movement models

-- D --

difference	Estimate the proximity of two individuals
dimfig	Scientific formatting of numbers
distance	Calculate the square distance between two distributions or location estimates
distances	Estimate the proximity of two individuals
dt.plot	Functions for diagnosing sampling schedules

-- E --

emulate	Draw a random model-fit from the sampling distribution
emulate.ctmm	Draw a random model-fit from the sampling distribution
emulate.telemetry	Draw a random model-fit from the sampling distribution
encounter	Encounter statistics
Exp	Log transformation of parameter estimates and their uncertainties
export	Export ctmm data formats
extent	Extent
extent-method	Extent

-- F --

funnel

Meta-analysis of movement-model parameters

-- G --

gazelle

Mongolian gazelle GPS dataset from the Mongolia's Eastern Steppe.

-- H --

head	Import, coerce, summarize, and combine MoveBank data
head.telemetry	Import, coerce, summarize, and combine MoveBank data
homerange	Calculate a range distribution estimate

-- I --

intensity

Compare empirical and theoretical intensity (resource-selection) functions [IN DEVELOPMENT]

-- J --

jaguar

Jaguar data from the Jaguar movement database.

-- L --

lasso	Spatial selection methods for telemetry objects.
Log	Log transformation of parameter estimates and their uncertainties

-- M --

mag	Calculate model fit residuals and assess their autocorrelation
mag.telemetry	Calculate model fit residuals and assess their autocorrelation
marquee	Spatial selection methods for telemetry objects.
mean.ctmm	Average movement models and autocorrelated kernel density estimates
mean.UD	Average movement models and autocorrelated kernel density estimates
mean.variogram	Compute a number-weighted average of variogram objects
median	Projection
median.telemetry	Projection
meta	Meta-analysis of movement-model parameters
midpoint	Estimate the proximity of two individuals

-- N --

npr	Calculate a non-parametric regression surface

-- O --

occurrence	Calculate a Kriged occurrence distribution estimate
optimizer	Minimize a function
outlie	Methods to facilitate outlier detection.
outlier	Methods to facilitate outlier detection.
overlap	Calculate the overlap between two stationary distributions

-- P --

pelican	Brown Pelican GPS and ARGOS data.
periodogram	Calculate the Lomb-Scargle periodogram of animal-tracking data
pkde	Calculate an autocorrelated kernel density estimate
plot	Plotting methods for telemetry objects
plot.outlie	Methods to facilitate outlier detection.
plot.periodogram	Calculate the Lomb-Scargle periodogram of animal-tracking data
plot.telemetry	Plotting methods for telemetry objects
plot.variogram	Plotting methods for variogram objects.
predict	Predict or simulate from a continuous-time movement model
predict.ctmm	Predict or simulate from a continuous-time movement model
predict.telemetry	Predict or simulate from a continuous-time movement model
projection	Projection
projection-method	Projection
projection<--method	Projection
proximity	Estimate the proximity of two individuals

-- R --

raster-method	Export ctmm data formats
residuals	Calculate model fit residuals and assess their autocorrelation
residuals.ctmm	Calculate model fit residuals and assess their autocorrelation
residuals.telemetry	Calculate model fit residuals and assess their autocorrelation
revisitation	Calculate an revisitation distribution estimate
rsf.fit	Fit integrated resource selection functions (iRSFs) with autocorrelation-adjusted weighted likelihood
rsf.select	Fit integrated resource selection functions (iRSFs) with autocorrelation-adjusted weighted likelihood

-- S --

sdm.fit	Fit species distribution models (SDMs) [IN DEVELOPMENT]
sdm.integrate	Fit species distribution models (SDMs) [IN DEVELOPMENT]
sdm.select	Fit species distribution models (SDMs) [IN DEVELOPMENT]
sigfig	Scientific formatting of numbers
simulate	Predict or simulate from a continuous-time movement model
simulate.ctmm	Predict or simulate from a continuous-time movement model
simulate.telemetry	Predict or simulate from a continuous-time movement model
SpatialPoints.telemetry	Export ctmm data formats
SpatialPointsDataFrame.telemetry	Export ctmm data formats
SpatialPolygonsDataFrame.telemetry	Export ctmm data formats
SpatialPolygonsDataFrame.UD	Export ctmm data formats
speed	Estimate the average speed of a tracked animal
speed.ctmm	Estimate the average speed of a tracked animal
speed.telemetry	Estimate the average speed of a tracked animal
speeds	Estimate the average speed of a tracked animal
speeds.ctmm	Estimate the average speed of a tracked animal
speeds.telemetry	Estimate the average speed of a tracked animal
suitability	Calculate a range distribution estimate
summary.ctmm	Summarize a continuous-time movement model
summary.telemetry	Import, coerce, summarize, and combine MoveBank data
summary.UD	Summarize a range distribution
summary.UERE	Estimate RMS UERE from calibration data

-- T --

tail	Import, coerce, summarize, and combine MoveBank data
tail.telemetry	Import, coerce, summarize, and combine MoveBank data
tbind	Import, coerce, summarize, and combine MoveBank data
turtle	Wood turtle GPS and calibration dataset from Working Land and Seascapes.

-- U --

uere	Estimate RMS UERE from calibration data
uere.fit	Estimate RMS UERE from calibration data
uere<-	Estimate RMS UERE from calibration data

-- V --

variogram	Calculate an empirical variogram from movement data
variogram.fit	Visually fit a movement model to a variogram
video	Video record animated telemetry objects.

-- W --

wolf	Maned wolf GPS dataset from The Maned Wolf Conservation Program.
writeRaster-method	Export ctmm data formats
writeVector	Export ctmm data formats
writeVector-method	Export ctmm data formats

-- Z --

zoom-method	Plotting methods for telemetry objects
zoom-method	Plotting methods for variogram objects.

-- misc --

%#%	Convert dimensionful quantities to and from SI units