Continuous-Time Movement Modeling

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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

ctmm-package 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