# Continuous-Time Movement Modeling

## Documentation for package ‘ctmm’ version 1.3.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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 --

pd.logdet | Postive-definite matrix operations
pd.solve | Postive-definite matrix operations
pd.sqrtm | Postive-definite matrix operations
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
transition | Make a sequence of transition slide figures
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