# Dive Analysis and Calibration

## Documentation for package ‘diveMove’ version 1.6.1

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

## Help Pages

A B C D E F G L O P R S T misc

diveMove-package | Dive Analysis and Calibration

## -- A --

as.data.frame-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
as.TDRspeed | Coerce, Extractor, and Replacement methods for class "TDR" objects
as.TDRspeed-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
austFilter | Filter satellite locations

## -- B --

bec | Calculate bout ending criteria from model coefficients
bec-method | Calculate bout ending criteria from model coefficients
boutfreqs | Histogram of log-transformed frequencies
boutinit | Fit "broken stick" model to log frequency data for identification of bouts of behaviour
boutinit-method | Fit "broken stick" model to log frequency data for identification of bouts of behaviour
Bouts | Class "Bouts" for representing Poisson mixtures for identification of behavioural bouts
Bouts-class | Class "Bouts" for representing Poisson mixtures for identification of behavioural bouts
boutsCDF | Estimated cumulative frequency for two- or three-process Poisson mixture models
boutsNLSll | Generalized log likelihood function taking any number of Poisson processes in a "broken-stick" model
boutsNLSll-method | Generalized log likelihood function taking any number of Poisson processes in a "broken-stick" model

## -- C --

calibrateDepth | Calibrate Depth and Generate a "TDRcalibrate" object
calibrateSpeed | Calibrate and build a "TDRcalibrate" object
ccData<- | Coerce, Extractor, and Replacement methods for class "TDR" objects
ccData<--method | Coerce, Extractor, and Replacement methods for class "TDR" objects
coerce-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
createTDR | Read comma-delimited file with "TDR" data

## -- D --

depth<- | Coerce, Extractor, and Replacement methods for class "TDR" objects
depth<--method | Coerce, Extractor, and Replacement methods for class "TDR" objects
distSpeed | Calculate distance and speed between locations
diveModel | Class "diveModel" for representing a model for identifying dive phases
diveModel-class | Class "diveModel" for representing a model for identifying dive phases
diveMove | Dive Analysis and Calibration
dives | Sample of TDR data from a fur seal
diveStats | Per-dive statistics
divesTDR | Sample of TDR data from a fur seal
divesTDRzoc | Sample of TDR data from a fur seal

## -- E --

extractDive | Extract Dives from "TDR" or "TDRcalibrate" Objects
extractDive-method | Extract Dives from "TDR" or "TDRcalibrate" Objects

## -- F --

fitMLEbouts | Maximum Likelihood Model of mixtures of 2 or 3 Poisson Processes
fitMLEbouts-method | Maximum Likelihood Model of mixtures of 2 or 3 Poisson Processes
fitNLSbouts | Fit mixture of Poisson Processes to Log Frequency data via Non-linear Least Squares regression
fitNLSbouts-method | Fit mixture of Poisson Processes to Log Frequency data via Non-linear Least Squares regression

## -- G --

getCCData | Coerce, Extractor, and Replacement methods for class "TDR" objects
getCCData-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
getDAct | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDAct-method | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDepth | Coerce, Extractor, and Replacement methods for class "TDR" objects
getDepth-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
getDiveDeriv | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDiveDeriv-method | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDiveModel | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDiveModel-method | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDPhaseLab | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDPhaseLab-method | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDtime | Coerce, Extractor, and Replacement methods for class "TDR" objects
getDtime-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
getFileName | Coerce, Extractor, and Replacement methods for class "TDR" objects
getFileName-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
getGAct | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getGAct-method | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getSpeed | Coerce, Extractor, and Replacement methods for class "TDR" objects
getSpeed-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
getSpeedCoef | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getSpeedCoef-method | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getTDR | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getTDR-method | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getTime | Coerce, Extractor, and Replacement methods for class "TDR" objects
getTime-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
grpSpeedFilter | Filter satellite locations

## -- L --

labelBouts | Label each vector element or matrix row with bout membership number
labelBouts-method | Label each vector element or matrix row with bout membership number

## -- O --

oneDiveStats | Per-dive statistics

## -- P --

plotBouts | Plot fitted Poisson mixture model and data
plotBouts-method | Plot fitted Poisson mixture model and data
plotBoutsCDF | Plot empirical and deterministic cumulative frequency distribution Poisson mixture data and model
plotBoutsCDF-method | Plot empirical and deterministic cumulative frequency distribution Poisson mixture data and model
plotDiveModel | Methods for plotting models of dive phases
plotDiveModel-method | Methods for plotting models of dive phases
plotTDR | Methods for plotting objects of class "TDR" and "TDRcalibrate"
plotTDR-method | Methods for plotting objects of class "TDR" and "TDRcalibrate"
plotZOC | Methods for visually assessing results of ZOC procedure
plotZOC-method | Methods for visually assessing results of ZOC procedure

## -- R --

readLocs | Read comma-delimited file with location data
readTDR | Read comma-delimited file with "TDR" data
rmixexp | Generate samples from a mixture of exponential distributions
rmsDistFilter | Filter satellite locations
rqPlot | Plot of quantile regression for speed calibrations

## -- S --

sealLocs | Ringed and Gray Seal ARGOS Satellite Location Data
show-method | Coerce, Extractor, and Replacement methods for class "TDR" objects
show-method | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
speed<- | Coerce, Extractor, and Replacement methods for class "TDR" objects
speed<--method | Coerce, Extractor, and Replacement methods for class "TDR" objects
stampDive | Per-dive statistics

## -- T --

TDR | Classes "TDR" and "TDRspeed" for representing TDR information
TDR-accessors | Coerce, Extractor, and Replacement methods for class "TDR" objects
TDR-class | Classes "TDR" and "TDRspeed" for representing TDR information
TDR-methods | Coerce, Extractor, and Replacement methods for class "TDR" objects
TDRcalibrate | Class "TDRcalibrate" for dive analysis
TDRcalibrate-accessors | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
TDRcalibrate-class | Class "TDRcalibrate" for dive analysis
TDRcalibrate-methods | Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
TDRspeed | Classes "TDR" and "TDRspeed" for representing TDR information
TDRspeed-class | Classes "TDR" and "TDRspeed" for representing TDR information
timeBudget | Describe the Time Budget of Major Activities from "TDRcalibrate" object.
timeBudget-method | Describe the Time Budget of Major Activities from "TDRcalibrate" object.

## -- misc --

.runquantile | Quantile of Moving Window
[-method | Coerce, Extractor, and Replacement methods for class "TDR" objects