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diveMove

diveMove is a GNU R package with tools to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. It also provides miscellaneous functions for handling location data.

Read ?diveMove for a quick overview of the major functionality. A vignette is also available by doing vignette("diveMove").

Dive analysis usually involves handling of large amounts of data, as new instruments allow for frequent sampling of variables over long periods of time. The aim of this package is to make this process more efficient for summarizing and extracting information gathered by time-depth recorders (TDRs, hereafter). The principal motivation for developing diveMove was to provide more flexibility during the various stages of analysis than is available in popular commercial software. This is achieved by making the results from intermediate calculations easily accessible, allowing the user to make his/her own summaries beyond the default choices the package provides.

Installation

Get the released version from CRAN:

install.packages("diveMove")

Or the development version from GitHub:

# install.packages("devtools")
devtools::install_github("spluque/diveMove")

Python users can access the package's functionality via scikit-diveMove.

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Install

install.packages('diveMove')

Monthly Downloads

1,687

Version

1.6.4

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Sebastian Luque

Last Published

October 13th, 2024

Functions in diveMove (1.6.4)

detDive-internal

Detect dives from depth readings
boutsCDF

Estimated cumulative frequency for two- or three-process Poisson mixture models
distSpeed

Calculate distance and speed between locations
boutsMLEll.chooser

Log likelihood function of parameters given observed data
diveModel-class

Class "diveModel" for representing a model for identifying dive phases
.detPhase

Detect phases of activity from depth readings
boutsNLSll,Bouts-method

Generalized log likelihood function taking any number of Poisson processes in a "broken-stick" model
calibrateDepth

Calibrate Depth and Generate a "TDRcalibrate" object
createTDR

Read comma-delimited file with "TDR" data
calibrateSpeed

Calibrate and build a "TDRcalibrate" object
diveStats

Per-dive statistics
diveMove-package

Dive Analysis and Calibration
dives

Sample of TDR data from a fur seal
diveMove-internal

Internal diveMove Functions
fitNLSbouts,data.frame-method

Fit mixture of Poisson Processes to Log Frequency data via Non-linear Least Squares regression
fitMLEbouts,numeric-method

Maximum Likelihood Model of mixtures of 2 or 3 Poisson Processes
extractDive,TDR,numeric,numeric-method

Extract Dives from "TDR" or "TDRcalibrate" Objects
diveMove-defunct

Defunct functions in package ‘diveMove’
diveMove-deprecated

Deprecated functions in diveMove
.runquantile

Quantile of Moving Window
plotDiveModel,diveModel,missing-method

Methods for plotting models of dive phases
rmixexp

Generate samples from a mixture of exponential distributions
readLocs

Read comma-delimited file with location data
plotTDR,POSIXt,numeric-method

Methods for plotting objects of class "TDR" and "TDRcalibrate"
plotZOC,TDR,matrix-method

Methods for visually assessing results of ZOC procedure
sealLocs

Ringed and Gray Seal ARGOS Satellite Location Data
labDive-internal

Internal Functions used for Detection of Dives
plotBoutsCDF,nls,numeric-method

Plot empirical and deterministic cumulative frequency distribution Poisson mixture data and model
plotBouts,nls,data.frame-method

Plot fitted Poisson mixture model and data
labelBouts,numeric-method

Label each vector element or matrix row with bout membership number
timeBudget,TDRcalibrate,logical-method

Describe the Time Budget of Major Activities from "TDRcalibrate" object.
rqPlot

Plot of quantile regression for speed calibrations
boutinit,data.frame-method

Fit "broken stick" model to log frequency data for identification of bouts of behaviour
calc.p

Utilities for Poisson mixture analyses
boutfreqs

Histogram of log-transformed frequencies
TDRcalibrate-accessors

Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
Bouts-class

Class "Bouts" for representing Poisson mixtures for identification of behavioural bouts
bec,nls-method

Calculate bout ending criteria from model coefficients
TDR-accessors

Coerce, Extractor, and Replacement methods for class "TDR" objects
TDRcalibrate-class

Class "TDRcalibrate" for dive analysis
TDR-class

Classes "TDR" and "TDRspeed" for representing TDR information
austFilter

Filter satellite locations