R: Dive Analysis and Calibration

diveMove-package {diveMove} | R Documentation

## Dive Analysis and Calibration

### Description

This package is a collection of functions for visualizing and analyzing depth and speed data from time-depth recorders TDRs. These can be used to zero-offset correct depth, calibrate speed, and divide the record into different phases, or time budget. Functions are provided for calculating summary dive statistics for the whole record, or at smaller scales within dives.

### Author(s)

Sebastian P. Luque spluque@gmail.com

### See Also

A vignette with a guide to this package is available by doing `vignette("diveMove")`. `TDR-class`, `calibrateDepth`, `calibrateSpeed`, `timeBudget`, `stampDive`.

### Examples

    ## Too long for checks
    ## read in data and create a TDR object
    zz <- system.file(file.path("data", "dives.csv"),
                      package="diveMove", mustWork=TRUE)
    (sealX <- readTDR(zz, speed=TRUE, sep=";", na.strings="", as.is=TRUE))

    if (dev.interactive(orNone=TRUE)) plotTDR(sealX)  # html plotly

    ## detect periods of activity, and calibrate depth, creating
    ## a "TDRcalibrate" object
    if (dev.interactive(orNone=TRUE)) dcalib <- calibrateDepth(sealX)
    ## Use the "offset" ZOC method to zero-offset correct depth at 3 m
    (dcalib <- calibrateDepth(sealX, zoc.method="offset", offset=3))

    if (dev.interactive(orNone=TRUE)) {
        ## plot all readings and label them with the phase of the record
        ## they belong to, excluding surface readings
        plotTDR(dcalib, surface=FALSE)
        ## plot the first 300 dives, showing dive phases and surface readings
        plotTDR(dcalib, diveNo=seq(300), surface=TRUE)
    }

    ## calibrate speed (using changes in depth > 1 m and default remaining arguments)
    (vcalib <- calibrateSpeed(dcalib, z=1))

    ## Obtain dive statistics for all dives detected
    dives <- diveStats(vcalib)
    head(dives)

    ## Attendance table
    att <- timeBudget(vcalib, FALSE) # taking trivial aquatic activities into account
    att <- timeBudget(vcalib, TRUE)  # ignoring them
    ## Identify which phase each dive belongs to
    stamps <- stampDive(vcalib)
    sumtab <- data.frame(stamps, dives)
    head(sumtab)

[Package diveMove version 1.6.0 Index]