R: Methods to Show and Extract Basic Information from...

TDRcalibrate-accessors {diveMove} | R Documentation

## Methods to Show and Extract Basic Information from "TDRcalibrate" Objects

### Description

Show and extract information from `TDRcalibrate` objects.

### Usage

    ## S4 method for signature 'TDRcalibrate,missing'
    getDAct(x)
    ## S4 method for signature 'TDRcalibrate,character'
    getDAct(x, y)
    ## S4 method for signature 'TDRcalibrate,missing'
    getDPhaseLab(x)
    ## S4 method for signature 'TDRcalibrate,numeric'
    getDPhaseLab(x, diveNo)
    ## S4 method for signature 'TDRcalibrate,missing'
    getDiveModel(x)
    ## S4 method for signature 'TDRcalibrate,numeric'
    getDiveModel(x, diveNo)
    ## S4 method for signature 'diveModel'
    getDiveDeriv(x, phase=c("all", "descent", "bottom", "ascent"))
    ## S4 method for signature 'TDRcalibrate'
    getDiveDeriv(x, diveNo, phase=c("all", "descent", "bottom", "ascent"))
    ## S4 method for signature 'TDRcalibrate,missing'
    getGAct(x)
    ## S4 method for signature 'TDRcalibrate,character'
    getGAct(x, y)
    ## S4 method for signature 'TDRcalibrate'
    getSpeedCoef(x)
    ## S4 method for signature 'TDRcalibrate'
    getTDR(x)

### Arguments

`x` | `TDRcalibrate` object.
`diveNo` | numeric vector with dive numbers to extract information from.
`y` | string; “dive.id”, “dive.activity”, or “postdive.id” in the case of `getDAct`, to extract the numeric dive ID, the factor identifying activity phases (with underwater and diving levels possibly represented), or the numeric postdive ID, respectively. In the case of `getGAct` it should be one of “phase.id”, “activity”, “begin”, or “end”, to extract the numeric phase ID for each observation, a factor indicating what major activity the observation corresponds to (where diving and underwater levels are not represented), or the beginning and end times of each phase in the record, respectively.
`phase` | character vector indicating phase of the dive for which to extract the derivative.

### Value

The extractor methods return an object of the same class as elements of the slot they extracted.

### Show Methods

show

  `signature(object="TDRcalibrate")`: prints an informative summary of the data.

show

  `signature(object="diveModel")`: prints an informative summary of a dive model.

### Extractor Methods

getDAct

  `signature(x="TDRcalibrate", y="missing")`: this accesses the `dive.activity` slot of `TDRcalibrate` objects. Thus, it extracts a data frame with vectors identifying all readings to a particular dive and postdive number, and a factor identifying all readings to a particular activity.

getDAct

  `signature(x="TDRcalibrate", y="character")`: as the method for missing `y`, but selects a particular vector to extract. See `TDRcalibrate` for possible strings.

getDPhaseLab

  `signature(x="TDRcalibrate", diveNo="missing")`: extracts a factor identifying all readings to a particular dive phase. This accesses the `dive.phases` slot of `TDRcalibrate` objects, which is a factor.

getDPhaseLab

  `signature(x="TDRcalibrate", diveNo="numeric")`: as the method for missing `y`, but selects data from a particular dive number to extract.

getDiveModel

  `signature(x="TDRcalibrate", diveNo="missing")`: extracts a list with all dive phase models. This accesses the dive.models slot of `TDRcalibrate` objects.

getDiveModel

  `signature(x="TDRcalibrate", diveNo="numeric")`: as the method for missing `diveNo`, but selects data from a particular dive number to extract.

getDiveDeriv

  `signature(x="TDRcalibrate")`: extracts the derivative (list) of the dive model (smoothing spline) from the dive.models slot of `TDRcalibrate` objects for one or all phases of a dive.

getDiveDeriv

  `signature(x="diveModel")`: as the method for `TDRcalibrate`, but selects data from one or all phases of a dive.

getGAct

  `signature(x="TDRcalibrate", y="missing")`: this accesses the `gross.activity` slot of `TDRcalibrate` objects, which is a named list. It extracts elements that divide the data into major wet and dry activities.

getGAct

  `signature(x="TDRcalibrate", y="character")`: as the method for missing `y`, but extracts particular elements.

getTDR

  `signature(x="TDRcalibrate")`: this accesses the tdr slot of `TDRcalibrate` objects, which is a `TDR` object.

getSpeedCoef

  `signature(x="TDRcalibrate")`: this accesses the `speed.calib.coefs` slot of `TDRcalibrate` objects; the speed calibration coefficients.

### Author(s)

Sebastian P. Luque spluque@gmail.com

### See Also

`diveModel`, `plotDiveModel`, `plotTDR`.

### Examples

    ## Too long for checks
    ## Continuing the Example from '?calibrateDepth':
    utils::example("calibrateDepth", package="diveMove",
                   ask=FALSE, echo=FALSE, , run.donttest=TRUE)
    dcalib		# the 'TDRcalibrate' that was created

    ## Beginning times of each successive phase in record
    getGAct(dcalib, "begin")

    ## Factor of dive IDs
    dids <- getDAct(dcalib, "dive.id")
    table(dids[dids > 0])		# samples per dive

    ## Factor of dive phases for given dive
    getDPhaseLab(dcalib, 19)
    ## Full dive model
    (dm <- getDiveModel(dcalib, 19))
    str(dm)

    ## Derivatives
    getDiveDeriv(dcalib, diveNo=19)
    (derivs.desc <- getDiveDeriv(dcalib, diveNo=19, phase="descent"))
    (derivs.bott <- getDiveDeriv(dcalib, diveNo=19, phase="bottom"))
    (derivs.asc <- getDiveDeriv(dcalib, diveNo=19, phase="ascent"))
    if (require(lattice)) {
        fl <- c("descent", "bottom", "ascent")
        bwplot(~ derivs.desc$y + derivs.bott$y + derivs.asc$y,
               outer=TRUE, allow.multiple=TRUE, layout=c(1, 3),
               xlab=expression(paste("Vertical rate (", m %.% s^-1, ")")),
               strip=strip.custom(factor.levels=fl))
    }

[Package diveMove version 1.6.0 Index]