plotTDR-methods: Methods for plotting objects of class "TDR" and...
In diveMove: Dive analysis and calibration

Description Usage Arguments Details Value Methods Author(s) See Also Examples

Main plotting method for objects of these classes. Plot and optionally set zero-offset correction windows in TDR records, with the aid of a graphical user interface (GUI), allowing for dynamic selection of offset and multiple time windows to perform the adjustment.

## S4 method for signature 'POSIXt,numeric'
plotTDR(x, y, concurVars=NULL, xlim=NULL, depth.lim=NULL,
        xlab="time (dd-mmm hh:mm)", ylab.depth="depth (m)",
        concurVarTitles=deparse(substitute(concurVars)),
        xlab.format="%d-%b %H:%M", sunrise.time="06:00:00",
        sunset.time="18:00:00", night.col="gray60",
        dry.time=NULL, phase.factor=NULL, plot.points=FALSE,
        interact=TRUE, key=TRUE, cex.pts=0.4, ...)
## S4 method for signature 'TDR,missing'
plotTDR(x, y, concurVars, concurVarTitles, ...)
## S4 method for signature 'TDRcalibrate,missing'
plotTDR(x, y, what=c("phases", "dive.model"),
        diveNo=seq(max(getDAct(x, "dive.id"))), ...)

`x`	`POSIXct` object with date and time, `TDR`, or `TDRcalibrate` object.
`y`	numeric vector with depth in m.
`concurVars`	matrix with additional variables in each column to plot concurrently with depth. For the (`TDR`,`missing`) and (`TDRcalibrate`,`missing`) methods, a `character` vector naming additional variables from the `concurrentData` slot to plot, if any.
`xlim`	`POSIXct` or numeric vector of length 2, with lower and upper limits of time to be plotted.
`depth.lim`	numeric vector of length 2, with the lower and upper limits of depth to be plotted.
`xlab, ylab.depth`	character strings to label the corresponding y-axes.
`concurVarTitles`	character vector of titles to label each new variable given in `concurVars`.
`xlab.format`	character: format string for formatting the x axis; see `strptime`.
`sunrise.time, sunset.time`	character string with time of sunrise and sunset, respectively, in 24 hr format. This is used for shading night time.
`night.col`	color for shading night time.
`dry.time`	subset of time corresponding to observations considered to be dry.
`phase.factor`	factor dividing rows into sections.
`plot.points`	logical: whether to plot points.
`interact`	logical: whether to provide interactive tcltk controls and access to the associated ZOC functionality.
`key`	logical: whether to draw a key.
`cex.pts`	Passed to `points` to set the relative size of points to plot (if any).
`...`	For the `(POSIXt,numeric)` method, arguments passed to `par` for all methods; useful defaults `las=1`, `bty="n"`, and `mar` (the latter depending on whether additional concurrent data will be plotted) are provided, but they can be overridden. For other methods, except `(TDRcalibrate,missing)`, these can be any of the arguments for the `(POSIXt,numeric)` method. For `(TDRcalibrate,missing)`, these are arguments for the appropriate methods.
`diveNo`	numeric vector or scalar with dive numbers to plot.
`what`	character: what aspect of the `TDRcalibrate` to plot, which selects the method to use for plotting.

This function is used primarily to correct drifts in the pressure transducer of TDR records and noise in depth measurements via method=“visual” in calibrateDepth.

If called with the interact argument set to TRUE, returns a list (invisibly) with as many components as sections of the record that were zero-offset corrected, each consisting of two further lists with the same components as those returned by locator.

plotTDR

signature(x="TDR", y="numeric"): interactive graphical display of time-depth data, with zooming and panning capabilities.

plotTDR

signature(x="TDR", y="missing"): As method above.

plotTDR

signature(x="TDRcalibrate", y="missing"): plot selected aspects of TDRcalibrate object. Currently, two aspects have plotting methods:

phases (Optional arguments: concurVars, surface) Plots all dives, labelled by the activity phase they belong to. It produces a plot consisting of one or more panels; the first panel shows depth against time, and additional panels show other concurrent data in the object. Optional argument concurVars is a character vector indicating which additional components from the concurrentData slot to plot, if any. Optional argument surface is a logical: whether to plot surface readings.
dive.model Plots the dive model for the selected dive number (diveNo argument).

Sebastian P. Luque spluque@gmail.com, with many ideas from CRAN package sfsmisc.

calibrateDepth, .zoc

## Continuing the Example from '?calibrateDepth':
utils::example("calibrateDepth", package="diveMove",
               ask=FALSE, echo=FALSE)
## Use interact=TRUE (default) to set an offset interactively
## Plot the 'TDR' object
plotTDR(getTime(divesTDR), getDepth(divesTDR), interact=FALSE)
plotTDR(divesTDR, interact=FALSE)

## Plot different aspects of the 'TDRcalibrate' object
plotTDR(dcalib, interact=FALSE)
plotTDR(dcalib, diveNo=19:25, interact=FALSE)
plotTDR(dcalib, what="dive.model", diveNo=25)
if (dev.interactive(orNone=TRUE)) {
    ## Add surface observations and interact
    plotTDR(dcalib, surface=TRUE)
    ## Plot one dive
    plotTDR(dcalib, diveNo=200)
}