plot.profile {oce}R Documentation

Plot a CTD profile of various quantities

Description

Plot a CTD profile, in any of several common formats.

Usage

plot.profile(x,
xtype="S", 
ytype=c("pressure", "z"),
col.S="darkgreen",
col.t="red",
col.rho="blue",
col.N2="brown",
col.dpdt="darkgreen",
col.time="darkgreen",
grid=TRUE,
col.grid="lightgray",
lty.grid="dotted",
Slim, Tlim, densitylim, N2lim, dpdtlim, timelim, ylim,
lwd,
xaxs="r", yaxs="r",
mgp=getOption("oce.mgp"),
mar=c(mgp[1]+1, mgp[1]+1, mgp[1] + 1.5, 0.5),
...)

Arguments

x A cdt object, e.g. as read by read.ctd.
xtype Type of profile to plot, from the list below.
S
Profile of salinity.
T
Profile of in-situ temperature.
density
Profile of density (expressed as sigma_theta).
index
Index of sample (very useful for working with ctd.trim).
S+T
Profile of salinity and temperature within a single axis frame.
N2
Profile of square of buoyancy frequency N^2, calculated with sw.N2 with an optional argument setting of df=length(x$p)/4 to do some smoothing.
density+N2
Profile of sigma-theta and the square of buoyancy frequency within a single axis frame.
density+dpdt
Profile of sigma-theta and dP/dt for the sensor. The latter is useful in indicating problems with the deployment. It is calculated by first differencing pressure and then using a smoothing spline on the result (to avoid grid-point wiggles that result because the SBE software only writes 3 decimal places in pressure). Note that dP/dt may be off by a scale factor; this should not be a problem if there is a x$data$time column, or a x$metadata$sample.rate value in the header.
ytype variable to use on y axis.
col.S Color for salinity profile.
col.t Color for temperature.
col.rho Color for density.
col.N2 Color for square of buoyancy frequency.
col.dpdt Color for dP/dt.
col.time Color for delta-time.
grid logical, set to TRUE to get a grid.
col.grid colour for grid.
lty.grid line type for grid.
Slim Optional limit for S axis
Tlim Optional limit for T axis
densitylim Optional limit for density axis
N2lim Optional limit for N2 axis
dpdtlim Optional limit for dp/dt axis
timelim Optional limit for delta-time axis
ylim Optional limit for y axis
lwd lwd value for data line
xaxs value of par xaxs to use
yaxs value of par yaxs to use
mgp 3-element numerical vector to use for par(mgp), and also for par(mar), computed from this. The default is tighter than the R default, in order to use more space for the data and less for the axes.
mar value to be used with par("mar").
... Optional arguments passed to other functions. A common example is to set df, for use in sw.N2 calculations.

Value

None.

Author(s)

Dan Kelley

See Also

read.ctd scans ctd information from a file, and plot.TS plots a temperature-salinity diagram.

Examples

library(oce)
data(ctd)
plot.profile(ctd, xtype="T")

[Package oce version 0.1-80 Index]