Creates a temperature-salinity plot for a CTD cast, with labeled isopycnals.
plotTS(
x,
inSitu = FALSE,
type = "p",
referencePressure = 0,
nlevels = 6,
levels,
grid = TRUE,
col.grid = "lightgray",
lty.grid = "dotted",
rho1000 = FALSE,
eos = getOption("oceEOS", default = "gsw"),
cex = par("cex"),
col = par("col"),
pch = par("pch"),
bg = "white",
pt.bg = "transparent",
col.rho = gray(0.5),
cex.rho = 3/4 * par("cex"),
rotate = TRUE,
useSmoothScatter = FALSE,
xlab,
ylab,
Slim,
Tlim,
drawFreezing = TRUE,
trimIsopycnals = TRUE,
mgp = getOption("oceMgp"),
mar = c(mgp[1] + 1.5, mgp[1] + 1.5, mgp[1], mgp[1]),
lwd = par("lwd"),
lty = par("lty"),
lwd.rho = par("lwd"),
lty.rho = par("lty"),
add = FALSE,
inset = FALSE,
debug = getOption("oceDebug"),
...
)A boolean indicating whether to use in-situ temperature or
(the default) potential temperature, calculated with reference pressure
given by referencePressure. This is ignored if eos="gsw",
because those cases the y axis is necessarily the conservative formulation
of temperature.
representation of data, "p" for points, "l" for
connecting lines, or "n" for no indication.
reference pressure, to be used in calculating
potential temperature, if inSitu is FALSE.
Number of automatically-selected isopycnal levels (ignored if
levels is supplied).
Optional vector of desired isopycnal levels.
a flag that can be set to TRUE to get a grid.
color for grid.
line type for grid.
if TRUE, label isopycnals as e.g. 1024; if FALSE, label as e.g. 24
equation of state to be used, either "unesco" or
"gsw".
character-expansion factor for symbols, as in par("cex").
color for symbols.
symbol type, as in par("pch").
optional color to be painted under plotting area, before
plotting. (This is useful for cases in which inset=TRUE.)
inside color for symbols with pch in 21:25
color for isopycnal lines and their labels.
size of the isopycnal labels.
if TRUE, labels in right-hand margin are written vertically
if TRUE, use smoothScatter() to plot the
points.
optional label for the x axis, with default "Salinity [PSU]".
optional label for the y axis, with default "Temperature [C]".
optional limits for salinity axis, otherwise inferred from visible data (i.e. the data that have finite values for both salinity and temperature).
as Slim, but for temperature.
logical indication of whether to draw a freezing-point
line. This is based on zero pressure. If eos="unesco" then
swTFreeze() is used to compute the curve, whereas if
eos="gsw" then gsw::gsw_CT_freezing() is used;
in each case, zero pressure is used.
logical value (TRUE by default) that
indicates whether to trim isopycnal curves
to the region of temperature-salinity space for which density
computations are considered to be valid in the context of the
chosen eos; see “Details”.
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.
line width of lines or symbols.
line type of lines or symbols.
line width for density curves.
line type for density curves.
a flag that controls whether to add to an existing plot. (It
makes sense to use add=TRUE in the panel argument of a
coplot(), for example.)
set to TRUE for use within plotInset(). The
effect is to prevent the present function from adjusting margins, which is
necessary because margin adjustment is the basis for the method used by
plotInset().
a flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more.
optional arguments passed to plotting functions.
A list is silently returned, containing xat and yat,
values that can be used by oce.grid() to add a grid to the plot.
The isopycnal curves (along which density is constant) are
drawn with drawIsopycnals(), which also places
labels in the margins showing density minus 1000 \(kg/m^3\).
If trimIsopycnals is TRUE (which is the default), these curves
are trimmed to the region within which the results of density calculation
in the chosen equation of state (eos) are considered to be reliable.
With eos="unesco" this region includes
Practical Salinity from 0 to 42 and Potential Temperature
from -2C to 40C, in accordance with Fofonoff and Millard
(1983, page 23).
With eos="gsw" the lower
limit of Absolute Salinity validity is taken as 0 g/kg,
in accordance with both McDougall et al. (2003 section 3)
and the TEOS-10/gsw Matlab code for the so-called "funnel" of validity.
However, an appropriate upper limit on Absolute Salinity is not as clear.
Here, the value 42 g/kg is chosen to match the "funnel" Matlab code
as of July 2020, but two other choices might have been
made. One is 50 g/kg, since gsw::gsw_SA_from_rho() returns NA values
for Absolute Salinities exceeding that value, and another is
40 g/kg, as in McDougall et al. (2003 section 3).
The Conservative Temperature range is set to run from -2C
to 33C, as in McDougall et al. (2003 section 3), even though the
"funnel" imposes no upper limit on this variable.
Fofonoff, N. P., and R. C. Millard. "Algorithms for Computation of Fundamental Properties of Seawater." UNESCO Technical Papers in Marine Research. SCOR working group on Evaluation of CTD data; UNESCO/ICES/SCOR/IAPSO Joint Panel on Oceanographic Tables and Standards, 1983. https://unesdoc.unesco.org/ark:/48223/pf0000059832.
McDougall, Trevor J., David R. Jackett, Daniel G. Wright, and Rainer Feistel.
"Accurate and Computationally Efficient Algorithms for Potential Temperature and Density of Seawater."
Journal of Atmospheric and Oceanic Technology 20, no. 5 (May 1, 2003): 730-41.
https://journals.ametsoc.org/jtech/article/20/5/730/2543/Accurate-and-Computationally-Efficient-Algorithms.
summary,ctd-method() summarizes the information, while
read.ctd() scans it from a file.
Other functions that plot oce data:
download.amsr(),
plot,adp-method,
plot,adv-method,
plot,amsr-method,
plot,argo-method,
plot,bremen-method,
plot,cm-method,
plot,coastline-method,
plot,ctd-method,
plot,gps-method,
plot,ladp-method,
plot,landsat-method,
plot,lisst-method,
plot,lobo-method,
plot,met-method,
plot,odf-method,
plot,rsk-method,
plot,satellite-method,
plot,sealevel-method,
plot,section-method,
plot,tidem-method,
plot,topo-method,
plot,windrose-method,
plot,xbt-method,
plotProfile(),
plotScan(),
tidem-class
Other things related to ctd data:
CTD_BCD2014666_008_1_DN.ODF.gz,
[[,ctd-method,
[[<-,ctd-method,
as.ctd(),
cnvName2oceName(),
ctd-class,
ctd.cnv,
ctdDecimate(),
ctdFindProfiles(),
ctdRaw,
ctdTrim(),
ctd,
d200321-001.ctd,
d201211_0011.cnv,
handleFlags,ctd-method,
initialize,ctd-method,
initializeFlagScheme,ctd-method,
oceNames2whpNames(),
oceUnits2whpUnits(),
plot,ctd-method,
plotProfile(),
plotScan(),
read.ctd.itp(),
read.ctd.odf(),
read.ctd.odv(),
read.ctd.sbe(),
read.ctd.woce.other(),
read.ctd.woce(),
read.ctd(),
setFlags,ctd-method,
subset,ctd-method,
summary,ctd-method,
woceNames2oceNames(),
woceUnit2oceUnit(),
write.ctd()
# NOT RUN {
library(oce)
data(ctd)
plotTS(ctd)
# }
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