ctdFindProfiles | R Documentation |
Examine the pressure record looking for extended periods of either ascent or descent, and return either indices to these events or a vector of CTD records containing the events.
ctdFindProfiles(
x,
cutoff = 0.5,
minLength = 10,
minHeight,
smoother = smooth.spline,
direction = c("descending", "ascending"),
breaks,
arr.ind = FALSE,
distinct,
debug = getOption("oceDebug"),
...
)
x |
a ctd object. |
cutoff |
criterion on pressure difference; see “Details”. If not provided, this defaults to 0.5. |
minLength |
lower limit on number of points in candidate profiles. If not provided, this defaults to 10. |
minHeight |
lower limit on height of candidate profiles. If not provided, this defaults to 0.1 times the pressure span. |
smoother |
The smoothing function to use for identifying down/up
casts. The default is |
direction |
String indicating the travel direction to be selected. |
breaks |
optional integer vector indicating the indices of last
datum in each profile stored within |
arr.ind |
logical value indicating whether the array indices should be returned; the alternative is to return a vector of ctd objects. |
distinct |
An optional string indicating how to identify profiles
by unique values. Use |
debug |
an integer specifying whether debugging information is
to be printed during the processing. This is a general parameter that
is used by many |
... |
Optional extra arguments that are passed to the smoothing function, |
The method works by examining the pressure record. First, this is smoothed using
smoother()
(see “Arguments”), and then the result is first-differenced
using diff()
. Median values of the positive and
negative first-difference values are then multiplied by cutoff
. This establishes criteria
for any given point to be in an ascending profile, a descending profile, or a non-profile.
Contiguous regions are then found, and those that have fewer than minLength
points are
discarded. Then, those that have pressure ranges less than minHeight
are discarded.
Caution: this method is not well-suited to all datasets. For example, the default
value of smoother
is smooth.spline()
, and this works well for just a few
profiles, but poorly for a tow-yo with a long sequence of profiles; in the latter case,
it can be preferable to use simpler smoothers (see “Examples”). Also, depending
on the sampling protocol, it is often necessary to pass the resultant profiles through
ctdTrim()
, to remove artifacts such as an equilibration phase, etc.
Generally, one is well-advised to use the present function for a quick look at the data,
relying on e.g. plotScan()
to identify profiles visually, for a final product.
If arr.ind=TRUE
, a data frame with columns start
and end
, the indices
of the downcasts. Otherwise, a vector of ctd
objects. In this second case,
the station names are set to a form like "10/3"
, for the third profile within an
original ctd object with station name "10"
, or to "3"
, if the original
ctd object had no station name defined.
Dan Kelley and Clark Richards
The documentation for ctd explains the structure of CTD objects, and also outlines the other functions dealing with them.
Other things related to ctd data:
CTD_BCD2014666_008_1_DN.ODF.gz
,
[[,ctd-method
,
[[<-,ctd-method
,
as.ctd()
,
cnvName2oceName()
,
ctd-class
,
ctd.cnv.gz
,
ctdDecimate()
,
ctdFindProfilesRBR()
,
ctdRaw
,
ctdRepair()
,
ctdTrim()
,
ctd_aml.csv.gz
,
ctd
,
d200321-001.ctd.gz
,
d201211_0011.cnv.gz
,
handleFlags,ctd-method
,
initialize,ctd-method
,
initializeFlagScheme,ctd-method
,
oceNames2whpNames()
,
oceUnits2whpUnits()
,
plot,ctd-method
,
plotProfile()
,
plotScan()
,
plotTS()
,
read.ctd.aml()
,
read.ctd.itp()
,
read.ctd.odf()
,
read.ctd.odv()
,
read.ctd.sbe()
,
read.ctd.ssda()
,
read.ctd.woce.other()
,
read.ctd.woce()
,
read.ctd()
,
setFlags,ctd-method
,
subset,ctd-method
,
summary,ctd-method
,
woceNames2oceNames()
,
woceUnit2oceUnit()
,
write.ctd()
library(oce)
## Not run:
# Example 1. Find profiles within a towyo file, as can result
# if the CTD is cycled within the water column as the ship
# moves.
profiles <- ctdFindProfiles(towyo)
## End(Not run)
## Not run:
# Example 2. Use a moving average to smooth pressure, instead of the
# default smooth.spline() method. This might avoid a tendency of
# the default scheme to miss some profiles in a long towyo.
movingAverage <- function(x, n = 11, ...)
{
f <- rep(1/n, n)
stats::filter(x, f, ...)
}
casts <- ctdFindProfiles(towyo, smoother=movingAverage)
## End(Not run)
## Not run:
# Example 3: glider data read into a ctd object. Chop
# into profiles by looking for pressure jumps exceeding
# 10 dbar.
breaks <- which(diff(gliderAsCtd[["pressure"]]) > 10)
profiles <- ctdFindProfiles(gliderAsCtd, breaks=breaks)
## End(Not run)
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