ctdFindProfiles: Find profiles within a towyow CTD record

Description

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.

Usage

ctdFindProfiles(x,
  cutoff=0.5, minLength=10, minHeight=0.1*diff(range(x[["pressure"]])),
  direction=c("descending", "ascending"), arr.ind=FALSE,
  debug=getOption("oceDebug"), ...)

Arguments

A ctd object, as read by read.ctd or created by as.ctd.

cutoff

criterion on pressure difference; see Details.

minLength

lower limit on number of points in candidate profiles.

minHeight

lower limit on height of candidate profiles.

direction

string indicating the travel direction to be selected

arr.ind

should array indices be returned, or a vector of ctd objects?

debug

a flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more.

...

extra arguments that are passed to smooth.spline.

Value

If arr.ind=TRUE, a data frame with columns start and end, the indices of the downcasts. Otherwise, a vector of ctd objects.

Details

The method works by examining the pressure record. First, this is smoothed using smooth.spline, which is provided with any extra arguments as supplied to the present function, e.g. ctdFindProfiles(..., df=10) uses a spline with 10 degrees of freedom. The spline is then first differenced with 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.

It is often necessary to pass the resultant profiles through ctdTrim, to remove artifacts such as an equilibration phase, etc.

Examples

Run this code

library(oce)
d <- read.csv("towyow.csv", header=TRUE)
towyow <- as.ctd(d$salinity, d$temperature, d$pressure)

casts <- ctdFindProfiles(towyow)
par(mfrow=c(length(casts), 3))
for (cast in casts) {
  plotProfile(cast, "salinity")
  plotProfile(cast, "temperature")
  plotTS(cast, type='o')
}