ctd.decimate {oce}R Documentation

Decimate a CTD profile

Description

Smooth and decimate a CTD profile.

Usage

ctd.decimate(x, p, method=c("approx","boxcar","lm"), e=1.5)

Arguments

x a ctd object, e.g. as read by read.ctd.
p an optional pressure increment, or list of pressures. If p is not supplied, a list of regularly-spaced pressures is computed based on the mean pressure difference between samples (converted to a round value using pretty). This list goes from 0 to the maximum pressure in the profile (rounded to the pressure increment). If a single p value is specified, then it is used as the increment. Finally, if a list of pressures is provided, then interpolation is done to these pressures.
method the method to be used for calculating decimated values. The default "approx" method is based on the R function approx and is a simple linear interpolation between neighbouring points. The "boxcar" method is based on the mean of local data , while the "lm" method is based on a local linear regression model. (The e parameter sets the locality, as explained in the next item.)
e is an expansion coefficient used to calculate the local neighbourhoods for the "boxcar" and "lm" methods. If e=1, then the neighbourhood for the i-th pressure extends from the (i-1)-th pressure to the (i+1)-th pressure. At the endpoints it is assumed that the outside bin is of the same pressure range as the first inside bin. For other values of e, the neighbourhood is expanded linearly in each direction. If the "lm" method produces warnings about "prediction from a rank-deficient fit", a larger value of "e" should be used.

Details

The "approx" method is best for bottle data, in which the usual task is to interpolate from a coarse sampling grid to a finer one. For CTD data, the "boxcar" method is probably the best choice, because the task is normally to sub-sample, and some degree of smoothing is usually desired. (The "lm" method is quite slow, and the results are similar to those of the boxcar method.)

NB. A sort of numerical cabeling effect can result from this procedure, but it can be avoided as follows

xd <- ctd.decimate(x)
xd$data$sigma.theta <- sw.sigma.theta(xd$data$salinity, xd$data$temperature, xd$data$pressure)

Value

An object of class "ctd", with pressures that are as set by the "p" parameter. In other respects, the return value is identical with the input ctd object (apart from its having an additional log entry indicating that the data have been altered.)

Author(s)

Dan Kelley

See Also

A ctd object may be read with read.ctd, and ctd.trim is useful in trimming spurious data (e.g. those obtained during the upcast).

Examples

library(oce)
data(ctd.raw) 
ctd.clean <- ctd.decimate(ctd.trim(ctd.raw))
summary(ctd.clean)

[Package oce version 0.1-76 Index]