ctd.trim {oce} | R Documentation |
Trim start/end portions of a CTD cast.
ctd.trim(x, method="downcast",parameters, verbose=FALSE)
x |
A ctd object, e.g. as read by read.ctd . |
method |
Various methods exist, some of which use parameters:
|
parameters |
A list whose elemetns depend on the method; see above. |
verbose |
If set to TRUE, some debugging information is provided, including a suggested call based on the scan number, which can serve as a good starting point for manual trimming. |
For normal CTD profiling, the goal is to isolate only the
downcast, discarding measurements made in the air, in an equilibration
phase in which the device is held below the water surface, and then
the upcast phase that follows the downcast. This is handled
reasonably well by ctd.trim
with method="downcast"
.
(The datasets provided with oce
were produced this way.)
However, for detailed work it makes sense to do things semi-manually.
The eye is simply better at handling exceptional cases. The process
is simple: use plot.ctd.scan()
to get an idea of the scan
indices of the downacast, and then use ctd.trim
with
method="index"
. A few trials will normally identify the
downcast very well.
An object of class
"ctd"
, with data having been trimmed in some way.
Dan Kelley
The Seabird CTD instrument is described at http://www.seabird.com/products/spec_sheets/19plusdata.htm.
The ctd
object may be read with read.ctd
.
plot.ctd.scan
is very useful in providing guidance
for trimming with ctd.trim
.
library(oce) data(ctd.raw) plot(ctd.raw) # barely recognizable, due to pre- and post-cast junk plot(ctd.trim(ctd.raw)) # looks like a real profile ... plot(ctd.decimate(ctd.trim(ctd.raw),method="boxcar")) # ... smoothed