oce (version 0.1-76)

read.tdr: Read an TDR temperature-depth recorder data file

Description

Read an TDR temperature-depth recorder file, producing an object of type tdr.

Usage

read.tdr(file, tz=getOption("oce.tz"), log.action, debug=FALSE)

Arguments

file

a connection or a character string giving the name of the file to load.

tz

time zone. The default value, oce.tz, is set to UTC at setup.

log.action

if provided, the action item to be stored in the log. (Typically only provided for internal calls; the default that it provides is better for normal calls by a user.)

debug

a flag that can be set to TRUE to turn on debugging.

Value

• An object of class "tdr", which is a list with elements detailed below.
• data
  a data table containing the (t, temperature, pressure) data.
• metadata
  a list containing the following items [object Object],[object Object],[object Object],[object Object]
• processing.log
  a processing log, in the standard oce format.

Details

Read an TDR (temperature-depth recorder) file. At the moment, three styles are understood: (1) a two-column style, containing temperature and pressure (in which case time is inferred from information in the header); (2) a four-column style, in which the date the time of day are given in the first two columns, followed by the temperature, and pressure; and (3) a five-column style, in which depth in the water column is given after the pressure.

See Also

The generic function read.oce provides an alternative to this. Objects of type tdr can be plotted with plot.tdr, and summarized with summary.tdr, both of which are generic functions. In-air samples (collected before and after deployment) may be removed in a crude way with tdr.trim, but the best scheme is to use subset.oce, based on a temporal window (see Examples). Removal of the atmospheric component of pressure is left up to the user; in many cases, it makes sense to treat this as a constant (see Examples).

Examples

library(oce)
data(tdr)
# trim automatically
tdr.trim.auto <- tdr.trim(tdr)
# trim manually
plot(tdr, which=2)
# try a few times near start of record (15:00:00 seems good)
abline(v=as.POSIXct("2008-06-25 00:00:00"),col="red")
abline(v=as.POSIXct("2008-06-26 00:00:00"),col="red")
abline(v=as.POSIXct("2008-06-25 15:00:00"),col="red")
# try a few times near end of record (15:00:00 seems ok)
abline(v=as.POSIXct("2008-07-04 00:00:00"),col="blue")
abline(v=as.POSIXct("2008-07-05 10:00:00"),col="blue")
abline(v=as.POSIXct("2008-07-04 12:00:00"),col="blue")
tdr.trim.manual <- subset(tdr, as.POSIXct("2008-06-25 15:00:00") <= t &
t <= as.POSIXct("2008-07-04 12:00:00"))
plot(tdr.trim.manual)