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

Description

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

Usage

read.pt(file, from=1, to, by=1, tz=getOption("oceTz"), 
        history, debug=getOption("oceDebug"))

Arguments

file

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

from

indication of the first datum to read. This can a positive integer to indicate sequence number, the POSIX time of the first datum, or a character string that can be converted to a POSIX time. (For POSIX times, be careful about the tz

to

an indication of the last datum to be read, in the same
    format as from.  If to is missing, data will be read
    to the end of the file.

by

an indication of the stride length to use while walking
    through the file.  If this is an integer, then by-1
    profiles are skipped between each pair of profiles that is read.  If
    this is a string representing a time interval, in col

tz

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

history

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 "pt", which is a
  list with elements detailed below.
dataa data table containing the time,
    temperature, and pressure data.
metadataa list containing the following items
    [object Object],[object Object],[object Object],[object Object]
historya history of processing, in the standard oce format.

`Implementation notes`

The end time for measurement
  (metadata$measurement.start) is inferred from the Logger
  time field in the header, not from Logging end.  The datasets
  available to the author suggest this is the proper scheme when the
  recorders are turned off manually before the end time that was
  programmed in.  In other cases, the assumption may or may not be
  correct.  Still, the end time for subsampling
  (metdata$subsample.end) should be correct.

`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 pt can be plotted with
  plot.pt, and summarized with summary.pt,
  both of which are generic functions.  In-air samples (collected before
  and after deployment) may be removed in a crude way with
  ptTrim, but the best scheme is to use
  subset.oce, based on a temporal window.  Removal of the
  atmospheric component of pressure is best done by the user, using
  measured records of atmospheric pressure.  However, if such data are
  unavailable, and if the p-T data set contains pre- and post-deployment
  data, ptPatm may provide a useful estimate of
  atmospheric pressure.

`Examples`

Run this codept <- read.pt("sl08_011855.dat", by=600)
save(pt, file="oce/data/pt.rda")
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