read.cm: Read a cm File

Description

Read a current-meter data file, producing a cm object.

Usage

read.cm(
  file,
  from = 1,
  to,
  by = 1,
  tz = getOption("oceTz"),
  type = c("s4"),
  longitude = NA,
  latitude = NA,
  debug = getOption("oceDebug"),
  encoding = "latin1",
  monitor = FALSE,
  processingLog
)

Value

An cm object.

The data slot will contain all the data in the file, with names determined from the tokens in line 3 in that file, passed through make.names(), except that Vnorth is renamed v (after conversion from cm/s to m/s), Veast is renamed u (after conversion from cm/s to m/s), Cond is renamed conductivity, T.Temp is renamed temperature

and Sal is renamed salinity, and a new column named time (a POSIX time) is constructed from the information in the file header, and another named pressure is constructed from the column named Depth. At least in the single file studied in the creation of this function, there are some columns that are unnamed in line 3 of the header; these yield data items with names X, X.1, etc.

Arguments

file: a connection or a character string giving the name of the file to load.
from: index number of the first measurement to be read, or the time of that measurement, as created with as.POSIXct() (hint: use tz="UTC").
to: indication of the last measurement to read, in a format matching that of from.
by: an indication of the stride length to use while walking through the file. If this is an integer, then by-1 measurements are skipped between each pair of profiles that is read. This may not make much sense, if the data are not equi-spaced in time. If by is a string representing a time interval, in colon-separated format, then this interval is divided by the sampling interval, to get the stride length. BUG: if the data are not equi-spaced, then odd results will occur.
tz: character string indicating time zone to be assumed in the data.
type: character string indicating type of file (ignored at present).
longitude: optional signed number indicating the longitude in degrees East.
latitude: optional signed number indicating the latitude in degrees North.
debug: a flag that turns on debugging. The value indicates the depth within the call stack to which debugging applies.
encoding: a character value that indicates the encoding to be used for this data file, if it is textual. The default value for most functions is "latin1", which seems to be suitable for files containing text written in English and French.
monitor: ignored.
processingLog: if provided, the action item to be stored in the log. This parameter is typically only provided for internal calls; the default that it provides is better for normal calls by a user.

Historical note

Prior to late July, 2016, the direction of current flow was stored in the return value, but it is no longer stored, since it can be derived from the u and v values.

Changes

On 2023-02-09 an item named north was added to the metadata slot. This is initialized to "magnetic" by read.cm(), but this is really just a guess, and users ought to consider using applyMagneticDeclination() to take magnetic declination into account.

Sample of Usage


library(oce)
cm <- read.oce("cm_interocean_0811786.s4a.tab")
summary(cm)
plot(cm)

Author

Dan Kelley

Details

There function has been tested on only a single file, and the data-scanning algorithm was based on visual inspection of that file. Whether it will work generally is an open question. It should be noted that the sample file had several odd characteristics, some of which are listed below.

file contained two columns named "Cond", which was guessed to stand for conductivity. Since only the first contained data, the second was ignored, but this may not be the case for all files.
The unit for "Cond" was stated in the file to be "mS", which makes no sense, so the unit was assumed to be mS/cm.
The file contained a column named "T-Temp", which is not something the author has seen in his career. It was assumed to stand for in-situ temperature.
The file contained a column named "Depth", which is not something an instrument can measure. Presumably it was calculated from pressure (with what atmospheric offset, though?) and so pressure was inferred from it using swPressure().
The file contained several columns that lacked names. These were ignored.
The file contained several columns that seem to be derived from the actual measured data, such as "Speed", "Dir", "N-S Dist", etc. These are ignored.
The file contained several columns that were basically a mystery to the author, e.g. "Hx", "Hy", "Vref", etc. These were ignored.

Based on such considerations, read.cm() reads only the columns that were reasonably well-understood based on the sample file. Users who need more columns should contact the author. And a user who could produce a document explaining the data format would be especially appreciated!