R: Read a CM file

read.cm {oce} | R Documentation

## 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"),
      monitor = FALSE,
      processingLog
    )

### 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.
`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.

### 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!

### 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.

### 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.

### Author(s)

Dan Kelley

### See Also

Other things related to cm data: `[[,cm-method`, `[[<-,cm-method`, `as.cm()`, `cm-class`, `cm`, `plot,cm-method`, `rotateAboutZ()`, `subset,cm-method`, `summary,cm-method`

### Examples

    ## Not run:
      library(oce)
      cm <- read.oce("cm_interocean_0811786.s4a.tab")
      summary(cm)
      plot(cm)

    ## End(Not run)

[Package oce version 1.7-2 Index]