R: Read a Seabird CTD File

read.ctd.sbe {oce} | R Documentation

## Read a Seabird CTD File

### Description

Read a Seabird CTD File

### Usage

    read.ctd.sbe(file, columns = NULL, station = NULL, missingValue,
      monitor = FALSE, debug = getOption("oceDebug"), processingLog, ...)

### Arguments

`file` | A connection or a character string giving the name of the file to load. For `read.ctd.sbe()` and `read.ctd.woce()`, this may be a wildcard (e.g. `"*.cnv"` or `"*.csv"`) in which case the return value is a vector containing CTD objects created by reading the files from `list.files` with `pattern` set to the specified wildcard pattern.
`columns` | An optional `list` that can be used to convert unrecognized data names to resultant variable names. This is used only by `read.ctd.sbe` and `read.ctd.odf`; see “Examples”.
`station` | Optional character string containing an identifying name or number for the station. This can be useful if the routine cannot determine the name automatically, or if another name is preferred.
`missingValue` | Optional missing-value flag; data matching this value will be set to `NA` upon reading. If this is provided, then it overrules any missing-value flag found in the data. For Seabird (`.cnv`) files, there is usually no need to set `missingValue`, because it can be inferred from the header (typically as -9.990e-29). Set `missingValue=NULL` to turn off missing-value detection, even in `.cnv` files that contain missing-value codes in their headers.
`monitor` | Boolean, set to `TRUE` to provide an indication of progress. This is useful if `filename` is a wildcard.
`debug` | An integer specifying whether debugging information is to be printed during the processing. This is a general parameter that is used by many `oce` functions. Generally, setting `debug=0` turns off the printing, while higher values suggest that more information be printed.
`processingLog` | If provided, the action item to be stored in the log. This is typically only provided for internal calls; the default that it provides is better for normal calls by a user.
`...` | additional arguments, passed to called routines.

### Details

This function reads files stored in Seabird `.cnv` format. Note that these files can contain multiple sensors for a given field. For example, the file might contain a column named `t090C` for one temperature sensor and `t190C` for a second. The first will be denoted `temperature` in the `data` slot of the return value, and the second will be denoted `temperature1`. This means that the first sensor will be used in any future processing that accesses `temperature`. This is for convenience of processing, and it does not pose a limitation, because the data from the second sensor are also available as e.g. `x[["temperature1"]]`, where `x` is the name of the returned value. For the details of the mapping from `.cnv` names to `ctd` names, see `cnvName2oceName`.

The original data names as stored in `file` are stored within the `metadata` slot as `dataNamesOriginal`, and are displayed with `summary` alongside the numerical summary. See the Appendix VI of [2] for the meanings of these names (in the "Short Name" column of the table spanning pages 161 through 172).

### Value

An object of `ctd-class`. The details of the contents depend on the source file. The `metadata` slot is particularly variable across data formats, because the meta-information provided in those formats varies widely.

### Author(s)

Dan Kelley

### References

1. The Sea-Bird SBE 19plus profiler is described at http://www.seabird.com/products/spec_sheets/19plusdata.htm. Some more information is given in the Sea-Bird data-processing manaual http://www.seabird.com/document/sbe-data-processing-manual.

2. A SBE data processing manual is at http://www.seabird.com/document/sbe-data-processing-manual.

### See Also

Other things related to `ctd` data: `[[,ctd-method`, `[[<-,ctd-method`, `as.ctd`, `cnvName2oceName`, `ctd-class`, `ctdDecimate`, `ctdFindProfiles`, `ctdRaw`, `ctdTrim`, `ctd`, `handleFlags,ctd-method`, `plot,ctd-method`, `plotProfile`, `plotScan`, `plotTS`, `read.ctd.itp`, `read.ctd.odf`, `read.ctd.woce.other`, `read.ctd.woce`, `read.ctd`, `subset,ctd-method`, `summary,ctd-method`, `woceNames2oceNames`, `write.ctd`

### Examples

    f <- system.file("extdata", "ctd.cnv", package="oce")
    ## Read the file in the normal way
    d <- read.ctd(f)
    ## Read an imaginary file, in which salinity is named 'salt'
    d <- read.ctd(f, columns=list(
      salinity=list(name="salt", unit=list(expression(), scale="PSS-78"))))

[Package oce version 0.9-20 Index]