R: Read a CTD file in ODF format

read.ctd.odf {oce} | R Documentation

## Read a CTD file in ODF format

### Description

Read a CTD file in ODF format

### Usage

    read.ctd.odf(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

`read.ctd.odf` reads files stored in Ocean Data Format, used in some Canadian hydrographic databases.

### 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

The ODF format, used by the Canadian Department of Fisheries and Oceans, is described to some extent in the documentation for `read.odf`. It is not clear that ODF format is handled correctly in `read.ctd.odf`, or the more general function `read.odf`, because the format varies between some sample files the author has encountered in his research.

### 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.sbe`, `read.ctd.woce.other`, `read.ctd.woce`, `read.ctd`, `subset,ctd-method`, `summary,ctd-method`, `woceNames2oceNames`, `write.ctd`

[Package oce version 0.9-20 Index]