R: Read a Section File

read.section {oce} | R Documentation

## Read a Section File

### Description

Read a file that contains a series of `ctd` profiles that make up an oceanographic section. Only exchange BOT comma-separated value format is permitted at this time, but other formats may be added later. It should also be noted that the parsing scheme was developed after inspection of the A03 data set (see Examples). This may cause problems if the format is not universal. For example, the header must name the salinity column "`CTDSAL`"; if not, salinity values will not be read from the file.

### Usage

    read.section(file, directory, sectionId = "", flags, ship = "",
      scientist = "", institute = "", missingValue = -999,
      debug = getOption("oceDebug"), processingLog)

### Arguments

`file` | A file containing a set of CTD observations. At present, only the exchange BOT format is accepted (see Details).
`directory` | A character string indicating the name of a directory that contains a set of CTD files that hold individual stations in the section.
`sectionId` | Optional string indicating the name for the section. If not provided, the section ID is determined by examination of the file header.
`flags` | Ignored, and deprecated (will be disallowed in a future version).
`ship` | Name of the ship carrying out the sampling.
`scientist` | Name of chief scientist aboard ship.
`institute` | Name of chief scientist's institute.
`missingValue` | Numerical value used to indicate missing data.
`debug` | Logical. If `TRUE`, print some information that might be helpful during debugging.
`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.

### Value

An object of class `section-class`.

### Disambiguating salinity

WOCE datasets commonly have a column named `CTDSAL` for salinity inferred from a CTD and `SALNTY` (not a typo) for salinity derived from bottle data. If only one of these is present in the data file, the data will be called `salinity` in the `data` slot of the return value. However, if both are present, then `CTDSAL` is stored as `salinity` and `SALNTY` is stored as `salinityBottle`.

### Author(s)

Dan Kelley

### References

Several repository sites provide section data. An example that is perhaps likely to exist for years is https://cchdo.ucsd.edu, but a search on `"WOCE bottle data"` should turn up other sites, if this one ceases to exist. Only the so-called exchange BOT data format can be processed by read.section() at this time. Data names are inferred from column headings using `woceNames2oceNames`.

### See Also

Other things related to section data: `[[,section-method`, `[[<-,section-method`, `as.section`, `handleFlags,section-method`, `initializeFlagScheme,section-method`, `plot,section-method`, `section-class`, `sectionAddStation`, `sectionGrid`, `sectionSmooth`, `sectionSort`, `section`, `subset,section-method`, `summary,section-method`

[Package oce version 1.1-1 Index]