read.ctd {oce} | R Documentation

## Read a CTD data file

### Description

Read a CTD data file, producing an object of type `ctd`.

### Usage

    read.ctd(file, type=NULL, columns=NULL, station=NULL,
      monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
    read.ctd.sbe(file, columns=NULL, station=NULL, missing.value,
      monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
    read.ctd.woce(file, columns=NULL, station=NULL, missing.value=-999,
      monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
    read.ctd.woce.other(file, columns=NULL, station=NULL, missing.value=-999,
      monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
    read.ctd.odf(file, columns=NULL, station=NULL, missing.value=-999,
      monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
    read.ctd.odv(file, columns=NULL, station=NULL, missing.value=-999,
      monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
    read.ctd.itp(file, columns=NULL, station=NULL, missing.value=-999,
      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.
`type` | if `NULL`, then the first line is studied, in order to determine the file type. If `type="SBE19"`, then a Seabird 19 (or similar) CTD format is assumed. If `type="WOCE"` then a WOCE-exchange file is assumed. If `type="ITP"` then an ice-tethered profiler file is assumed. If `type="ODF"` an ODF file is assumed. If `type="ODV"` an ascii-ODV file is assumed.
`debug` | a flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more.

`columns`

if `NULL`, then `read.ctd` tries to infer column names from the header. For SBE files only, the `column` argument can control the column selection. It is a list that names data types and the columns containing them, starting at 1. The list must include `"pressure"`, `"temperature"` and `"salinity"`, with any other values being ignored (in this version of the function). Note that SBE headers count the "name" from zero, e.g. if the header line says `# name 1 = prDM: Pressure, Digiquartz [db]` then the correct specification to get this pressure would be `columns=list(pressure=2, ...)`.

`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.)
`missing.value` | optional missing-value flag; data matching this value will be set to `NA` upon reading.
`monitor` | boolean, set to `TRUE` to provide an indication of progress. This is useful if `filename` is a wildcard.
`processingLog` | if provided, the action item to be stored in the log. (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

These functions read CTD datasets that have been stored in common formats, and could be extended to accommodate other formats if needed. The basic function is `read.ctd`, which analyzes some of the file contents, and then calls one of the following, any of which can be called directly.

- `read.ctd.sbe()` reads files files created by Seabird CTD instruments. These are recognized by a first line with first ten characters “`* Sea-Bird`.”

- `read.ctd.woce()` reads files stored in the exchange format used by the World Ocean Circulation Experiment (WOCE) (first 4 characters of the first line being “`CTD,`”), and also in a rarer format with the first 3 characters being “`CTD`” followed by a blank or the end of the line).

- `read.ctd.woce.other()` reads the format called “CTD” in the section of the archive websites named “Other formats.” These data are stored in filenames ending `.WCT`, and they do not have a great deal of metadata (e.g. longitude), so the user is forced to infer such things from a separate file. Support for this data type is limited, e.g. requiring a header of a certain length and data columns in a certain order. Improvements are unlikely to be added to the function, since this data type seems to offer no advantages over the type handled by `read.ctd.woce()`.

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

Different file types provide different meta-information. For example, the WOCE exchange format binds together the institute name and the initials of the chief scientist into a single string that `read.ctd` cannot parse, so both `object@metadata$institute` and `object@metadata$scientist` are left blank for WOCE files.

### Value

An object of `class` `"ctd"`, which is a list with elements detailed below. The most important elements are the station name and position, along with the profile data that are contained in the data frame named `data`. (Other elements in the list may be deleted in future versions of the package, if they prove to be of little use in practice, or if they prove to have been idiosyncratic features of the particular files used in early development of `oce`.)

``data``

: a list containing the profile data. The column names are discovered from the header, and may differ from file to file. For example, some CTD instruments may have a fluorometer connected, others may not. The order of the columns may vary from case to case, and so it is important to refer to them by name. The following vectors are normally present: `data$pressure`, `data$salinity`, `data$temperature`, and `data$sigmatheta`. (sigma-theta is calculated using `swSigmaTheta`.)

``metadata``

: a list containing the following items

`header`

  the header itself, normally containing several dozen lines of information.

`filename`

  name of the file passed to `read.ctd`.

`filename.orig`

  name of the original file saved by the instrument (normally a hex file).

`system.upload.time`

  system upload time.

`ship`

  name of vessel from which the CTD was deployed.

`scientist`

  name of the scientist leading the work at sea.

`institute`

  name of the institute behind the work.

`address`

  the address of the institute where the scientist works.

`cruise`

  name of cruise.

`station`

  station number or name.

`date`

  date of lowering of CTD into the water.

`startTime`

  time when instrument started recording data.

`latitude`

  latitude, in decimal degrees, positive north of equator.

`longitude`

  longitude, in decimal degrees, positive if east of Greenwich and west of dateline.

`recovery`

  date of recovery of CTD.

`waterDepth`

  the water depth at the site.

`sampleInterval`

  time interval between samples, in seconds.

``processingLog`` | : a log of processing, in the standard `oce` format.

### Issues

The functions attempt to infer a wide range of meta-information from file headers, but variations in these headers limit generality. For example, `read.ctd.sbe` handles water depths in any of the following forms, but ostensibly similar forms may not work.

    ** DEPTH = 100
    ** Water Depth:   40 m
    ** Depth (m): 3447
    ** Depth: 16
    ** Profondeur: 92

Similar issues come up for other items in CTD headers. For example, date variants can cause a problem if, say, a date is stored in American notation but the user is in another locale, where dates are represented differently; a solution is to call `Sys.setlocale("LC_TIME", "en_US")` before reading the data.

Even when `read.ctd` appears to have read the data without error, the prudent user will do some plots and summaries on a sample file. It is also a good idea to examine some inferred numerical values in comparison with the information in the data file. CTD profiles are not cheap to acquire, and publishing erroneous results is highly embarrassing. The rewards of having confidence in the data surely outweigh the cost of a half hour spent looking at the data.

### Sample files

Three sample files are provided with the package, in

- `system.file("extdata", "ctd.cnv", package="oce")`

- `system.file("extdata", "d200321-001.ctd", package="oce")`

- `system.file("extdata", "CTD_BCD2010666_01_01_DN.ODF", package="oce")`

and an examination of these in relationship with the existing code should help users to understand the present implementation, providing insights on extending it for their own data.

### Author(s)

Dan Kelley

### References

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/old-manuals/Software_Manuals/SBE_Data_Processing/SBEDataProcessing_7.20g.pdf.

The WOCE-exchange format is described at `http://woce.nodc.noaa.gov/woce_v3/wocedata_1/whp/exchange/exchange_format_desc.htm`, and a sample file is at http://woce.nodc.noaa.gov/woce_v3/wocedata_1/whp/exchange/example_ct1.csv

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 seems to be somewhat variable and some of the R code is designed mainly by examination of some particular files being used in the author's research.

The `ODV` format, used by the ODV software and some European/British data providers, is described in a file stored on the website of the British Oceanographic Data Center, `bodc.ac.uk`, in a directory named `data/codes_and_formats/odv_format`. (The URL is not provided here because it is unreliable, which causes problems with CRAN submission of the oce package.)

Information about ice-tethered profile data is provided at http://www.whoi.edu/page.do?pid=23096, which also provides a link for downloading data. Note that the present version only handles data in profiler-mode, not fixed-depth mode.

### See Also

The documentation for `ctd-class` explains the structure of `ctd` objects, and also outlines the other functions dealing with them.

### Examples

    library(oce)
    ## Not run:
    ## Labrador Sea data, file 0001919.tar.gz from website
    ## http://www.nodc.noaa.gov/cgi-bin/OAS/prd/accession/download
    d <- read.ctd.woce("*.csv")
    data(coastlineWorld)
    plot(coastlineWorld, clat=55, clon=-50, span=5000)
    longitude <- sapply(d, function(stn) stn[['longitude']])
    latitude <- sapply(d, function(stn) stn[['latitude']])
    points(longitude, latitude, col='red')

    ## End(Not run)

[Package oce version 0.9-18 Index]