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.

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

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]