ctd.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, ...)read.ctd.sbe() and read.ctd.woce(), this may be
a wildcard (e.g. "*.cnv" or "*.csv") in which case the
retuNULL, 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-exchangeNULL, 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 conNA upon reading.TRUE to provide an indication
of progress. This is useful if filename is a wildcard.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$pressure,
data$salinity, data$temperature, and
data$sigmatheta. ($\sigma_\theta$ is calculated
using swSigmaTheta.)oce format.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.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")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 byread.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.
The ODF format, used by the Canadian Department of Fisheries and Oceans, is
described at
read.ctd.odf. However, it was only a
starting point, for examination of data files revealed many variants in the
names of the data columns. If anything odd happens with ODF files (e.g. if
they cannot be plotted), the first thing to do is to reread the files with
debug=1, to see if column names were converted properly.
The ODV format, used by the ODV software and some European/British
data providers, is described at
Information about ice-tethered profile data is provided at
ctd-class explains the structure
of ctd objects, and also outlines the other functions dealing with
them.library(oce)
## 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')Run the code above in your browser using DataLab