read.section {oce} | R Documentation |
Read a file that contains a series of ctd
profiles that make
up an oceanographic section.
read.section(file, directory, sectionId="", flags, ship="", scientist="", institute="", missingValue=-999, debug=getOption("oceDebug"), processingLog)
file |
a file containing a set of CTD observations. At present, only the exchange BOT format is accepted (see Details). |
directory |
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. |
ship |
name of the ship carrying out the sampling |
scientist |
name of chief scientist aboard ship |
institute |
name of chief scientist's institute |
flags |
optional list of salinity-quality flags that will be
demanded of the salinity data. If not given, an appropriate flag will be
chosen based on the data type. For example, for WOCE data, any
data with salinity flag not equal to 2 will be rejected.
|
missingValue |
numerical value used to indicate missing data |
debug |
logical. If |
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.) |
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.
An object of class section-class
.
Dan Kelley
Several repository sites provide section data. An example that is
perhaps likely to exist for years is http://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.
Sections can also be created with as.section
. The
documentation for section-class
explains the structure of
section objects, and outlines other functions dealing with them.