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.
read.section(
file,
directory,
sectionId = "",
flags,
ship = "",
scientist = "",
institute = "",
missingValue = -999,
encoding = "latin1",
debug = getOption("oceDebug"),
processingLog
)
A section object.
A file containing a set of CTD observations. At present, only the exchange BOT format is accepted (see “Details”).
A character string indicating the name of a directory that contains a set of CTD files that hold individual stations in the section.
Optional string indicating the name for the section. If not provided, the section ID is determined by examination of the file header.
Ignored, and deprecated (will be disallowed in a future version).
Name of the ship carrying out the sampling.
Name of chief scientist aboard ship.
Name of chief scientist's institute.
Numerical value used to indicate missing data.
a character value that indicates the encoding to be used for
this data file, if it is textual. The default value for most functions is
"latin1"
, which seems to be suitable for files containing text written in
English and French.
an integer specifying whether debugging information is
to be printed during the processing. This is a general parameter that
is used by many oce
functions. Generally, setting debug=0
turns off the printing, while higher values suggest that more information
be printed. If one function calls another, it usually reduces the value of
debug
first, so that a user can often obtain deeper debugging
by specifying higher debug
values.
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.
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
.
Dan Kelley
Several repository sites provide section data. A reasonably stable example is
https://cchdo.ucsd.edu
, but a search on "WOCE bottle data"
should
turn up other sites, if this 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()
.
Other things related to section data:
[[,section-method
,
[[<-,section-method
,
as.section()
,
handleFlags,section-method
,
initializeFlagScheme,section-method
,
plot,section-method
,
section
,
section-class
,
sectionAddStation()
,
sectionGrid()
,
sectionSmooth()
,
sectionSort()
,
subset,section-method
,
summary,section-method