oce (version 0.1.69)

read.section: Read a section containing multiple CTD profiles

Description

Read a file that contains a series of CTD profiles that make up an oceanographic section.

Usage

read.section(file, section.id, debug=FALSE)

Arguments

file

a file containing a set of CTD observations. At present, only the exchange BOT format is accepted (see Details).

section.id

optional string indicating the name for the section. If not provided, the section ID is determined by examination of the file header.

debug

logical. If TRUE, print some information that might be helpful during debugging.

Value

• A section object.

Details

Only exchange BOT comma-separated value format is permitted at this time, but other formats may be added later.

This function is very limited at the moment. As it evolves, the section object is likely to be modified (in a user-transparent way), and make.section will be modified as well.

Bug 1: the parsing is primitive, having been designed by inspection of the A03 data set (see Examples). For example, it is assumed that the header names the salinity column as CTDSAL, and if another name is used, no salinity will be read from the file. (Possibly this is not a problem; the author has just not checked yet on the strictness of the header format.)

Bug 2: the routine does not read measurements other than temperature (CTDTMP), salinity (CTDSAL) and pressure (CTDPRS). It should check for other items, e.g. nutrients and tracers.

Bug 3: missing-value codes are ignored.

References

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.

See Also

make.section can be used to manually bind together CTD objects into a section.

Examples

library(oce)
# http://cchdo.ucsd.edu/data_access?ExpoCode=90CT40_1
# ExpoCode 90CT40_1, Chief Scientist Tereschenkov/SOI
a03 <- read.section("a03_hy1.csv") 
summary(a03)
a03.gridded <- section.grid(a03, pressure="levitus")
plot(a03.gridded)