oce (version 0.9-18)

read.odf: Read an ODF file, producing an oce object

Description

Read an ODF file, producing an oce object

Usage

read.odf(file, debug = getOption("oceDebug"))

Arguments

file

the file containing the data.

debug

a debugging flag, 0 for none, 1 for some debugging

Value

• an object of class oce. It is up to a calling function to determine what to do with this object.

Details

ODF (Ocean Data Format) is a format developed at the Bedford Institute of Oceanography and also used at other Canadian Department of Fisheries and Oceans (DFO) facilities. It can hold various types of time-series data, which includes a variety of instrument types. Thus, read.odf is used by read.ctd.odf for CTD data, etc. As of mid-2015, read.odf is still in development, with features being added as a project with DFO makes available more files.

Note that some elements of the metadata are particular to ODF objects, e.g. depthMin, depthMax and sounding, which are inferred from ODF items named MIN_DEPTH, MAX_DEPTH and SOUNDING, respectively. In addition, the more common metadata item waterDepth, which is used in ctd objects to refer to the total water depth, is here identical to sounding.

References

Anthony W. Isenor and David Kellow, 2011. ODF Format Specification Version 2.0. (A .doc file downloaded from a now-forgotten URL by Dan Kelley, in June 2011.)

See Also

ODF2oce will be an alternative to this, once (or perhaps if) a ODF package is released by the Canadian Department of Fisheries and Oceans.

Examples

library(oce)
odf <- read.odf(system.file("extdata", "CTD_BCD2014666_008_1_DN.ODF", package="oce")) 
# Figure 1. make a CTD, and plot (with span to show NS)
plot(as.ctd(odf), span=500, fill='lightgray')
# show levels with bad QC flags
subset(odf, flag!=0)
# Figure 2. highlight bad data on TS diagram
plotTS(odf, type='o') # use a line to show loops
bad <- odf[["flag"]]!=0
points(odf[['salinity']][bad],odf[['temperature']][bad],col='red',pch=20)