read.odf {oce} | R Documentation |
Read an ODF file, producing an oce object
read.odf(file, debug = getOption("oceDebug"))
file |
the file containing the data. |
debug |
a debugging flag, 0 for none, 1 for some debugging |
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
.
an object of class oce
. It is up to a calling function to determine what to do with this object.
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.)
ODF2oce
will be an alternative to this, once (or perhaps if) a ODF
package is released by the Canadian Department of Fisheries and Oceans.
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)