read.odf {oce} | R Documentation |
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.
read.odf(file, columns = NULL, debug = getOption("oceDebug"))
file |
the file containing the data. |
columns |
An optional |
debug |
an integer specifying whether debugging information is
to be printed during the processing. This is a general parameter that
is used by many |
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 set to sounding
if that is finite,
or to maxDepth
otherwise.
The function ODFNames2oceNames
is used to translate
data names from the ODF file to standard oce
names, and
handles conversion for a few non-standard units. The documentation
of ODFNames2oceNames
should be consulted for more
details.
An object of class oce
. It is up to a calling function to determine what to do with this object.
ODF files do not store information on the temperature or salinity scale, and read.odf
assumes them to be ITS-90 and PSS-78, respectively. These scales will not be correct for old
data files. Note that the temperature scale can be converted from old scales
using T90fromT68
and T90fromT48
, although the change will be in
a fraction of a millidegree, which probably exceeds reasonable confidence in old data.
Anthony W. Isenor and David Kellow, 2011. ODF Format Specification Version 2.0. (This is 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.
Other things related to odf
data: ODF2oce
,
ODFNames2oceNames
,
[[,odf-method
,
[[<-,odf-method
, odf-class
,
plot,odf-method
,
read.ctd.odf
,
subset,odf-method
,
summary,odf-method
library(oce) # Read a CTD cast made on the Scotian Shelf. Note that the file's metadata # states that conductivity is in S/m, but it is really conductivity ratio, # so we must alter the unit before converting to a CTD object. Note that # read.odf() on this data file produces a warning suggesting that the user # repair the unit, using the method outlined here. odf <- read.odf(system.file("extdata", "CTD_BCD2014666_008_1_DN.ODF", package="oce")) odf[["conductivityUnit"]] <- list(unit=expression(), scale="") # # Figure 1. make a CTD, and plot (with span to show NS) plot(as.ctd(odf), span=500) # Figure 2. highlight bad data on TS diagram plotTS(odf, type='o') # use a line to show loops bad <- odf[["QCFlag"]]!=0 points(odf[['salinity']][bad],odf[['temperature']][bad],col='red',pch=20)