read.argo is used to read an Argo file, producing an object of type
argo. The file must be in the ARGO-style NetCDF format described at
in the Argo documentation [2,3].
read.argo(file, debug = getOption("oceDebug"), processingLog, ...)a character string giving the name of the file to load.
a flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more.
if provided, the action item to be stored in the log. (Typically only provided for internal calls; the default that it provides is better for normal calls by a user.)
additional arguments, passed to called routines.
An object of argo-class.
Argo data are made available at several websites. A bit of detective work can be required to track down the data.
Some servers provide data for floats that surfaced in a given ocean on a given day, the anonymous FTP server ftp://usgodae.org/pub/outgoing/argo/geo/ being an example.
Other servers provide data on a per-float basis. A complicating
factor is that these data tend to be categorized by "dac" (data
archiving centre), which makes it difficult to find a particular
float. For example,
https://www.usgodae.org/ftp/outgoing/argo/ is the top level of
a such a repository. If the ID of a float is known but not the
"dac", then a first step is to download the text file
http://www.usgodae.org/ftp/outgoing/argo/ar_index_global_meta.txt
and search for the ID. The first few lines of that file are header,
and after that the format is simple, with columns separated by slash
(/). The dac is in the first such column and the float ID in the
second. A simple search will reveal the dac.
For example data(argo) is based on float 6900388, and the line
containing that token is
bodc/6900388/6900388_meta.nc,846,BO,20120225005617, from
which the dac is seen to be the British Oceanographic Data Centre
(bodc). Armed with that information, visit
https://www.usgodae.org/ftp/outgoing/argo/dac/bodc/6900388
and see a directory called `profiles` that contains a NetCDF
file for each profile the float made. These can be read with
read.argo. It is also possible, and probably more common,
to read a NetCDF file containing all the profiles together and for
that purpose the file
https://www.usgodae.org/ftp/outgoing/argo/dac/bodc/6900388/6900388_prof.nc
should be downloaded and provided as the file argument to
read.argo. This can be automated as in Example 2,
although readers are cautioned that URL structures tend to change
over time.
Similar steps can be followed on other servers.
Items are inferred from the data file in a straightforward way, using
ncvar_get, converting from one-column matrices
to vectors, and trimming leading and trailing blank space in character
values, using trimString.
Items are renamed from the argo ('snake case') forms to oce ('camel
case') forms with argoNames2oceNames. For example,
FIRMWARE_VERSION in the data file is renamed as
firmwareVersion in the return value.
Note that some files use upper-case for items, while other files
use lower-case for the same things; read.argo attempts
to ignore this variation.
See the Argo documentation [2,3] for some details on what files contain.
Many items listed in section 2.2.3 of [3] are read from the
file and stored in the metadata slot, with the exception of
longitude and latitude, which are stored in the
data slot, alongside hydrographic information.
The following global attributes stored within the netcdf file are stored in the
metadata slot: title, institution, source,
history, references, userManualVersion, conventions,
and featureType. These names are identical to those in the netcdf
file, except that userManualVersion is named
user_manual_version in the file, and conventions is
named Conventions in the file.
It is assumed that the profile data are as listed in the NetCDF variable
called STATION_PARAMETERS. Each item can have variants, as
described in Sections 2.3.4 of [3].
For example, if "PRES" is found in STATION_PARAMETERS,
then PRES (pressure) data are sought in the file, along with
PRES_QC, PRES_ADJUSTED, PRES_ADJUSTED_QC, and
PRES_ERROR. The same pattern works for other profile data. The variables
are stored with different names within the resultant argo-class
object, to match with oce conventions. Thus, PRES gets renamed
pressure, while PRES_ADJUSTED gets renamed pressureAdjusted,
and PRES_ERROR gets renamed pressureError; all of these are
stored in the data slot. Meanwhile, the quality-control flags
PRES_QC and PRES_ADJUSTED_QC are stored as pressure
and pressureAdjusted in the metadata$flags slot.
Once a predefined series of items are inferred and stored in either the
metadata or data slot, read.argo then reads all
non-empty variables in the file, storing them in the metadata
slot, using with the original ('snake case') name that is used in
the data file. (Note that the sample dataset accessed with data(argo)
lacks metadata items with names starting with HISTORY_, because
those are zero-length in the source file.)
2. Argo User's Manual Version 3.2, Dec 29th, 2015, available at https://archimer.ifremer.fr/doc/00187/29825/40575.pdf (but note that this is a draft; newer versions may have replaced this by now).
3. User's Manual (ar-um-02-01) 13 July 2010, available at http://www.argodatamgt.org/content/download/4729/34634/file/argo-dm-user-manual-version-2.3.pdf, which is the main document describing argo data.
The documentation for argo-class explains the structure of argo
objects, and also outlines the other functions dealing with them.
Other things related to argo data: [[,argo-method,
[[<-,argo-method, argo-class,
argoGrid, argoNames2oceNames,
argo, as.argo,
handleFlags,argo-method,
plot,argo-method,
subset,argo-method,
summary,argo-method
# NOT RUN {
## Example 1: read from a local file
library(oce)
d <- read.argo("/data/OAR/6900388_prof.nc")
summary(d)
plot(d)
## Example 2: construct URL for download (brittle)
id <- "6900388"
url <- "https://www.usgodae.org/ftp/outgoing/argo"
if (!length(list.files(pattern="argo_index.txt")))
download.file(paste(url, "ar_index_global_meta.txt", sep="/"), "argo_index.txt")
index <- readLines("argo_index.txt")
line <- grep(id, index)
if (0 == length(line)) stop("id ", id, " not found")
if (1 < length(line)) stop("id ", id, " found multiple times")
dac <- strsplit(index[line], "/")[[1]][1]
profile <- paste(id, "_prof.nc", sep="")
float <- paste(url, "dac", dac, id, profile, sep="/")
download.file(float, profile)
argo <- read.argo(profile)
summary(argo)
# }
# NOT RUN {
# }
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