This function provides an easy way to look up values within an argoFloats
object, without the need to know the exact structure of the data. The action
taken by [[ depends on the type element in the metadata slot of
the object (which is set by the function that created the object), on the
value of i and, in some cases, on the value of j; see “Details”.
# S4 method for argoFloats
[[(x, i, j, ...)an argoFloats object.
a character value that specifies the item to be looked up; see “Details”.
supplemental index value, used for some x types
and i values; see “Details”.
ignored.
the indicated item, or NULL if it is neither stored within the first argument nor computable from its contents.
There are several possibilities, depending on the object type, as
listed below. Note that these possibilities are checked in the
order listed here.
For all object types:
If i is "metadata" then the metadata slot of x is returned.
Otherwise, if i is "data" then the data slot of x is returned.
Otherwise, if i is "cycle" then a character vector of the cycle
numbers is returned.
Otherwise, if i is "processingLog" then the processingLog slot of
x is returned.
Otherwise, if i is "ID" then a character vector of the ID numbers
is returned.
Otherwise, the following steps are taken, depending on type.
If type is "index", i.e. if x was created with getIndex()
or with subset,argoFloats-method() acting on the result of getIndex(),
then:
If i is numeric and j is unspecified, then i is taken to
be an index that identifies the row(s) of the data frame that
was constructed by getIndex() based on the remote index file
downloaded from the Argo server. This has elements file for
the remote file name, date for the date of the entry, latitude
and longitude for the float position, etc.
If i is the name of an item in the metadata slot, then that item
is returned. The choices are:
"destdir", "destfileRda", "filename", "ftpRoot", "header",
"server", "type", and "url".
Otherwise, if i is the name of an item in the data slot, then that item
is returned. The choices are:
"date", "date_update", "file", "institution", "latitude",
"longitude", "ocean", and "profiler_type". Note that "time" and
"time_update" may be used as synonyms for "date" and "date_update".
Otherwise, if i=="index" then that item from the data slot of x is returned.
(For the possible names, see the previous item in this sub-list.)
Otherwise, if i is an integer, then the i-th row of the index item in
the data slot is returned. This is a good way to learn the
longitude and latitude of the profile, the file name on the server,
etc.
Otherwise, if i is "ID" then the return value is developed from the
index$file item within the data slot of x, in one of three cases:
If j is not supplied, the return value is a vector holding the
identifiers (character codes for numbers) for all the data files
referred to in the index.
Otherwise, if j is numeric, then the return value is a subset of
the ID codes, as indexed by j.
Otherwise, an error is reported.
If i is "length", the number of remote files pointed to by the index
is returned.
Otherwise, if type is "profiles", i.e. if x was created with getProfiles(), then:
If i is numeric and j is unspecified, then return the local file name(s)
that are identified by using i as an index.
If i is the name of an item in the metadata slot, then that item
is returned. The choices are:
"type" and "destdir".
Otherwise, if i is the name of an item in the data slot, then that item
is returned. There is only one choice: "file".
If i is "length", the number of local file names that were downloaded
by getProfiles() is returned.
Otherwise, if type is "argos", i.e. if x was created with readProfiles(), then:
If i is equal to "argos", and j is unspecified, then a list
holding the oce::argo objects stored within x is returned.
If i is equal to "argos", and j is provided, then the associated
oce::argo object is returned.
If i is numeric and j is unspecified, then return the argo objects identified
by using i as an index.
If i is the name of an item in the metadata slot, then that item
is returned. There is only choice, "type".
Otherwise, if i is the name of an item in the data slot, then that item
is returned as a named list. (At present, there is only one choice: "argos".)
Otherwise, if i is "length" then the number of oce-type argo objects in x is returned.
Otherwise, if i is a character value then it is taken to be
an item within the metadata or data slots of the argo objects
stored in x, and the returned value is a list containing that
information with one (unnamed) item per profile.
If j is provided
and equal to "byLevel", then the items from the metadata are
repeated (if necessary) and formed into matrix or vector of the same
shape as the "pressure" field; this can be convenient for computations
involving items that only occur once per profile, such as "longitude",
but it should not be used for items that are not level-specific, such
as the various "HISTORY_*" elements, which apply to a dataset, not to
a level
Otherwise, NULL is reported.
Otherwise, an error is reported.
Kelley, D. E., Harbin, J., & Richards, C. (2021). argoFloats: An R package for analyzing Argo data. Frontiers in Marine Science, (8), 636922. doi:10.3389/fmars.2021.635922
data(index)
# Full remote filename for first two item in index
paste0(index[["server"]], "/dac/", index[["cycle", 1:2]])
#> [1] "https://data-argo.ifremer.fr/dac/124"
#> [2] "https://data-argo.ifremer.fr/dac/125"
# File names and geographical locations of first 5 items in index
index5 <- subset(index, 1:5)
#> Kept 5 cycles (0.496%)
data.frame(file=gsub(".*/", "", index5[["file"]][1]),
lon=index5[["longitude"]],
lat=index5[["latitude"]])
#> file lon lat
#> 1 D1901584_124.nc -76.231 27.705
#> 2 D1901584_124.nc -76.024 27.773
#> 3 D1901584_124.nc -76.320 28.064
#> 4 D1901584_124.nc -76.520 28.101
#> 5 D1901584_124.nc -77.108 27.794