This takes an index constructed with getIndex(), possibly
after focusing with subset,argoFloats-method(), and creates
a list of files to download from the server named in the index.
Then these files are downloaded to the destdir directory,
using filenames inferred from the source filenames. The
value returned by getProfiles() is suitable for use
by readProfiles().
getProfiles(
index,
destdir = argoDefaultDestdir(),
age = argoDefaultProfileAge(),
retries = 3,
skip = TRUE,
quiet = TRUE,
debug = 0
)an argoFloats object of type "index", as created
by getIndex().
character value indicating the directory in which to store
downloaded files. The default value is to compute this using
argoDefaultDestdir(), which returns ~/data/argo by default,
although it also provides ways to set other values using
options().
Set destdir=NULL
if destfile is a filename with full path information.
File clutter is reduced by creating a top-level directory called
data, with subdirectories for various file types; see
“Examples”.
Option 1) a numerical value indicating a time interval, in days. If the file to be downloaded from the server already exists locally, and was created is less than age days in the past, it will not be downloaded. The default is one year. Setting age=0 will force a download. Option 2) "latest" meaning the file will only be downloaded if A) the file doesn't exist or B) the file does exist and the time it was created is older than the date_update in the index file
integer telling how many times to retry a download, if the first attempt fails.
A logical value indicating whether to skip over netcdf
files that cannot be downloaded from the server. This is FALSE by
default, so that getProfiles() will raise an error if it is
impossible to re-download an outdated file. This is not
unexpected with built-in index files, e.g. data(index),
because this package cannot be updated every time the Argo
servers change the names of netcdf files. However, users
are commonly working with index files they created with
getIndex(), so they ought to be up-to-date.
logical value; use FALSE to show more
verbose information when downloading files.
(Even if quiet is TRUE, problems will still be reported.)
integer value indicating level of debugging. If this
is less than 1, no debugging is done. Otherwise, some functions
will print debugging information. If a function call fails, the
first step should be to rerun the function with debug=1,
to see if the output suggests a problem in the call.
An object of class argoFloats with type="profiles", the
data slot of which contains two items: url,
which holds the URLs from which the NetCDF
files were downloaded, and file, which
holds the path names of the downloaded files; the latter
is used by readProfiles().
It should be noted that the constructed server URL follows
a different pattern on the USGODAE an Ifremer servers, and
so if some other server is used, the URL may be wrong, leading
to an error. Similarly, if the patterns on these two
servers change, then getProfiles() will fail. Users who
encounter such problems are requested to report them
to the authors.
If a particular data file cannot be downloaded after multiple trials, then
the behaviour depends on the value of the skip argument. If that is
TRUE then a NA value is inserted in the corresponding
spot in the return value, but if it is FALSE (the default), then an error is reported.
Note that readProfiles() skips over any such NA entries,
while reporting their positions within index.
For more on this function, see Kelley et al. (2021).
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