This works with either a vector of NetCDF files,
or a argoFloats object of type "profiles", as
created by getProfiles().
During the reading, argo profile objects are created with oce::read.argo()
or a replacement function provided as the FUN argument.
readProfiles(
profiles,
FUN,
destdir = argoDefaultDestdir(),
quiet = FALSE,
debug = 0
)either (1) a character vector that holds
the names of NetCDF files or (2) an argoFloats
object created by getProfiles(). In the first case, any
items that start with "ftp:" are taken to represent
the full paths to remote files, and these first downloaded
to the destdir directory using getProfileFromUrl().
a function that reads the NetCDF files in which the argo
profiles are stored. If FUN not provided, then it defaults
to oce::read.argo(). Only experts should consider anything
other than this default, or a wrapper to it.
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”.
logical value; use FALSE to show more
verbose information when downloading files.
(Even if quiet is TRUE, problems will still be reported.)
an integer specifying the level of debugging. If
this is zero, the work proceeds silently. If it is 1,
a small amount of debugging information is printed. Note that
debug-1 is passed to oce::read.argo(), which actually reads
the file, and so it will print messages if debug exceeds 1.
An argoFloats object
with type="argos", in which the data slot
contains a list named argos that holds objects
that are created by oce::read.argo().
By default, warnings are issued about any
profiles in which 10 percent or more of the measurements are flagged
with a quality-control code of 0, 3, 4, 6, 7, or 9 (see the
applyQC() documentation for the meanings of these codes). For more
on this function, see section 2 of 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
# Read from a local file
f <- system.file("extdata", "SR2902204_131.nc", package="argoFloats")
p <- readProfiles(f)
#> Warning: Of 1 profiles read, 1 has >10% of BBP700 values with QC flag of 4, signalling bad data.
#> The indices of the bad profiles are as follows.
#> 1
#> Warning: Of 1 profiles read, 1 has >10% of chlorophyllA values with QC flag of 4, signalling bad data.
#> The indices of the bad profiles are as follows.
#> 1
#> Warning: Of 1 profiles read, 1 has >10% of oxygen values with QC flag of 4, signalling bad data.
#> The indices of the bad profiles are as follows.
#> 1
#> Warning: Of 1 profiles read, 1 has >10% of pressure values with QC flag of 4, signalling bad data.
#> The indices of the bad profiles are as follows.
#> 1