Nothing
R/read.R
In argoFloats: Analysis of Oceanographic Argo Floats
Defines functions
readProfiles
Documented in
readProfiles
## vim:textwidth=128:expandtab:shiftwidth=4:softtabstop=4
#' Read Argo Profiles From Local Files
#'
#' This works with either a vector of NetCDF files,
#' or a [`argoFloats-class`] 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.
#'
#' 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).
#'
#' @param profiles either (1) a character vector that holds
#' the names of NetCDF files or (2) an [`argoFloats-class`]
#' 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()].
#'
#' @param FUN 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.
#'
#' @template destdir
#'
#' @template quiet
#'
#' @param debug 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.
#'
#' @return An [`argoFloats-class`] object
#' with `type="argos"`, in which the `data` slot
#' contains a list named `argos` that holds objects
#' that are created by [oce::read.argo()].
#'
#' @examples
## # Omit this, because rhub errors out, evidently because it is running donttest blocks.
## # Example 1: read 5 profiles and plot TS for the first, in raw and QC-cleaned forms.
## # This example involves downloading to a local repository, so it is not run on CRAN.
##\donttest{
## library(argoFloats)
## data(index)
## index1 <- subset(index, 1)
## profiles <- getProfiles(index1)
## raw <- readProfiles(profiles)
## clean <- applyQC(raw)
## par(mfrow=c(1, 2))
## file <- gsub(".*/", "", profiles[[1]])
## aWithNA <- clean[[1]]
## oce::plotTS(raw[[1]], eos="unesco", type="o")
## mtext(file, cex=0.7*par("cex"))
## aWithoutNA <- raw[[1]]
## oce::plotTS(clean[[1]], eos="unesco", type="o")
## mtext(paste(file, "\n (after applying QC)"), cex=0.7*par("cex"))
##}
##
#' # Read from a local file
#' f <- system.file("extdata", "SR2902204_131.nc", package="argoFloats")
#' p <- readProfiles(f)
#'
#' @references
#' 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}
#'
#' @export
#'
#' @importFrom utils setTxtProgressBar txtProgressBar
#'
#' @author Dan Kelley
readProfiles <- function(profiles, FUN, destdir=argoDefaultDestdir(), quiet=FALSE, debug=0)
{
if (!requireNamespace("oce", quietly=TRUE))
stop("must install.packages(\"oce\") for readProfiles() to work")
if (!requireNamespace("ncdf4", quietly=TRUE))
stop("must install.packages(\"ncdf4\") for readProfiles() to work")
res <- NULL
argoFloatsDebug(debug, "readProfiles() {\n", style="bold", sep="", unindent=1)
if (missing(FUN)) {
FUN <- oce::read.argo
} else {
if (!is.function(FUN))
stop("FUN must be a function, e.g. oce::read.argo")
}
## show the ncdf4 version. Frankly, this is just to prevent errors in R CMD check. The problem
## has to do with oce::read.argo() doing a require(ncdf4), which causes an error message in
## checking argoFloats.
ncversion <- ncdf4::nc_version()
argoFloatsDebug(debug, "ncdf4 version: ", ncversion, "\n")
res <- new("argoFloats", type="argos")
if (is.character(profiles)) {
argoFloatsDebug(debug, "Case 1: vector of ", length(profiles), " character valuesn", sep="")
# find subtype, and don't permit mixed subtypes
istraj <- grepl("traj", profiles)
if (any(istraj) && any(!istraj))
stop("cannot mix \"trajectories\" and \"cycle\" subtypes for case where 'profiles' is a character vector")
res@metadata$subtype <- if (istraj[1]) "trajectories" else "cycles"
# get storage for the oce::argo objects
n <- length(profiles)
res@data$argos <- vector("list", length=n)
for (i in seq_len(n)) {
if (grepl("^ftp:", profiles[i])) {
localFile <- getProfileFromUrl(profiles[i], destdir=destdir, debug=debug, quiet=quiet)
res@data$argos[[i]] <- FUN(localFile, debug=debug-1)
} else {
argoFloatsDebug(debug, "Attempting to read file '", profiles[i], "'.\n", sep="")
if (!file.exists(profiles[i]))
stop("cannot find the local file: '", profiles[i], "'")
res@data$argos[[i]] <- FUN(profiles[i], debug=debug-1)
}
}
# res@data$argos <- lapply(profiles, FUN, debug=debug-1)
n <- length(res@data$argos)
argoFloatsDebug(debug, "initializing the flag-mapping scheme in the profiles (over-rides oce defaults).\n")
for (i in seq_len(n)) {
res@data$argos[[i]]@metadata$flagScheme <- list(name="argo",
mapping=list(not_assessed=0,
passed_all_tests=1,
probably_good=2,
probably_bad=3,
bad=4,
changed=5,
not_used_6=6,
not_used_7=7,
estimated=8,
missing=9),
default=c(0, 3, 4, 6, 7, 9))
res@data$argos[[i]]@processingLog <- oce::processingLogAppend(res@data$argos[[i]]@processingLog,
"override existing flagScheme to be mapping=list(not_assessed=0, passed_all_tests=1, probably_good=2, probably_bad=3, bad=4, changed=5, not_used_6=6, not_used_7=7, estimated=8, missing=9)), default=c(0, 3, 4, 9)")
}
} else if (inherits(profiles, "argoFloats")) {
# Handle result of previous call to getProfiles(), i.e. a 'profiles' type.
type <- profiles[["type"]]
filenames <- profiles[["file"]]
istraj <- grepl("traj", filenames)
if (any(istraj) && any(!istraj))
stop("cannot mix \"trajectories\" and \"cycle\" subtypes for case where 'profiles' is an argoFloats object")
res@metadata$subtype <- if (istraj[1]) "trajectories" else "cycles"
if (type == "profiles") {
argoFloatsDebug(debug, "case 2: object created by getProfiles()\n")
mustSkip <- is.na(profiles@data$file)
if (sum(mustSkip)) {
if (sum(mustSkip) == 1) {
warning("skipping a profile with NA file name, at index ", which(mustSkip))
} else {
warning("skipping ", sum(mustSkip), " profiles with NA file names, at indices: ",
paste(which(mustSkip), collapse=" "))
}
}
if (all(mustSkip))
stop("No valid files found in the \"", destdir, "\" directory. Perhaps getProfiles() was unable to download them, or they were deleted after downloading.")
fileNames <- gsub(".*/(.*).nc", "\\1.nc", profiles@data$file[!mustSkip])
fullFileNames <- paste0(destdir, "/", fileNames)
n <- length(fullFileNames)
argoFloatsDebug(debug, "reading", length(fullFileNames), "NetCDF files ...\n")
useProgressBar <- !quiet && interactive()
if (useProgressBar)
pb <- txtProgressBar(0, n, 0, style=3)
res@data$argos <- lapply(seq_along(fullFileNames), function(i) {
if (useProgressBar)
setTxtProgressBar(pb, i)
oce::read.argo(fullFileNames[i], debug=debug-1)
})
if (useProgressBar)
close(pb)
argoFloatsDebug(debug, "initializing the flag-mapping scheme in the profiles (over-rides oce defaults).\n")
for (i in seq_len(n)) {
res@data$argos[[i]]@metadata$flagScheme <- list(name="argo",
mapping=list(not_assessed=0,
passed_all_tests=1,
probably_good=2,
probably_bad=3,
bad=4,
changed=5,
not_used_6=6,
not_used_7=7,
estimated=8,
missing=9),
default=c(0, 3, 4, 9))
res@data$argos[[i]]@processingLog <- oce::processingLogAppend(res@data$argos[[i]]@processingLog,
"override existing flagScheme to be mapping=list(not_assessed=0, passed_all_tests=1, probably_good=2, probably_bad=3, bad=4, changed=5, not_used_6=6, not_used_7=7, estimated=8, missing=9)), default=c(0, 3, 4, 9)")
}
} else {
stop("'profiles' must be a character vector or an object created by getProfiles()")
}
} else {
stop("'profiles' must be a character vector or an object created by getProfiles().")
}
## tabulate flags (ignore "Adjusted" items)
if (!quiet || debug) {
flagNamesAll <- unique(sort(unlist(lapply(res@data$argos, function(a) names(a@metadata$flags)))))
flagNames <- flagNamesAll[!grepl("Adjusted$", flagNamesAll)]
for (flagName in flagNames) {
percentBad <- sapply(res@data$argos,
function(x) {
if (flagName %in% names(x@metadata$flags)) {
nbad <- sum(x@metadata$flags[[flagName]] %in% c(0, 3, 4, 6, 7, 9))
100 * nbad / length(x@metadata$flags[[flagName]])
} else {
NA
}
})
badCases <- percentBad > 10
if (any(badCases, na.rm=TRUE)) {
warning("Of ", length(badCases), " profiles read, ",
sum(badCases, na.rm=TRUE),
if (sum(badCases, na.rm=TRUE) > 1) " have " else " has ",
">10% of ", flagName, " values with QC flag of 4, signalling bad data.",
"\n The indices of the bad profiles are as follows.",
"\n ", paste(which(badCases), collapse=" "), immediate. = TRUE)
}
}
}
argoFloatsDebug(debug, "} # readProfiles\n", style="bold", sep="", unindent=1)
res@processingLog <- oce::processingLogAppend(res@processingLog, paste(deparse(match.call()), sep="", collapse=""))
res
}
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Defines functions readProfiles
Documented in readProfiles
## vim:textwidth=128:expandtab:shiftwidth=4:softtabstop=4
#' Read Argo Profiles From Local Files
#'
#' This works with either a vector of NetCDF files,
#' or a [`argoFloats-class`] 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.
#'
#' 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).
#'
#' @param profiles either (1) a character vector that holds
#' the names of NetCDF files or (2) an [`argoFloats-class`]
#' 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()].
#'
#' @param FUN 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.
#'
#' @template destdir
#'
#' @template quiet
#'
#' @param debug 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.
#'
#' @return An [`argoFloats-class`] object
#' with `type="argos"`, in which the `data` slot
#' contains a list named `argos` that holds objects
#' that are created by [oce::read.argo()].
#'
#' @examples
## # Omit this, because rhub errors out, evidently because it is running donttest blocks.
## # Example 1: read 5 profiles and plot TS for the first, in raw and QC-cleaned forms.
## # This example involves downloading to a local repository, so it is not run on CRAN.
##\donttest{
## library(argoFloats)
## data(index)
## index1 <- subset(index, 1)
## profiles <- getProfiles(index1)
## raw <- readProfiles(profiles)
## clean <- applyQC(raw)
## par(mfrow=c(1, 2))
## file <- gsub(".*/", "", profiles[[1]])
## aWithNA <- clean[[1]]
## oce::plotTS(raw[[1]], eos="unesco", type="o")
## mtext(file, cex=0.7*par("cex"))
## aWithoutNA <- raw[[1]]
## oce::plotTS(clean[[1]], eos="unesco", type="o")
## mtext(paste(file, "\n (after applying QC)"), cex=0.7*par("cex"))
##}
##
#' # Read from a local file
#' f <- system.file("extdata", "SR2902204_131.nc", package="argoFloats")
#' p <- readProfiles(f)
#'
#' @references
#' 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}
#'
#' @export
#'
#' @importFrom utils setTxtProgressBar txtProgressBar
#'
#' @author Dan Kelley
readProfiles <- function(profiles, FUN, destdir=argoDefaultDestdir(), quiet=FALSE, debug=0)
{
if (!requireNamespace("oce", quietly=TRUE))
stop("must install.packages(\"oce\") for readProfiles() to work")
if (!requireNamespace("ncdf4", quietly=TRUE))
stop("must install.packages(\"ncdf4\") for readProfiles() to work")
res <- NULL
argoFloatsDebug(debug, "readProfiles() {\n", style="bold", sep="", unindent=1)
if (missing(FUN)) {
FUN <- oce::read.argo
} else {
if (!is.function(FUN))
stop("FUN must be a function, e.g. oce::read.argo")
}
## show the ncdf4 version. Frankly, this is just to prevent errors in R CMD check. The problem
## has to do with oce::read.argo() doing a require(ncdf4), which causes an error message in
## checking argoFloats.
ncversion <- ncdf4::nc_version()
argoFloatsDebug(debug, "ncdf4 version: ", ncversion, "\n")
res <- new("argoFloats", type="argos")
if (is.character(profiles)) {
argoFloatsDebug(debug, "Case 1: vector of ", length(profiles), " character valuesn", sep="")
# find subtype, and don't permit mixed subtypes
istraj <- grepl("traj", profiles)
if (any(istraj) && any(!istraj))
stop("cannot mix \"trajectories\" and \"cycle\" subtypes for case where 'profiles' is a character vector")
res@metadata$subtype <- if (istraj[1]) "trajectories" else "cycles"
# get storage for the oce::argo objects
n <- length(profiles)
res@data$argos <- vector("list", length=n)
for (i in seq_len(n)) {
if (grepl("^ftp:", profiles[i])) {
localFile <- getProfileFromUrl(profiles[i], destdir=destdir, debug=debug, quiet=quiet)
res@data$argos[[i]] <- FUN(localFile, debug=debug-1)
} else {
argoFloatsDebug(debug, "Attempting to read file '", profiles[i], "'.\n", sep="")
if (!file.exists(profiles[i]))
stop("cannot find the local file: '", profiles[i], "'")
res@data$argos[[i]] <- FUN(profiles[i], debug=debug-1)
}
}
# res@data$argos <- lapply(profiles, FUN, debug=debug-1)
n <- length(res@data$argos)
argoFloatsDebug(debug, "initializing the flag-mapping scheme in the profiles (over-rides oce defaults).\n")
for (i in seq_len(n)) {
res@data$argos[[i]]@metadata$flagScheme <- list(name="argo",
mapping=list(not_assessed=0,
passed_all_tests=1,
probably_good=2,
probably_bad=3,
bad=4,
changed=5,
not_used_6=6,
not_used_7=7,
estimated=8,
missing=9),
default=c(0, 3, 4, 6, 7, 9))
res@data$argos[[i]]@processingLog <- oce::processingLogAppend(res@data$argos[[i]]@processingLog,
"override existing flagScheme to be mapping=list(not_assessed=0, passed_all_tests=1, probably_good=2, probably_bad=3, bad=4, changed=5, not_used_6=6, not_used_7=7, estimated=8, missing=9)), default=c(0, 3, 4, 9)")
}
} else if (inherits(profiles, "argoFloats")) {
# Handle result of previous call to getProfiles(), i.e. a 'profiles' type.
type <- profiles[["type"]]
filenames <- profiles[["file"]]
istraj <- grepl("traj", filenames)
if (any(istraj) && any(!istraj))
stop("cannot mix \"trajectories\" and \"cycle\" subtypes for case where 'profiles' is an argoFloats object")
res@metadata$subtype <- if (istraj[1]) "trajectories" else "cycles"
if (type == "profiles") {
argoFloatsDebug(debug, "case 2: object created by getProfiles()\n")
mustSkip <- is.na(profiles@data$file)
if (sum(mustSkip)) {
if (sum(mustSkip) == 1) {
warning("skipping a profile with NA file name, at index ", which(mustSkip))
} else {
warning("skipping ", sum(mustSkip), " profiles with NA file names, at indices: ",
paste(which(mustSkip), collapse=" "))
}
}
if (all(mustSkip))
stop("No valid files found in the \"", destdir, "\" directory. Perhaps getProfiles() was unable to download them, or they were deleted after downloading.")
fileNames <- gsub(".*/(.*).nc", "\\1.nc", profiles@data$file[!mustSkip])
fullFileNames <- paste0(destdir, "/", fileNames)
n <- length(fullFileNames)
argoFloatsDebug(debug, "reading", length(fullFileNames), "NetCDF files ...\n")
useProgressBar <- !quiet && interactive()
if (useProgressBar)
pb <- txtProgressBar(0, n, 0, style=3)
res@data$argos <- lapply(seq_along(fullFileNames), function(i) {
if (useProgressBar)
setTxtProgressBar(pb, i)
oce::read.argo(fullFileNames[i], debug=debug-1)
})
if (useProgressBar)
close(pb)
argoFloatsDebug(debug, "initializing the flag-mapping scheme in the profiles (over-rides oce defaults).\n")
for (i in seq_len(n)) {
res@data$argos[[i]]@metadata$flagScheme <- list(name="argo",
mapping=list(not_assessed=0,
passed_all_tests=1,
probably_good=2,
probably_bad=3,
bad=4,
changed=5,
not_used_6=6,
not_used_7=7,
estimated=8,
missing=9),
default=c(0, 3, 4, 9))
res@data$argos[[i]]@processingLog <- oce::processingLogAppend(res@data$argos[[i]]@processingLog,
"override existing flagScheme to be mapping=list(not_assessed=0, passed_all_tests=1, probably_good=2, probably_bad=3, bad=4, changed=5, not_used_6=6, not_used_7=7, estimated=8, missing=9)), default=c(0, 3, 4, 9)")
}
} else {
stop("'profiles' must be a character vector or an object created by getProfiles()")
}
} else {
stop("'profiles' must be a character vector or an object created by getProfiles().")
}
## tabulate flags (ignore "Adjusted" items)
if (!quiet || debug) {
flagNamesAll <- unique(sort(unlist(lapply(res@data$argos, function(a) names(a@metadata$flags)))))
flagNames <- flagNamesAll[!grepl("Adjusted$", flagNamesAll)]
for (flagName in flagNames) {
percentBad <- sapply(res@data$argos,
function(x) {
if (flagName %in% names(x@metadata$flags)) {
nbad <- sum(x@metadata$flags[[flagName]] %in% c(0, 3, 4, 6, 7, 9))
100 * nbad / length(x@metadata$flags[[flagName]])
} else {
NA
}
})
badCases <- percentBad > 10
if (any(badCases, na.rm=TRUE)) {
warning("Of ", length(badCases), " profiles read, ",
sum(badCases, na.rm=TRUE),
if (sum(badCases, na.rm=TRUE) > 1) " have " else " has ",
">10% of ", flagName, " values with QC flag of 4, signalling bad data.",
"\n The indices of the bad profiles are as follows.",
"\n ", paste(which(badCases), collapse=" "), immediate. = TRUE)
}
}
}
argoFloatsDebug(debug, "} # readProfiles\n", style="bold", sep="", unindent=1)
res@processingLog <- oce::processingLogAppend(res@processingLog, paste(deparse(match.call()), sep="", collapse=""))
res
}
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