argoFloats package makes it easy identify, download,cache, and analyze oceanographic data collected by Argo profiling floats, while handling quality control. Our goal in making this package was to eliminate the gap between the freely available Argo data and the end user.
argoFloats package provides tools for downloading and processing Argo profile data. It allows users to focus on core, biogeochemical (“BGC”) , or deep Argo profiles, and also allows the user to sift these profiles based on ID, time, geography, variable, institution, ocean, cycle, direction, profile, dataStateIndicator, etc. Once downloaded, such data sets can be analyzed within
argoFloats or using other R tools and packages.
As an adjunct to the written documentation, the following videos are provided, to introduce concepts and show how to accomplish some every-day tasks. In some cases, sample code is also made available at https://github.com/ArgoCanada/argoFloats/tree/develop/videos.
|argoFloats R 01: Introduction||Dan Kelley & Jaimie Harbin||Apr 9, 2020||
|argoFloats R 02: TS plot near Bermuda||Jaimie Harbin & Dan Kelley||Apr 24, 2020||
|argoFloats R 03: New website||Jaimie Harbin & Dan Kelley||Apr 30, 2020||
|argoFloats R 04: Subset by ocean or polygon||Jaimie Harbin & Dan Kelley||May 7, 2020||
|argoFloats R 05: TS diagram, colour-coded by oxygen||Jaimie Harbin & Dan Kelley||May 14, 2020||
|argoFloats R 06: Trajectory plot, colour coded by time||Jaimie Harbin & Dan Kelley||May 28, 2020||
|argoFloats R 07: Maps with bathymetry||Jaimie Harbin & Dan Kelley||Jun 4, 2020||
|argoFloats R 08: Introduction to quality control flags||Jaimie Harbin & Dan Kelley||Aug 12, 2020||
|argoFloats R 09: Advanced Quality Control||Dan Kelley & Jaimie Harbin||Aug 27, 2020||
|argoFloats R 10: Using adjusted data streams||Dan Kelley & Jaimie Harbin||Sep 3, 2020||
|argoFloats R 11: mapApp()||Dan Kelley & Jaimie Harbin||Sep 21, 2020||
|argoFloats R 12: dataStateIndicator()||Dan Kelley & Jaimie Harbin||Nov 13, 2020||
Since argoFloats is in an active phase of development, it is not yet available on CRAN. Still, it is easily installed in R with
library(devtools) install_github("ArgoCanada/argoFloats", ref="develop")
` where, of course, the devtools package must be installed first, if it is not already present on the user’s system.
Figure 1 illustrates the typical workflow with the package, with descriptions of the steps on the left, and names of the relevant functions on the right.
As shown above, the central functions for the
argoFloats package are
Some built-in data sets are provided for concreteness of illustration and for testing, but actual work always starts with a call to
getIndex() to download a full index of float data, which we will demonstrate later in this vignette.
To begin to get familiar with how the
argoFloats package works, we will begin looking at the built in data sets. Built into the
argoFloats package is the
indexDeep indices, referring to core Argo, BGC-Argo, a combination, and deep Argo respectively. It should be noted that as of September 21, 2020,
indexMerged no longer exists as the switch to
indexSynthetic has been made. For the sake of this vignette we will focus on the
index data set.
The first step is to access the required packages that will be needed during this tutorial, with
library(oce) library(ocedata) library(argoFloats)
To access the embedded index within
argoFloats, the following code is used:
It is now possible to process the downloaded index using the
argoFloats specialized versions of R “generic” functions,
show() as shown below.
The following subsections use built-in data.
plot() command within the
argoFloats package provides simple ways to plot aspects of
argoFloats-class objects. To produce the built in plot and visualize the coordinates of a section of Argo floats off of the Bahamas, the following code is used:
plot(index, bathymetry=FALSE) # also, try using bathymetry=TRUE
[[ command provides a way to extract items from
argoFloats objects, without getting lost in the details of storage. For example, if the user wanted to extract the
file within the
index data set, instead of doing
index@data$index$file, instead they can simply do
index[["file"]]. (Note that
[[<- is not specialized, since the user is highly discouraged from altering values within
summary() command displays key features of
argoFloats-class objects such as the type, server, file, URL etc. See
summary,argoFloats-method() further details.
show() command provides a one-line sketch of
argoFloats-class objects. This gets used by the
print() function. For example if the user types in:
The following output occurs:
argoFloats object of type "index" with 953 items
Hint: This command can be particularly useful when doing the
merge() command, which will be explained in greater detail further down.
It should be noted that the profile elements within
argoFloats objects are stored as in the form of
argo objects as defined by the
oce package. This means that
argoFloats users can rely on a wide variety of
oce functions to analyze their data. The full suite of R tools is also available, and the vastness of that suite explains why
argoFloats is written in R.
Until this point, we have demonstrated how the user can become familiar with embedded indices. As previously described, however, actual work always starts with downloading a full index of float data. As shown by Figure 1, the
getIndex() command is used to get an index of available Argo float profiles, either by downloading information from a data repository or by reusing an index (stored as an .rda file) that was prepared by a recent call to the function.
getIndex() command works by specifying the server, with first trying the Ifremer server and then the USGODAE server if that does not work. The next step is to specify the file name. The table below can be obtained using
?getIndex(). As shown, the user has the ability to write the specific file name from the server, or to simply use the embedded nicknames within the package:
"synthetic". The following table summarizes the contents of the various files indicated by the
||Biogeochemical data (without S or T)|
||-||Biogeochemical trajectory files|
||Synthetic data, successor to
destdir argument has a default of
~/data/argo, where it should be noted that
~ is a short cut for
?getIndex() for further description about the additional arguments for this command.
To get the index from the Ifremer server, the following code is used:
As shown by Figure 1, the next step when working with the
argoFloats package is to use the
subset() function to focus on a subset of profiles. The
argoFloats package provides tools to sift through profiles based on ID, time, geography, variable, institution, ocean, dataMode, cycle, direction, profile, dataStateIndicator, section, etc.
For geographic subsetting, the user has the ability to subset by
To subset for specific groups of Argo profiling floats off the coast of Bahamas, the following code is used:
# Subsetting by circle <- subset(ai, circle=list(longitude=-77.5, latitude=27.5, radius=50)) aiCircle # Subsetting by polygon <- c(-76.5, -76.0, -75.5) lonPoly <- c(25.5, 26.5, 25.5) latPoly <- subset(ai, polygon=list(longitude=lonPoly, latitude=latPoly)) aiPoly # Plotting the subsets together <- merge(aiCircle, aiPoly) CP plot(CP, bathymetry=FALSE) # also, try using bathymetry=TRUE
Exercise 1: Use the subset by rectangle function to add a rectangle subset onto Figure 3 and subset all of the data to only include samples between 2012 and 2020.
As of March, 2021, a subset by
section was developed to create a section of Argo data, similarly to what is done with CTD data. A subset by
section combined with subset by
time can provide insightful information of Argo vs CTD sampling efforts. An example of this is highlighted below, which compares a section of Argo data from the Mediterranean outflow region across to North America to the line A03 CTD section data collected in 1993-09-11.
Exercise 2: Use the information from Figure 4 to compare Argo and CTD section sampling methods.
library(oce) library(argoFloats) <- par(no.readonly=TRUE) oldpar par(mfrow=c(2,1)) data(section, package="oce") #getIndex() <- getIndex() ai #subset by section <- c(-70, -64,-10) lonlim <-c(40,35,35) latlim <- subset(ai, section=list(longitude=lonlim, latitude=latlim, width=100)) index1 #subset by time <- as.POSIXct("2020-09-23", tz="UTC") from <- as.POSIXct("2020-10-25", tz="UTC") to <- subset(index1, time=list(from=from, to=to)) index2 plot(index2, bathymetry=FALSE, asp=1/cos(mean(range(unlist(index2[["latitude"]]), na.rm=TRUE))*pi/180), mgp=getOption("oceMgp") )points(lonlim, latlim, pch=21, col="black", bg="red", type="o") plot(section, which="map", col="tan") par(oldpar)
The next step within the
argoFloats package is the
getProfiles() function. 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() command works with either a list of local NetCDF files, or a
argoFloats object type
profiles, as created by
The command can be useful for analyzing individual profiles, for example:
<- subset(index, 1:2) # To subset for profiles index1 <- getProfiles(index1) profiles <- readProfiles(profiles) argos <- applyQC(argos) argosClean plot(argosClean, which="profile", type="p")
Exercise 3: Using the profile in the previous example, plot a TS diagram.
Exercise 1: Use the subset by rectangle function to add a rectangle subset onto Figure 3 and subset all of the data to only include data between 2012 and 2020.
library(argoFloats) <- getIndex() ai # Subset by circle <- subset(ai, circle=list(longitude=-77.5, latitude=27.5, radius=50)) index1 # Subset by polygon <- c(-76.5, -76.0, -75.5) lonPoly <- c(25.5, 26.5, 25.5) latPoly <- subset(ai, polygon=list(longitude=lonPoly, latitude=latPoly)) index2 # Subset by rectangle <- c(-76.5, -76) lonRect <- c(27, 28) latRect <- subset(ai, rectangle=list(longitude=lonRect, latitude=latRect)) index3 # Merge the subsets together <- merge(index1, index2) index4 <- merge(index3, index4) # Note right now can only merge 2 indices together index5 # Subset for year 2012-2020 <- subset(index5, time=list(from="2012-01-01", to="2020-01-01")) index6 # Plot data plot(index6, bathymetry=FALSE) # also, try using bathymetry=TRUE
Exercise 2: Use the information from Figure 4 to compare Argo and CTD section sampling efforts.
Figure 4 reveals that it takes almost 3 months of Argo sampling to reproduce a 1 month CTD section cruise. Additionally, it displayed that there are geographical gaps within the Argo data. On the other hand, it should be noted that by extending the latitude range, these gaps are quickly filled in. In conclusion, Argo sampling is much more cost effective, and it can allow for collection of more information (i.e. nutrients, oxygen, backscattering, etc.) if such thing is desired.
Exercise 3: Using the profile in the previous example, plot a TS diagram.
library(argoFloats) <- getIndex("synthetic") ai <- subset(ai, 1:2) # To subset for profiles sub <- getProfiles(sub) profiles <- readProfiles(profiles) argos <- applyQC(argos) argosClean plot(argosClean, which="TS")