This is the first release of this toolbox under the OneArgo-R name. It is a further development of the BGC-Argo-R toolbox.

This toolbox contains a variety of functions for accessing, processing, and visualizing Argo data, including Core, Deep, and Biogeochemical Argo. Functions are designed to be maximally efficient, to provide access to the most up-to-date data available, and to allow for downloading and plotting of those data based on numerous user-defined conditions.

Please cite this toolbox as:

M. Cornec, Y. Huang, Q. Jutard, R. Sauzede, and C. Schmechtig, 2022. OneArgo-R: An R toolbox for accessing and visualizing Argo data. Zenodo. https://doi.org/10.5281/zenodo.6604650

Note: This toolbox is adapted from the OneArgo-Mat MATLAB Toolbox (H. Frenzel, J. Sharp, A. Fassbender, N. Buzby, 2022. OneArgo-Mat: A MATLAB toolbox for accessing and visualizing Argo data. Zenodo. https://doi.org/10.5281/zenodo.6588041)

1. Rstudio version 1.4 and R version 3.4 (or more recent) are needed to use these functions without modifications.
2. OSmac users need to install the "xquartz" for figure plot.
3. An Internet connection is needed to get the latest versions of index and Sprof files.
4. Memory requirements depend on the number of profiles and variables that are simultaneously loaded into memory.

The sample code in Tutorial_101 folder shows an example of selecting floats that match geographic and temporal limits and visualizing some of the data. The sample code in Tutorial_extended folder shows extended functionalities of the toolbox.

This repository can be cloned using the command line or GitHub Desktop. Or the files can be directly downloaded in zipped format.

Before use, make sure the files are placed in a directory that is in the R search path. Or add the directory where they are located to the search path. Or run it in the directory where the Tutorial script was placed.

For an overview of how to use this toolbox, step through the 'Tutorial' script (launching it in the R Console, or in the Rstudio console using the Run button or Ctrl+Alt+Enter, the Run All shortcut in R studio), a tutorial that was developed for the 2021 GO-BGC Scientific Workshop.

initialize_argo.R : defines standard settings and paths and downloads synthetic profile index file
select_profiles.R : returns profiles and corresponding floats based on input criteria
load_float_data.R : loads data of one or more specified float(s) into memory
get_lon_lat_time.R : extracts the longitude, latitude, and time information for the specified floats)
qc_filter.R : filters the data according to selected QC flags
extract_qc_df.R : filters the data according to selected QC flags and data mode, and convert into dataframe
show_profiles.R : downloads float data and calls plot_profiles to create plot
show_sections.R : downloads float data and calls plot_sections to create plot
show_trajectories.R : downloads float data and calls plot_trajectories to create plot
show_time_series.R : downloads float data and calls plot_time_series to create plot

Tutorial_101.R : tutorial script for SOCCOM Workshop (7/31/24)
Tutorial_extended.R : tutorial script for GO-BGC Scientific Workshop (6/30/21)

calc_auxil.R : calculates various auxiliary variables from Argo float data
check_dir.R : determines if a directory needs to be created and does so if necessary
combine_variables.R : combines the given variables along with all associated variables and returns them
depth_interp.R : interpolates values for BGC-Argo parameters against depth
do_download.R : determines if a file should be downloaded or not
do_pause.R : pauses execution of Tutorial (if used without desktop)
download_float.R : downloads the Sprof NetCDF file for one float
download_multi_floats.R : calls download_float to download Sprof NetCDF files for multiple floats
get_dims : determines the number of profiles, parameters,and depth levels in an Sprof netcdf file
get_lon_lat_lims.R : obtains maximum/minimum latitude and longitude values from input data
get_multi_profile_mean : calculates the mean profile of multiple profiles
get_var_name_units.R : returns the long variable name and units name for a given short parameter name input
load_library.R : load/install the required functions
plot_profiles.R : plots profiles of one or more specified float(s) for the specified variable(s)
plot_time_series.R : plots time-series of one or more specified float(s) for the specified variable(s)
plot_sections.R : plots sections of one or more specified float(s) for the specified variable(s)
plot_trajectories.R : plots trajectories of one or more specified float(s)
try_download.R : attempts to download a file from any of the specified GDACs

You can open the corresponding R script file to check out the description of input and output parameters for individual functions.

Please feel free to use the GitHub Issues and Pull Requests features to report any problems with this code and to suggest bug fixes or additional features.

Video Youtube: R Tutorial with GO-BGC data
Demo Notebook

More detailed information about quality control flags, raw and adjusted modes, etc., can be found in H. C. Bittig et al., Front. Mar. Sci., 2019, https://doi.org/10.3389/fmars.2019.00502

This toolbox has been translated from MATLAB:
MATLAB Toolbox

A similar toolbox in Python:
Python toolbox

Video tutorials for the toolbox

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