This is the final release of this toolbox under the BGC-Argo-Mat name. All future development will be done under the OneArgo-R name.

This toolbox contains a variety of functions for accessing, processing, and visualizing Biogeochemical Argo data. 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.

This toolbox is created and maintained by M. Cornec (LOV, now at NOAA-PMEL), Y. Huang (NOAA-PMEL), Q. Jutard (OSU ECCE TERRA), R. Sauzede (IMEV) and C. Schmechtig (OSU ECCE TERRA), 2021 (All authors contributed equally to the code.)

This toolbox is adapted from the BGC-Argo-Mat MATLAB Toolbox: H. Frenzel*, J. Sharp*, A. Fassbender, J. Plant, T. Maurer, Y. Takeshita, D. Nicholson, A. Gray, 2021. BGC-Argo-Mat: A MATLAB toolbox for accessing and visualizing Biogeochemical Argo data. Zenodo. https://doi.org/10.5281/zenodo.4971318.

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 (https://www.xquartz.org/).
3. An Internet connection is needed to get the latest versions of index and Sprof files; but the repository includes versions of these files so that it can be run offline.
4. Memory requirements depend on the number of profiles and variables that are simultaneously loaded into memory.

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 https://support.rstudio.com/hc/en-us/articles/200711843-Working-Directories-and-Workspaces. Or run it in the directory where the main_workshop script was placed.

For an overview of how to use this toolbox, step through the 'Main_workshop' 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 (6/30/21).

initialize_argo.R : defines standard settings and paths and downloads synthetic profile index file
load_float_data.R : loads data of one or more specified float(s) into memory
select_profiles.R : returns profiles and corresponding floats based on input criteria
show_profiles.R : downloads float data and calls plot_profiles to create plot
show_time_series.R : downloads float data and calls plot_time_series 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
get_lon_lat_time.R : extracts the longitude, latitude, and time information for the specified floats)
Main_workshop.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 main_workshop (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.

Version 1 & 2: June 2021
Version 2.1: January 2022
Version 3.0: May 2022

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

This toolbox has been translated from MATLAB:
MATLAB toolbox

A similar toolbox in Python:
Python toolbox

https://www.youtube.com/watch?v=w_6pEGNXQQ4&feature=youtu.be

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

M. Cornec (LOV), Y. Huang (NOAA-PMEL), Q. Jutard (OSU ECCE TERRA), R. Sauzede (IMEV) and C. Schmechtig (OSU ECCE TERRA), 2021. BGC-Argo-R: A R toolbox for accessing and visualizing Biogeochemical Argo data. Zenodo. https://doi.org/10.5281/zenodo.5028138