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R package to download, visualize, and process data from the Simons CMAP (https://cmap.readthedocs.io/en/latest/) database.
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README.md

CMAP for R Users

Simons CMAP is an initiative from the CBIOMES collaboration that provides an open source database service to unify, visualize, and analyze ocean data sets from the field campaign observations, remote sensing satellite, and model outputs. The project is supported by the Simons Foundation.

The cmap4r R package makes it easy for users to download, visualize, and process data from the CMAP database.

Getting Started

CMAP hosts data on a Microsoft SQL Server. To retrieve data from the database, cmap4r requires an API key. For this, the user needs to register on the SimonsCMAP website and navigate to the "APIKeys" tab on the webpage to obtain an API key. The package allows the user to save the key as a keyring variable which will be used for data retrieval whenever required.

Installation

Currently, we host the latest version of the package on GitHub. Please follow the instructions below to install the package and some additional R packages for processing and visualizing the data.

## Install cmap4r:
devtools::install_github("simonscmap/cmap4r/cmap4r")

## Package for data processing:
install.packages("dplyr")  

## Packages for visualization:
install.packages("ggplot2")
install.packages("plotly")

Saving API Key

After installing cmap4r, use the set_authorization function to set/reset the API Key.

library(cmap4r)

# To set the API authorization key
set_authorization()

# To reset the authorization key
set_authorization(reset = TRUE)

A First Example

Suppose we are interested in how chlorophyll concentration varies with depth in a certain region of the ocean during a certain period of time. The function get_depthprofile gives us the average (and standard deviation) of a variable of interest at each depth, where the averaging is performed for each depth over a given range of longitudes, latitudes, and times. We will look at chlorophyll concentration as measured by the Argo Floats (which is the variable argo_merge_chl_adj in the table tblArgoMerge_REP).

get_depthprofile(table_name = "tblArgoMerge_REP",
                 sel_var = "argo_merge_chl_adj",
                 lat1 = 20, lat2 = 24,
                 lon1 = -170, lon2 = -150,
                 dt1 = "2016-04-30", dt2 = "2016-04-30",
                 depth1 = 0, depth2 = 1500)

This gives a tibble with the desired information.

There are many functions like get_depthprofile for retrieving data from the CMAP database, including

  • get_spacetime
  • get_section
  • get_timeseries
  • exec_manualquery

For a complete list and many more examples of data retrieval and visualization, please see the tutorial here: https://simonscmap.github.io/cmap4r/.

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