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.
cmap4r R package makes it easy for users to download, visualize, and process data from the CMAP database.
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
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
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
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
For a complete list and many more examples of data retrieval and visualization, please see the tutorial here: https://simonscmap.github.io/cmap4r/.