Get started with the oceanexplorer
Ocean Atlas (WOA) of the US agency NOAA contains high-resolution and
high-quality data for oceanographic variables, such as temperature,
salinity and nutrients. This package facilitates easy access and
exploration of this data, and targets three different audiences:
- Users with no programming experience by means of graphical user
interface (Shiny app).
- Users with minimal programming experience as a hybrid
graphical-programming interface that can be easily integrated in an R
workflow (RStudio addin).
- Users with an R programming background.
In this document I will explain the basic use cases of all three
application types. But first a word on the back-end of this R package.
This package heavily relies on geospatial data analysis facilitated by
sf (Pebesma 2023a) for vectors
and stars (Pebesma 2023b) for
raster data (i.e., the native NOAA data format). I highly recommend
reading the accompanying documentation of these packages if you intend
to work with the NOAA datasets:
The shiny app can be found here: https://martinschobben.shinyapps.io/oceanexplorer/. The
app allows exploration of the NOAA database and selected data can be
extracted as a csv file.
Load NOAA data
The initial screen starts at the “parameter” tab of the left-most
field which allows the selection of the oceanographic variable of
- The drop down menu “variable” selects the oceanographic variable of
- The drop down menu “averaging” selects the time period over which
the mean is calculated. The period can be “annual”, North Hemisphere
seasonal (e.g., “Spring”, three-month periods) and monthly (e.g.,
- The drop down menu “resolution” selects the grid resolution for mean
fields on a 1- or 5-degree longitude/latitude grid.
The following document lists the technical details of the variable
collection and presentation: NOAA
World Ocean Atlas 2018 Product Documentation. The papers on this
page give in-depth information on the variable of interest: https://www.ncei.noaa.gov/products/world-ocean-atlas.
Clicking the “load data” button extracts the data from the NOAA WOA
database. This operation can take some time.
Filter NOAA data
The last action also automatically drops us in the “locations” tab
(in the left most field), which allows us to select specific regions on
the now displayed world map of the variable of interest.
Locations tab (Left)
This field allows filtering of the dataset.
- The text fields: “depth”, “longitude”, and “latitude” specify the
location to extract oceanographic variables. Alternatively, one can
click on the plot (“map” tab) to obtain the values. It is possible to
extract multiple locations at once by providing a comma separated list
(e.g., 120, 130, 140) to the text field on the left (“locations” tab).
Note, that depth and coordinate vectors should be of the same length, or
one of the two should have length one. The data is extracted only when
all three text fields have been filled, and by subsequently clicking the
- Data extraction can be achieved in two modes; “point” and “fuzzy”,
where the former results in a very precise search, the latter option
searches in an area with a circumference of 50\(\,\)km around the selected coordinate
point. The returned value of a fuzzy search is therefore an average of
the search area. Currently, fuzzy search is not yet implemented.
- The button “extract” uses the information supplied in the text
fields: “depth”, “longitude”, and “latitude” to extract the
oceanographic variable. Hence, the button is only active when those
fields have been filled, and otherwise remains greyed-out. The buttons:
“reset” and “back” revert all, or the last extraction, respectively.
These two operations can be used for both data extracted by clicking on
the interactive plot and/or obtained by using the text field
Map tab (right)
This field allows changing visual aspects of the NOAA data. In
addition the plot is interactive and can be clicked (single click). It
is therefore possible to only use the right-hand side of the screen to
select your data without touching any of the buttons and menus on the
- The “projections” drop-down menu enables selection some of commonly
used projections, such as “4326”. And, two stereographic projections
“3031” and “3995” of the Antarctic and Arctic regions,
- The checkbox “fix variable scale” determines whether the variable
scale is fixed for the current depth slice or the whole dataset.
Loosening the variable scale can help highlight nuanced differences in
certain variables (e.g., phosphate).
- The “depth” slider allows filter for depth slices.