The oceanexplorer

The goal of oceanexplorer is to enable easy access and exploration of the WORLD OCEAN ATLAS of the US agency NOAA.

Demo of the ocean explorer

Credits

The construction of the R (R Core Team 2021) package oceanexplorer and associated documentation was aided by the packages; devtools (Wickham, Hester, et al. 2021), roxygen2 (Wickham, Danenberg, et al. 2021), testthat (Wickham 2021), knitr (Xie 2014 ; Xie 2015), rmarkdown (Xie, Allaire, and Grolemund 2018; Xie, Dervieux, and Riederer 2020), and the superb guidance in the book: R packages: organize, test, document, and share your code, by Wickham (2015).

Data transformation, cleaning and visualization is performed with: dplyr (Wickham, François, et al. 2021), tibble (Müller and Wickham 2021), stringr (Wickham 2019), magrittr (Bache and Wickham 2020), and rlang (Henry and Wickham 2021).

In addition, this package relies on a set of packages for spatial data analysis: sf (Pebesma 2021a), stars (Pebesma 2021b), and ncmeta (Sumner 2020).

The app is build with shiny (Chang et al. 2021) and the guidance in the book: Mastering Shiny: Build Interactive Apps, Reports & Dashboards (Wickham 2020). was a great help in learning how to develop such applications. Furthermore, the packages waiter (Coene 2021), bslib (Sievert and Cheng 2021) and thematic (Sievert, Schloerke, and Cheng 2021) ensure user friendliness and visually pleasing graphics.

Installation

You can install the development version of oceanexplorer from GitHub

# Install oceanexplorer from GitHub: 
# install.packages("devtools")
devtools::install_github("UtrechtUniversity/oceanexplorer")

Example

The package allows extraction of global databases of several physical and chemical parameters of the ocean from the NOAA WORLD OCEAN ATLAS.

library(oceanexplorer)
# obtain the NOAA world ocean atlas for oxygen content
oxy_global <- get_NOAA("oxygen", 1, "annual")

Slice a specific interval from the array with filter_NOAA(), like so:

# filter a depth of 200 meters to show OMZs
(oxy_omz <- filter_NOAA(oxy_global, depth = 200))
#> stars object with 2 dimensions and 1 attribute
#> attribute(s):
#>            Min.  1st Qu.   Median     Mean  3rd Qu.     Max.  NA's
#> o_an  0.9701567 164.1833 218.6721 206.2584 266.9612 359.0279 26041
#> dimension(s):
#>     from  to offset delta                       refsys point values x/y
#> lon    1 360   -180     1 +proj=longlat +a=6378137 ...    NA   NULL [x]
#> lat    1 180    -90     1 +proj=longlat +a=6378137 ...    NA   NULL [y]

In addition, the sliced array can be plotted, like so:

# plot the NOAA world ocean atlas for oxygen content
plot_NOAA(oxy_omz)

The same plot can be produced by taking the original data and supplying a value to the depth argument and specifying the range of oxygen content to oxy_omz.

# plot the NOAA world ocean atlas for oxygen content
plot_NOAA(oxy_global, depth = 200, rng = range(oxy_omz[[1]]))

Interactive exploration

Lastly, the package can launch a Shiny app for interactive exploration of the datasets.

# launch an interactive shiny session
NOAA_app()

Or, the RStudio addin can be launched within the RStudio viewer pain by executing the following code, or by using the Addins drop down menu in the taskbar.

# launch an interactive shiny session
NOAA_addin()

References

Bache, Stefan Milton, and Hadley Wickham. 2020. Magrittr: A Forward-Pipe Operator for r. https://CRAN.R-project.org/package=magrittr.

Chang, Winston, Joe Cheng, JJ Allaire, Carson Sievert, Barret Schloerke, Yihui Xie, Jeff Allen, Jonathan McPherson, Alan Dipert, and Barbara Borges. 2021. Shiny: Web Application Framework for r. https://shiny.rstudio.com/.

Coene, John. 2021. Waiter: Loading Screen for Shiny. https://CRAN.R-project.org/package=waiter.

Henry, Lionel, and Hadley Wickham. 2021. Rlang: Functions for Base Types and Core r and Tidyverse Features. https://CRAN.R-project.org/package=rlang.

Müller, Kirill, and Hadley Wickham. 2021. Tibble: Simple Data Frames. https://CRAN.R-project.org/package=tibble.

Pebesma, Edzer. 2021a. Sf: Simple Features for r. https://CRAN.R-project.org/package=sf.

———. 2021b. Stars: Spatiotemporal Arrays, Raster and Vector Data Cubes. https://CRAN.R-project.org/package=stars.

R Core Team. 2021. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.

Sievert, Carson, and Joe Cheng. 2021. Bslib: Custom Bootstrap ’Sass’ Themes for Shiny and Rmarkdown. https://CRAN.R-project.org/package=bslib.

Sievert, Carson, Barret Schloerke, and Joe Cheng. 2021. Thematic: Unified and Automatic Theming of Ggplot2, Lattice, and Base r Graphics. https://CRAN.R-project.org/package=thematic.

Sumner, Michael. 2020. Ncmeta: Straightforward NetCDF Metadata. https://github.com/hypertidy/ncmeta.

Wickham, Hadley. 2015. R Packages: Organize, Test, Document, and Share Your Code. O’Reilly Media, Inc. https://r-pkgs.org/.

———. 2019. Stringr: Simple, Consistent Wrappers for Common String Operations. https://CRAN.R-project.org/package=stringr.

———. 2020. Mastering Shiny: Build Interactive Apps, Reports & Dashboards. O’Reilly Media, Inc. https://mastering-shiny.org/.

———. 2021. Testthat: Unit Testing for r. https://CRAN.R-project.org/package=testthat.

Wickham, Hadley, Peter Danenberg, Gábor Csárdi, and Manuel Eugster. 2021. Roxygen2: In-Line Documentation for r. https://CRAN.R-project.org/package=roxygen2.

Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller. 2021. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.

Wickham, Hadley, Jim Hester, Winston Chang, and Jennifer Bryan. 2021. Devtools: Tools to Make Developing r Packages Easier. https://CRAN.R-project.org/package=devtools.

Xie, Yihui. 2014. “Knitr: A Comprehensive Tool for Reproducible Research in R.” In Implementing Reproducible Computational Research, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC. http://www.crcpress.com/product/isbn/9781466561595.

———. 2015. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. https://yihui.org/knitr/.

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.