In UtrechtUniversity/oceanexplorer: Explore Our Planet's Oceans with NOAA

The oceanexplorer

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

# following code for loading and writing the bibtex references for the used pkgs
pkgs <- c(
  # data transformation and visualization
  "dplyr", "ggplot2", "purrr", 
  # package development
  "devtools", "shinytest", "vdiffr", "roxygen2", "testthat", 
  # documentation
  "knitr", "rmarkdown", 
  # spatial analysis
  "stars", "sf", "ncmeta",
  # shiny app
  "thematic", "bslib", "shiny", "waiter", "shinyjs"
)  
# Get the R reference
rref <- citation()
# Create ref key
rref$key <- "rversion"
hadley1 <- bibentry(
  key = "Wickham2015",
  bibtype = "Book",
  title = "R packages: organize, test, document, and share your code",
  author =  person("Hadley","Wickham"),
  year = "2015",
  publisher = " O'Reilly Media, Inc.",
  url = "https://r-pkgs.org/"
)
hadley2 <- bibentry(
  key = "Wickham2020",
  bibtype = "Book",
  title = "Mastering Shiny: Build Interactive Apps, Reports & Dashboards.",
  author =  person("Hadley","Wickham"),
  year = "2020",
  publisher = " O'Reilly Media, Inc.",
  url = "https://mastering-shiny.org/"
)
knitr::write_bib(pkgs, "vignettes/packages.bib", prefix = "")
pkgs <- bibtex::read.bib("vignettes/packages.bib")
bibtex::write.bib(
  purrr::reduce(list(rref, hadley1, hadley2, pkgs), append), 
  file = "vignettes/packages.bib"
)

The goal of oceanexplorer is to enable easy access and exploration of the World Ocean Atlas of the US agency NOAA.

{width=95%}

Check the app

Check the app here: https://martinschobben.shinyapps.io/oceanexplorer/

Funding

This project was funded by ERC Starting grant number 802835, OceaNice, awarded to Peter Bijl.

Credits

The construction of the R [@rversion] package oceanexplorer and associated documentation was aided by the packages; devtools [@devtools], roxygen2 [@roxygen2], testthat [@testthat], shinytest [@shinytest], vdiffr [@vdiffr], knitr [@knitr2014 ; @knitr2015], rmarkdown [@rmarkdown2018; @rmarkdown2020], and the superb guidance in the book: R packages: organize, test, document, and share your code, by @Wickham2015.

Data transformation, cleaning and visualization is performed with: dplyr [@dplyr], and ggplot2 [@ggplot2].

In addition, this package relies on a set of packages for spatial data analysis: sf [@sf] and stars [@stars].

The app is build with shiny [@shiny] and the guidance in the book: Mastering Shiny: Build Interactive Apps, Reports & Dashboards [@Wickham2020] was a great help in learning how to develop such applications. Furthermore, the packages shinyjs [@shinyjs], waiter [@waiter], bslib [@bslib] and thematic [@thematic] ensure user-friendliness of the interface and visually pleasing graphics.

Installation

You can install the latest version of oceanexplorer from CRAN

# Install oceanexplorer from CRAN: 
install.packages("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))

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

# plot the NOAA world ocean atlas for oxygen content
plot_NOAA(oxy_omz, depth = NULL)

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()

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 task-bar.

# launch an interactive shiny session
NOAA_addin()

Code of Conduct

Please note that the oceanexplorer project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

UtrechtUniversity/oceanexplorer documentation built on Oct. 23, 2023, 6:48 a.m.