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https://github.com/MartinSchobben/oceanexplorer

Easy exploration of the NOAA world ocean atlas
https://github.com/MartinSchobben/oceanexplorer

earth earth-observation earth-science noaa noaa-data ocean ocean-sciences oceanography open-data r r-package rstats shiny spatial spatial-analysis spatial-data

Last synced: 20 days ago
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Easy exploration of the NOAA world ocean atlas

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README 

        
---

output: github_document

bibliography: "vignettes/packages.bib"

---



# The oceanexplorer   



```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```



```{r pkgs, echo=FALSE, message=FALSE, eval=FALSE}

# 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"

)

```



[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

[![license](https://img.shields.io/github/license/mashape/apistatus.svg)](https://choosealicense.com/licenses/mit/)

[![Codecov test coverage](https://codecov.io/gh/MartinSchobben/Oceanexplorer/branch/main/graph/badge.svg)](https://app.codecov.io/gh/MartinSchobben/Oceanexplorer?branch=main)

[![R-CMD-check](https://github.com/MartinSchobben/oceanexplorer/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/MartinSchobben/oceanexplorer/actions/workflows/R-CMD-check.yaml)



The goal of oceanexplorer is to enable easy access and exploration of the [World Ocean Atlas](https://www.nodc.noaa.gov/OC5/SELECT/woaselect/woaselect.html) of the US agency [NOAA](https://www.ncei.noaa.gov/).



![Demo of the ocean explorer app](man/figures/oceanexplorer-demo.gif){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



``` r

# 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.



```{r load}

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:



```{r slice, eval=exists("oxy_global")}

# 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:



```{r plot1, eval=exists("oxy_omz")}

# 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`.



```{r plot2, eval=exists("oxy_global")}

# 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.



```{r app, eval = FALSE}

# 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.



```{r addin, eval = FALSE}

# launch an interactive shiny session

NOAA_addin()

```



## Code of Conduct



Please note that the oceanexplorer project is released with a [Contributor Code of Conduct](https://martinschobben.github.io/oceanexplorer/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.



# References