{"id":29111591,"url":"https://github.com/UtrechtUniversity/oceanexplorer","last_synced_at":"2025-06-29T10:01:57.254Z","repository":{"id":40546033,"uuid":"441203134","full_name":"MartinSchobben/oceanexplorer","owner":"MartinSchobben","description":"Easy exploration of the NOAA world ocean atlas","archived":false,"fork":false,"pushed_at":"2023-10-21T11:55:04.000Z","size":35652,"stargazers_count":9,"open_issues_count":1,"forks_count":4,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-06-20T13:00:40.193Z","etag":null,"topics":["earth","earth-observation","earth-science","noaa","noaa-data","ocean","ocean-sciences","oceanography","open-data","r","r-package","rstats","shiny","spatial","spatial-analysis","spatial-data"],"latest_commit_sha":null,"homepage":"https://martinschobben.github.io/oceanexplorer/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MartinSchobben.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-12-23T14:21:20.000Z","updated_at":"2024-08-29T09:04:55.000Z","dependencies_parsed_at":"2023-10-16T03:47:36.083Z","dependency_job_id":"3321f8b5-a89f-47d5-97a8-d490098204ea","html_url":"https://github.com/MartinSchobben/oceanexplorer","commit_stats":{"total_commits":148,"total_committers":4,"mean_commits":37.0,"dds":"0.22972972972972971","last_synced_commit":"ac6af8e6e6fe7a26a84f2d1a96883432a22e0372"},"previous_names":["utrechtuniversity/oceanexplorer"],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/MartinSchobben/oceanexplorer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MartinSchobben%2Foceanexplorer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MartinSchobben%2Foceanexplorer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MartinSchobben%2Foceanexplorer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MartinSchobben%2Foceanexplorer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MartinSchobben","download_url":"https://codeload.github.com/MartinSchobben/oceanexplorer/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MartinSchobben%2Foceanexplorer/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262574117,"owners_count":23330777,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["earth","earth-observation","earth-science","noaa","noaa-data","ocean","ocean-sciences","oceanography","open-data","r","r-package","rstats","shiny","spatial","spatial-analysis","spatial-data"],"created_at":"2025-06-29T10:01:32.952Z","updated_at":"2025-06-29T10:01:57.151Z","avatar_url":"https://github.com/MartinSchobben.png","language":"R","readme":"---\noutput: github_document\nbibliography: \"vignettes/packages.bib\"\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n\n# The oceanexplorer \u003ca href=\"https://github.com/MartinSchobben/oceanexplorer\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"138\" /\u003e\u003c/a\u003e  \n\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n\n```{r pkgs, echo=FALSE, message=FALSE, eval=FALSE}\n# following code for loading and writing the bibtex references for the used pkgs\npkgs \u003c- c(\n  # data transformation and visualization\n  \"dplyr\", \"ggplot2\", \"purrr\", \n  # package development\n  \"devtools\", \"shinytest\", \"vdiffr\", \"roxygen2\", \"testthat\", \n  # documentation\n  \"knitr\", \"rmarkdown\", \n  # spatial analysis\n  \"stars\", \"sf\", \"ncmeta\",\n  # shiny app\n  \"thematic\", \"bslib\", \"shiny\", \"waiter\", \"shinyjs\"\n)  \n# Get the R reference\nrref \u003c- citation()\n# Create ref key\nrref$key \u003c- \"rversion\"\nhadley1 \u003c- bibentry(\n  key = \"Wickham2015\",\n  bibtype = \"Book\",\n  title = \"R packages: organize, test, document, and share your code\",\n  author =  person(\"Hadley\",\"Wickham\"),\n  year = \"2015\",\n  publisher = \" O'Reilly Media, Inc.\",\n  url = \"https://r-pkgs.org/\"\n)\nhadley2 \u003c- bibentry(\n  key = \"Wickham2020\",\n  bibtype = \"Book\",\n  title = \"Mastering Shiny: Build Interactive Apps, Reports \u0026 Dashboards.\",\n  author =  person(\"Hadley\",\"Wickham\"),\n  year = \"2020\",\n  publisher = \" O'Reilly Media, Inc.\",\n  url = \"https://mastering-shiny.org/\"\n)\nknitr::write_bib(pkgs, \"vignettes/packages.bib\", prefix = \"\")\npkgs \u003c- bibtex::read.bib(\"vignettes/packages.bib\")\nbibtex::write.bib(\n  purrr::reduce(list(rref, hadley1, hadley2, pkgs), append), \n  file = \"vignettes/packages.bib\"\n)\n```\n\n\n\u003c!-- badges: start --\u003e\n[![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)\n[![license](https://img.shields.io/github/license/mashape/apistatus.svg)](https://choosealicense.com/licenses/mit/)\n[![Codecov test coverage](https://codecov.io/gh/MartinSchobben/Oceanexplorer/branch/main/graph/badge.svg)](https://app.codecov.io/gh/MartinSchobben/Oceanexplorer?branch=main)\n[![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)\n\u003c!-- badges: end --\u003e\n\n\nThe 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/).\n\n![Demo of the ocean explorer app](man/figures/oceanexplorer-demo.gif){width=95%}\n\n## Check the app\n\nCheck the app here: https://martinschobben.shinyapps.io/oceanexplorer/\n\n## Funding \u003ca href=\"https://www.uu.nl/en/news/erc-grant-for-peter-bijl-to-predict-future-sea-level\"\u003e\u003cimg src=\"man/figures/oceanice-logo.png\" style=\"float:right; height:50px;\"/\u003e\u003c/a\u003e \n\nThis project was funded by ERC Starting grant number 802835, OceaNice, awarded to Peter Bijl.\n\n## Credits\n\nThe 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. \n\nData transformation, cleaning and visualization is performed with: *dplyr* [@dplyr], and *ggplot2* [@ggplot2].\n\nIn addition, this package relies on a set of packages for spatial data analysis: *sf* [@sf] and *stars* [@stars].\n\nThe app is build with *shiny* [@shiny] and the guidance in the book: *Mastering Shiny: Build Interactive Apps, Reports \u0026 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.\n\n\n## Installation\n\nYou can install the latest version of oceanexplorer from CRAN\n\n``` r\n# Install oceanexplorer from CRAN: \ninstall.packages(\"oceanexplorer\")\n```\n\n\n## Example\n\nThe package allows extraction of global databases of several physical and chemical parameters of the ocean from the NOAA World Ocean Atlas.\n\n```{r load}\nlibrary(oceanexplorer)\n# obtain the NOAA world ocean atlas for oxygen content\noxy_global \u003c- get_NOAA(\"oxygen\", 1, \"annual\")\n```\n\n\nSlice a specific interval from the array with `filter_NOAA()`, like so:\n\n```{r slice, eval=exists(\"oxy_global\")}\n# filter a depth of 200 meters to show OMZs\n(oxy_omz \u003c- filter_NOAA(oxy_global, depth = 200))\n```\n\n\nIn addition, the sliced array can be plotted, like so:\n\n```{r plot1, eval=exists(\"oxy_omz\")}\n# plot the NOAA world ocean atlas for oxygen content\nplot_NOAA(oxy_omz, depth = NULL)\n```\n\nThe 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`.\n\n\n```{r plot2, eval=exists(\"oxy_global\")}\n# plot the NOAA world ocean atlas for oxygen content\nplot_NOAA(oxy_global, depth = 200, rng = range(oxy_omz[[1]]))\n```\n\n\n# Interactive exploration\n\nLastly, the package can launch a Shiny app for interactive exploration of the datasets.\n\n```{r app, eval = FALSE}\n# launch an interactive shiny session\nNOAA_app()\n```\n\n\nThe 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.\n\n```{r addin, eval = FALSE}\n# launch an interactive shiny session\nNOAA_addin()\n```\n\n## Code of Conduct\n\nPlease 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.\n\n# References\n","funding_links":[],"categories":["Projects"],"sub_categories":["Research software"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FUtrechtUniversity%2Foceanexplorer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FUtrechtUniversity%2Foceanexplorer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FUtrechtUniversity%2Foceanexplorer/lists"}