oceanexplorer

Easy exploration of the NOAA world ocean atlas

https://github.com/martinschobben/oceanexplorer

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
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Low similarity (19.2%) to scientific vocabulary

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

Last synced: 6 months ago · JSON representation ·

Repository

Easy exploration of the NOAA world ocean atlas

Basic Info

Host: GitHub
Owner: MartinSchobben
License: other
Language: R
Default Branch: main
Homepage: https://martinschobben.github.io/oceanexplorer/
Size: 34 MB

Statistics

Stars: 9
Watchers: 2
Forks: 4
Open Issues: 1
Releases: 5

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

Created about 4 years ago · Last pushed over 2 years ago

Metadata Files

Readme Changelog License Code of conduct Citation

README.Rmd

---
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

Owner

Name: Martin Schobben
Login: MartinSchobben
Kind: user
Location: Vienna, Austria

Website: https://martinschobben.github.io/webpage/
Repositories: 4
Profile: https://github.com/MartinSchobben

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.3.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------

cff-version: 1.2.0
message: 'To cite package "oceanexplorer" in publications use:'
type: software
license: MIT
title: 'oceanexplorer: Explore Our Planet''s Oceans with NOAA'
version: 0.1.0
abstract: 'Provides tools for easy exploration of the world ocean atlas of the US
  agency National Oceanic and Atmospheric Administration (NOAA). It includes functions
  to extract NetCDF data from the repository and code to visualize several physical
  and chemical parameters of the ocean. A Shiny app further allows interactive exploration
  of the data. The methods for data collecting and quality checks are described in
  several papers, which can be found here: <https://www.ncei.noaa.gov/products/world-ocean-atlas>.'
authors:
- family-names: Schobben
  given-names: Martin
  email: schobbenmartin@gmail.com
  orcid: https://orcid.org/0000-0001-8560-0037
repository: https://CRAN.R-project.org/package=oceanexplorer
repository-code: https://github.com/MartinSchobben/oceanexplorer
url: https://martinschobben.github.io/oceanexplorer/
contact:
- family-names: Schobben
  given-names: Martin
  email: schobbenmartin@gmail.com
  orcid: https://orcid.org/0000-0001-8560-0037
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
references:
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    orcid: https://orcid.org/0000-0001-8457-4658
  year: '2022'
  url: https://CRAN.R-project.org/package=cffr
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  title: covr
  abstract: 'covr: Test Coverage for Packages'
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    email: james.f.hester@gmail.com
  year: '2022'
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- type: software
  title: curl
  abstract: 'curl: A Modern and Flexible Web Client for R'
  notes: Suggests
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    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2022'
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- type: software
  title: devtools
  abstract: 'devtools: Tools to Make Developing R Packages Easier'
  notes: Suggests
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    given-names: Hadley
  - family-names: Hester
    given-names: Jim
  - family-names: Chang
    given-names: Winston
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@rstudio.com
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2022'
  url: https://CRAN.R-project.org/package=devtools
  version: '>= 2.4.3'
- type: software
  title: diffviewer
  abstract: 'diffviewer: HTML Widget to Show File Differences'
  notes: Suggests
  authors:
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    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Kunst
    given-names: Joshua
  - family-names: Chang
    given-names: Winston
    email: winston@rstudio.com
  year: '2022'
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- type: software
  title: globals
  abstract: 'globals: Identify Global Objects in R Expressions'
  notes: Suggests
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  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
  year: '2022'
  url: https://CRAN.R-project.org/package=globals
  version: '>= 0.14.0'
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
  url: https://CRAN.R-project.org/package=knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
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    given-names: Aron
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  - family-names: Wickham
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  - family-names: Chang
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  - family-names: Iannone
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    email: rich@rstudio.com
    orcid: https://orcid.org/0000-0003-3925-190X
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  abstract: 'roxygen2: In-Line Documentation for R'
  notes: Suggests
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    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Danenberg
    given-names: Peter
    email: pcd@roxygen.org
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    given-names: Gábor
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    given-names: Manuel
  year: '2022'
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  abstract: 'shinytest: Test Shiny Apps'
  notes: Suggests
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    given-names: Winston
    email: winston@rstudio.com
  - family-names: Csárdi
    given-names: Gábor
    email: gabor@rstudio.com
  - family-names: Wickham
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    email: hadley@rstudio.com
  year: '2022'
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  version: '>= 1.5.1'
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  title: spelling
  abstract: 'spelling: Tools for Spell Checking in R'
  notes: Suggests
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    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
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  year: '2022'
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- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
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    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=testthat
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  notes: Suggests
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    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
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  notes: Suggests
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  notes: Imports
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  notes: Imports
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    orcid: https://orcid.org/0000-0002-1576-2126
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  notes: Imports
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- type: software
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  notes: Imports
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  - family-names: Pebesma
    given-names: Edzer
    email: edzer.pebesma@uni-muenster.de
    orcid: https://orcid.org/0000-0001-8049-7069
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  notes: Imports
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    given-names: John
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  year: '2022'
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  notes: Imports
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  - family-names: Sievert
    given-names: Carson
    email: carson@rstudio.com
    orcid: https://orcid.org/0000-0002-4958-2844
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    given-names: Joe
    email: joe@rstudio.com
  year: '2022'
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  version: '>= 0.3.1'
- type: software
  title: thematic
  abstract: 'thematic: Unified and Automatic ''Theming'' of ''ggplot2'', ''lattice'',
    and ''base'' R Graphics'
  notes: Imports
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  - family-names: Sievert
    given-names: Carson
    email: carson@rstudio.com
    orcid: https://orcid.org/0000-0002-4958-2844
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    given-names: Barret
    email: barret@rstudio.com
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  - family-names: Cheng
    given-names: Joe
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    email: lionel@rstudio.com
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    given-names: Yihui
    email: xie@yihui.name
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    given-names: Xianying
  year: '2022'
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  abstract: 'fs: Cross-Platform File System Operations Based on ''libuv'''
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    given-names: Jim
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  year: '2022'
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  abstract: 'glue: Interpreted String Literals'
  notes: Imports
  authors:
  - family-names: Hester
    given-names: Jim
    orcid: https://orcid.org/0000-0002-2739-7082
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@rstudio.com
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2022'
  url: https://CRAN.R-project.org/package=glue
  version: '>= 1.6.0'
- type: software
  title: shinyjs
  abstract: 'shinyjs: Easily Improve the User Experience of Your Shiny Apps in Seconds'
  notes: Imports
  authors:
  - family-names: Attali
    given-names: Dean
    email: daattali@gmail.com
    orcid: https://orcid.org/0000-0002-5645-3493
  year: '2022'
  url: https://CRAN.R-project.org/package=shinyjs
  version: '>= 2.1.0'
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=rlang
  version: '>= 0.4.11'
- type: software
  title: maps
  abstract: 'maps: Draw Geographical Maps'
  notes: Imports
  authors:
  - family-names: Becker
    given-names: Original S code by Richard A.
  - family-names: Minka
    given-names: Allan R. Wilks. R version by Ray Brownrigg. Enhancements by Thomas
      P
  - family-names: Deckmyn.
    given-names: Alex
  year: '2022'
  url: https://CRAN.R-project.org/package=maps
  version: '>= 3.4.0'
- type: software
  title: ncmeta
  abstract: 'ncmeta: Straightforward ''NetCDF'' Metadata'
  notes: Imports
  authors:
  - family-names: Sumner
    given-names: Michael
    email: mdsumner@gmail.com
  year: '2022'
  url: https://CRAN.R-project.org/package=ncmeta
  version: '>= 0.3.0'
- type: software
  title: RNetCDF
  abstract: 'RNetCDF: Interface to ''NetCDF'' Datasets'
  notes: Imports
  authors:
  - family-names: Michna
    given-names: Pavel
    email: rnetcdf-devel@bluewin.ch
  - family-names: Woods
    given-names: Milton
    email: miltonjwoods@gmail.com
  year: '2022'
  url: https://CRAN.R-project.org/package=RNetCDF
  version: '>= 2.6.1'
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2022'
  url: https://CRAN.R-project.org/package=dplyr
  version: '>= 1.0.9'
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
  version: '>= 4.1.0'
identifiers:
- type: url
  value: https://utrecht-university.shinyapps.io/oceanexplorer/
- type: url
  value: https://www.ncei.noaa.gov/products/world-ocean-atlas

GitHub Events

Total

Last Year

Committers

Last synced: about 2 years ago

All Time

Total Commits: 148
Total Committers: 4
Avg Commits per committer: 37.0
Development Distribution Score (DDS): 0.23

Past Year

Commits: 32
Committers: 3
Avg Commits per committer: 10.667
Development Distribution Score (DDS): 0.125

Top Committers

Name	Email	Commits
MartinSchobben	m**n@h**m	114
MartinSchobben	s**n@g**m	28
MartinSchobben	M****n	5
Ilja Kocken	j****r	1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 4
Total pull requests: 2
Average time to close issues: 4 months
Average time to close pull requests: 10 days
Total issue authors: 3
Total pull request authors: 2
Average comments per issue: 0.75
Average comments per pull request: 2.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 1.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

MartinSchobben (2)
ConnorFlynn (1)
PythonCoderUnicorn (1)

Pull Request Authors

kequach (1)
japhir (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 235 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 3
Total maintainers: 1

cran.r-project.org: oceanexplorer

Explore Our Planet's Oceans with NOAA

Homepage: https://martinschobben.github.io/oceanexplorer/
Documentation: http://cran.r-project.org/web/packages/oceanexplorer/oceanexplorer.pdf
License: MIT + file LICENSE
Latest release: 0.1.0
published over 2 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 235 Last month

Rankings

Forks count: 14.1%

Stargazers count: 19.3%

Dependent repos count: 23.8%

Dependent packages count: 28.6%

Average: 33.8%

Downloads: 83.1%

Maintainers (1)

schobbenmartin@gmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 4.1.0 depends
DT >= 0.20 imports
RNetCDF >= 2.6.1 imports
bslib >= 0.3.1 imports
dplyr >= 1.0.9 imports
fs >= 1.5.2 imports
ggplot2 >= 3.3.5 imports
glue >= 1.6.0 imports
maps >= 3.4.0 imports
miniUI >= 0.1.1.1 imports
ncmeta >= 0.3.0 imports
purrr >= 0.3.4 imports
rlang >= 0.4.11 imports
rstudioapi >= 0.13 imports
sf >= 1.0.5 imports
shiny >= 1.7.1 imports
shinyFeedback >= 0.4.0 imports
shinyjs >= 2.1.0 imports
stars >= 0.5.5 imports
thematic >= 0.1.2.1 imports
waiter >= 0.2.5 imports
covr * suggests
devtools >= 2.4.3 suggests
diffviewer >= 0.1.1 suggests
globals >= 0.14.0 suggests
knitr * suggests
rmarkdown * suggests
roxygen2 * suggests
shinytest >= 1.5.1 suggests
spelling * suggests
testthat >= 3.1.2 suggests
vdiffr >= 1.0.2 suggests
withr * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v1 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

.github/workflows/pkgdown.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

.github/workflows/shiny-deploy.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

.github/workflows/update-citation-cff.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

oceanexplorer

Science Score: 44.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: oceanexplorer

Rankings

Maintainers (1)

Dependencies