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oce

oce: an R package for Oceanographic Analysis - Published in JOSS (2022)

https://github.com/dankelley/oce

Science Score: 95.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: springer.com, joss.theoj.org
  • ✓
    Committers with academic emails
    2 of 18 committers (11.1%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

oceanography r
Last synced: 4 months ago · JSON representation

Repository

R package for oceanographic processing

Basic Info
Statistics
  • Stars: 152
  • Watchers: 13
  • Forks: 43
  • Open Issues: 15
  • Releases: 7
Topics
oceanography r
Created almost 16 years ago · Last pushed 4 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Security Codemeta

README.md

oce oce logo

CRAN\_Status\_Badge status Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit R-CMD-check RStudio CRAN mirror downloads RStudio CRAN mirror downloads RStudio CRAN mirror downloads RStudio CRAN mirror downloads <!-- badges: end -->

Why use R for oceanographic analysis?

The R language is popular in many branches of science, and Oceanography is no exception. With its broad statistical support, R is a natural choice for oceanographers in the biological, chemical and geological sub-disciplines. However, some physical oceanographers have remained attached to Matlab, which was widely adopted during the 1990s. Lately, this has been changing, as oceanographers turn to open-source systems such as Python and R. A particular strength of R is its provision of many powerful and well-vetted packages for handling specialized calculations. The oce package is a prime example.

What the oce package provides

The oce package handles a wide variety of tasks that come up in the analysis of Oceanographic data. In addition to the present README file, a brief sketch of the package has been written by the core developers (Kelley Dan E., Clark Richards and Chantelle Layton, 2022. oce: an R package for Oceanographic Analysis. Journal of Open Source Software, 7(71), 3594), and the primary developer uses the package extensively in his book about the place of R in oceanographic analysis (Kelley, Dan E., 2018. Oceanographic Analysis with R. New York. Springer-Verlag ISBN 978-1-4939-8844-0). Details of oce functions are provided within the R help system, and in the package webpage.

Installing oce

Stable versions of oce are available from CRAN, and may be installed from within R, in the same way as other packages. However, the CRAN version is only updated a few times a year (pursuant to policy), so many users install the "develop" branch instead. This branch may be updated several times per day, as the authors fix bugs or add features that are motivated by day-to-day usage. This is the branch favoured by users who need new features or who would wish to contribute to Oce development.

To install a develop version that is usually under a week old, try using

install.packages("oce", repos = c("https://dankelley.r-universe.dev", "https://cloud.r-project.org"))

which does not require that you have compilers for C++, Fortran, etc. on your system. However, if you have those things, you can also try building straight from the github source using

remotes::install_github("dankelley/oce", ref="develop")

Note that most readers should also install Ocedata, with

remotes::install_github("dankelley/ocedata", ref="main")

which does not require compilers for C++, Fortran, etc.

Evolution of oce

Oce is emphatically an open-source system, and so the participation of users is very important. This is why Git is used for version control of the Oce source code, and why GitHub is the host for that code. Users are invited to take part in the development process, by suggesting features, by reporting bugs, or just by watching as others do such things. Oceanography is a collaborative discipline, so it makes sense that the evolution of Oce be similarly collaborative.

Examples using built-in datasets

CTD

library(oce)
data(ctd)
plot(ctd, which=c(1,2,3,5), type="l", span=150)

Sample CTD plot.

Acoustic Doppler profiler

library(oce)
data(adp)
plot(adp)

Sample adp plot.

Sealevel and tides

library(oce)
data(sealevel)
m <- tidem(sealevel)
par(mfrow=c(2, 1))
plot(sealevel, which=1)
plot(m)

Sample sealevel plot.

Echosounder

library(oce)
data(echosounder)
plot(echosounder, which=2, drawTimeRange=TRUE, drawBottom=TRUE)

Sample echosounder plot.

Map

library(oce)
par(mar=rep(0.5, 4))
data(endeavour, package="ocedata")
data(coastlineWorld, package="oce")
mapPlot(coastlineWorld, col="gray")
mapPoints(endeavour$longitude, endeavour$latitude, pch=20, col="red")

Sample map plot.

Landsat image

library(ocedata)
library(oce)
data(landsat)
plot(landsat)

Sample landsat image plot.

Owner

  • Name: Dan Kelley
  • Login: dankelley
  • Kind: user
  • Location: Halifax, NS, Canada
  • Company: Dalhousie University

Oceanographer, University Professor and former Senator (ORCID https://orcid.org/0000-0001-7808-5911)

JOSS Publication

oce: an R package for Oceanographic Analysis
Published
March 03, 2022
DOI
Volume 7, Issue 71, Page 3594
Authors
Dan E. Kelley ORCID
Dan E. Kelley, Professor, Dalhousie University
Clark Richards ORCID
Clark Richards, Research Scientist, Bedford Institute of Oceanography, Department of Fisheries and Oceans, Canada; also Adjunct Professor, Dalhousie University
Chantelle Layton ORCID
Chantelle Layton, Physical Scientist, Bedford Institute of Oceanography, Department of Fisheries and Oceans, Canada
Editor
Kristen Thyng ORCID
Tags
oceanography measurement data analysis
View PDF Review Thread Software Archive

CodeMeta (codemeta.json) 

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Papers & Mentions

Total mentions: 10

Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil
Last synced: 3 months ago
Geographic Variation of Melanisation Patterns in a Hornet Species: Genetic Differences, Climatic Pressures or Aposematic Constraints?
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The Unique Chemistry of Eastern Mediterranean Water Masses Selects for Distinct Microbial Communities by Depth
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Different drivers, common mechanism; the distribution of a reef fish is restricted by local-scale oxygen and temperature constraints on aerobic metabolism
Last synced: 3 months ago
Bats in a changing landscape: Linking occupancy and traits of a diverse montane bat community to fire regime
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Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean
Last synced: 3 months ago
Light intensity regulates flower visitation in Neotropical nocturnal bees
Last synced: 3 months ago
Environmental influences on foraging effort, success and efficiency in female Australian fur seals
Last synced: 3 months ago
The “Little MonSta” Deep-Sea Benthic, Precision Deployable, Multi-Sensor and Sampling Lander Array
Last synced: 3 months ago
Environmental variables driving species and genus level changes in annual plankton biomass
Last synced: 3 months ago

GitHub Events

Total
  • Issues event: 137
  • Watch event: 8
  • Delete event: 23
  • Issue comment event: 350
  • Push event: 149
  • Pull request event: 5
  • Create event: 7
Last Year
  • Issues event: 137
  • Watch event: 8
  • Delete event: 23
  • Issue comment event: 352
  • Push event: 149
  • Pull request event: 5
  • Create event: 7

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 9,196
  • Total Committers: 18
  • Avg Commits per committer: 510.889
  • Development Distribution Score (DDS): 0.169
Past Year
  • Commits: 227
  • Committers: 2
  • Avg Commits per committer: 113.5
  • Development Distribution Score (DDS): 0.022
Top Committers
Name Email Commits
Dan Kelley k****n@g****m 7,644
Dan.Kelley@Dal.Ca D****y@D****a@3****5 1,068
Clark Richards c****s@g****m 254
dan.kelley@dal.ca d****y@d****a@3****5 126
Pablo Valdés p****4@g****m 49
Jaimie Harbin j****6@d****a 19
akrenner m****r@n****v 8
jkennel j****l@u****a 5
Dan Kelley k****y@D****l 5
Chantelle c****3@h****m 4
Chisholm C****E@E****a 3
Dan Kelley k****y@e****a 3
Anna Victor 1****8 2
Jeff Jackson X****c 2
Andrew Barna a****a@g****m 1
SvenGastauer s****r@p****u 1
Dirk Eddelbuettel e****d@d****g 1
Zak Varty 4****y 1
Committer Domains (Top 20 + Academic)
dal.ca: 3 debian.org: 1 postgrad.curtin.edu.au: 1 emit.phys.ocean.dal.ca: 1 ent.dfo-mpo.ca: 1 uoguelph.ca: 1 noaa.gov: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 2,150
  • Total pull requests: 140
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 1 day
  • Total issue authors: 141
  • Total pull request authors: 14
  • Average comments per issue: 5.0
  • Average comments per pull request: 1.75
  • Merged pull requests: 131
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 95
  • Pull requests: 7
  • Average time to close issues: 6 days
  • Average time to close pull requests: 10 minutes
  • Issue authors: 8
  • Pull request authors: 2
  • Average comments per issue: 3.19
  • Average comments per pull request: 0.86
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dankelley (1,407)
  • richardsc (422)
  • j-harbin (43)
  • clayton33 (35)
  • EOGrady21 (8)
  • atcogswell (8)
  • MichaelFolkes (8)
  • janstrauss1 (6)
  • Bokoyea (6)
  • koRneel82 (6)
  • Vinterwoo (5)
  • Xandac (4)
  • tomvanengeland (4)
  • rvaillancourt (4)
  • edwardpmorris (4)
Pull Request Authors
  • richardsc (103)
  • j-harbin (9)
  • dankelley (5)
  • Xandac (4)
  • pablovaldes (3)
  • akrenner (3)
  • clayton33 (3)
  • EOGrady21 (3)
  • SvenGastauer (2)
  • JoaoFilipeResende (1)
  • zakvarty (1)
  • DocOtak (1)
  • eddelbuettel (1)
  • avictor88 (1)
Top Labels
Issue Labels
graphics (292) ctd (277) development (242) request (205) adp (145) mapping (139) bug (131) section (94) reporter recheck requested (88) high priority (86) argo (80) enhancement (60) adv (59) I/O (56) ODF (51) for next CRAN (49) ad2cp (47) low priority (44) rsk (41) documentation (37) landsat (34) imagep (29) flags (27) tidem (27) pinned (25) stale (24) advice:programming (22) coastline (21) sw (18) amsr (18)
Pull Request Labels
rsk (2) ODF (1) colormap (1)

Packages

  • Total packages: 3
  • Total downloads:
    • cran 2,949 last-month
  • Total docker downloads: 1,466
  • Total dependent packages: 14
    (may contain duplicates)
  • Total dependent repositories: 35
    (may contain duplicates)
  • Total versions: 86
  • Total maintainers: 1
proxy.golang.org: github.com/dankelley/oce
  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 4 months ago
cran.r-project.org: oce

Analysis of Oceanographic Data

  • Versions: 68
  • Dependent Packages: 13
  • Dependent Repositories: 33
  • Downloads: 2,949 Last month
  • Docker Downloads: 1,466
Rankings
Forks count: 1.7%
Stargazers count: 3.0%
Dependent packages count: 4.2%
Dependent repos count: 4.6%
Downloads: 6.6%
Average: 6.7%
Docker downloads count: 19.8%
Maintainers (1)
Dan.Kelley@Dal.Ca
Last synced: 4 months ago
conda-forge.org: r-oce
  • Versions: 13
  • Dependent Packages: 1
  • Dependent Repositories: 2
Rankings
Dependent repos count: 20.1%
Average: 26.6%
Forks count: 27.3%
Dependent packages count: 29.0%
Stargazers count: 30.3%
Last synced: 4 months ago

Dependencies

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