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https://dankelley.github.io/oce/

R package for oceanographic processing
https://dankelley.github.io/oce/

oceanography r

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R package for oceanographic processing

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README 

        



# oce oce logo



[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/oce)](https://cran.r-project.org/package=oce)

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## 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](https://doi.org/10.21105/joss.03594). 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](https://link.springer.com/book/10.1007/978-1-4939-8844-0). 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](https://dankelley.github.io/oce/).



## 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.



The easy way to install the `"develop"` branch is to execute the following

commands in R.



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



and most readers should also install Ocedata, with



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



## 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.](https://raw.githubusercontent.com/dankelley/oce/develop/oce-demo-1.png)



### Acoustic Doppler profiler



    library(oce)

    data(adp)

    plot(adp)



![Sample adp plot.](https://raw.githubusercontent.com/dankelley/oce/develop/oce-demo-2.png)



### Sealevel and tides



    library(oce)

    data(sealevel)

    m <- tidem(sealevel)

    par(mfrow=c(2, 1))

    plot(sealevel, which=1)

    plot(m)



![Sample sealevel plot.](https://raw.githubusercontent.com/dankelley/oce/develop/oce-demo-3.png)



### Echosounder



    library(oce)

    data(echosounder)

    plot(echosounder, which=2, drawTimeRange=TRUE, drawBottom=TRUE)



![Sample echosounder plot.](https://raw.githubusercontent.com/dankelley/oce/develop/oce-demo-4.png)



### 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.](https://raw.githubusercontent.com/dankelley/oce/develop/oce-demo-5.png)



### Landsat image



    library(ocedata)

    library(oce)

    data(landsat)

    plot(landsat)



![Sample landsat image plot.](https://raw.githubusercontent.com/dankelley/oce/develop/oce-demo-6.png)