whalestrike
whalestrike: An R package for simulating ship strikes on whales - Published in JOSS (2024)
Science Score: 93.0%
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 11 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: researchgate.net, joss.theoj.org, zenodo.org -
○Committers with academic emails
-
○Institutional organization owner
-
✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Repository
Numerical simulation of ship-whale collision
Basic Info
- Host: GitHub
- Owner: dankelley
- License: gpl-3.0
- Language: R
- Default Branch: main
- Homepage: https://dankelley.github.io/whalestrike/
- Size: 11.5 MB
Statistics
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
The whalestrike package
Purpose
This package provides tools for simulating the collisions of ships with whales, using a simplified dynamical structure involving point masses separated by compressible materials. Along with functions for computations of forces, deformations, accelerations, etc., the package provides a easy-to-use GUI tool that makes it easy to set up some common simulation scenarios, and to display the results in graphical form.
To learn more about the scientific background, and to see the results of some detailed computations placed in the context of a database of observed strikes, see Kelley et al. (2021). For more information on the coding, see Kelley (2024).
Installation
The package is not yet available on CRAN, and must be installed from source. This can be done either by downloading the source and building it locally, or by the simpler method of typing ```R
install.package("remotes")
remotes::install_github("dankelley/whalestrike", ref="main")
``
in an R session. (Uncomment the first line, if theremotes`
package is not yet installed on your machine.)
Usage
Most users will find that the GUI application is a good way to learn about the package. To start this, type
R
library(whalestrike)
app2()
in an R session. A window will open in your browser. On the
left-hand side is a region with controllers, many hidden in sub-panels
that can be opened by clicking on V-shaped icons. Before opening
those sub-panels, try adjusting the ship speed, to see what happens to
the plots, especially the one labelled Lethality Index. Think about
whether the tendency of variations to the index are in line with your
intuition. Next, open the Ship sub-panel, to explore the result of
altering the ship mass. This sub-panel also has controllers
specifying the geometry of the impact region, and you ought to explore
them, also. Continuing to explore the app's controllers ought to give
you a good indication of what the tool provides. To learn more, try
consulting the app's documentation, provided (a) as the response to
typing ? app2 in the R console, (b) as information in a dialog box
that opens when the Help button is clicked, and (c) in a youtube
video and a brief followup youtube
video that illustrates an alteration
made after a helpful comment from a review of a Journal of Open-Source
Software manuscript about the package.
Users who want more control, and who want to deal with the results in
numerical as opposed to graphical form, should try clicking the Code
button in app2(), to see the R code that runs the simulation outside
the app. The next step will be to explore the functions used in that
code. Documentation exists for each of these functions e.g. typing
R
library(whalestrike)
?strike
in an R session will provide information on strike(), which is a key
function in the package.
References
Kelley, Dan E., James P. Vlasic, and Sean W. Brillant. "Assessing the Lethality of Ship Strikes on Whales Using Simple Biophysical Models." Marine Mammal Science 37, no. 1 (January 2021): 251–67. https://doi.org/10.1111/mms.12745. (journal site; ResearchGate Preprint)
Kelley, Dan E. "Whalestrike: an R package for simulating ship strikes on whales". Submitted to Journal of Open Source Software, 2024-01-29.
Owner
- Name: Dan Kelley
- Login: dankelley
- Kind: user
- Location: Halifax, NS, Canada
- Company: Dalhousie University
- Website: http://dankelley.github.io
- Repositories: 72
- Profile: https://github.com/dankelley
Oceanographer, University Professor and former Senator (ORCID https://orcid.org/0000-0001-7808-5911)
JOSS Publication
whalestrike: An R package for simulating ship strikes on whales
Authors
Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
Editor
Renata Diaz
Tags
oceanography whales ship strikes marine policyCodeMeta (codemeta.json)
{
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"@type": "SoftwareSourceCode",
"identifier": "whalestrike",
"description": "Simple simulation of the mechanics of a boat striking a whale.",
"name": "whalestrike: Simulate Whale Ship Strikes",
"codeRepository": "https://github.com/dankelley/whalestrike",
"issueTracker": "https://github.com/dankelley/whalestrike/issues",
"license": "https://spdx.org/licenses/GPL-3.0",
"version": "0.4.3",
"programmingLanguage": {
"@type": "ComputerLanguage",
"name": "R",
"url": "https://r-project.org"
},
"runtimePlatform": "R version 4.3.3 (2024-02-29)",
"author": [
{
"@type": "Person",
"givenName": "Dan",
"familyName": "Kelley",
"email": "dan.kelley@dal.ca",
"@id": "https://orcid.org/0000-0001-7808-5911"
}
],
"maintainer": [
{
"@type": "Person",
"givenName": "Dan",
"familyName": "Kelley",
"email": "dan.kelley@dal.ca",
"@id": "https://orcid.org/0000-0001-7808-5911"
}
],
"softwareSuggestions": [
{
"@type": "SoftwareApplication",
"identifier": "knitr",
"name": "knitr",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=knitr"
},
{
"@type": "SoftwareApplication",
"identifier": "rmarkdown",
"name": "rmarkdown",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=rmarkdown"
},
{
"@type": "SoftwareApplication",
"identifier": "testthat",
"name": "testthat",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=testthat"
}
],
"softwareRequirements": {
"1": {
"@type": "SoftwareApplication",
"identifier": "bslib",
"name": "bslib",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=bslib"
},
"2": {
"@type": "SoftwareApplication",
"identifier": "deSolve",
"name": "deSolve",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=deSolve"
},
"3": {
"@type": "SoftwareApplication",
"identifier": "R",
"name": "R",
"version": ">= 3.5.0"
},
"4": {
"@type": "SoftwareApplication",
"identifier": "shiny",
"name": "shiny",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
"name": "Comprehensive R Archive Network (CRAN)",
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=shiny"
},
"SystemRequirements": null
},
"fileSize": "398.757KB",
"relatedLink": "https://dankelley.github.io/whalestrike/",
"releaseNotes": "https://github.com/dankelley/whalestrike/blob/master/NEWS.md",
"readme": "https://github.com/dankelley/whalestrike/blob/main/README.md",
"contIntegration": "https://github.com/dankelley/whalestrike/actions/workflows/R-CMD-check.yaml",
"developmentStatus": "https://www.repostatus.org/#active",
"keywords": [
"collision",
"r",
"ships",
"whales"
]
}GitHub Events
Total
- Push event: 1
Last Year
- Push event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| dankelley | k****n@g****m | 324 |
| James Vlasic | j****c@d****a | 8 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 28
- Total pull requests: 0
- Average time to close issues: 5 months
- Average time to close pull requests: N/A
- Total issue authors: 3
- Total pull request authors: 0
- Average comments per issue: 1.93
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dankelley (24)
- alexee-mayette (3)
- mkcarr-28 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- R >= 3.5.0 depends
- bslib * depends
- deSolve * depends
- shiny * depends
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests