TropFishR
A collection of fisheries models based on the FAO Manual "Introduction to tropical fish stock assessment".
https://github.com/tokami/TropFishR
Category: Biosphere
Sub Category: Marine Life and Fishery
Keywords
assessment fao-manual fish fish-stocks
Keywords from Contributors
fisheries-management fisheries-stock-assessment spict fisheries
Last synced: about 3 hours ago
JSON representation
Repository metadata
Tropical Fisheries Analysis with R
- Host: GitHub
- URL: https://github.com/tokami/TropFishR
- Owner: tokami
- Created: 2015-10-02T12:57:02.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2024-02-29T11:25:35.000Z (about 1 year ago)
- Last Synced: 2024-04-04T10:02:55.184Z (about 1 year ago)
- Topics: assessment, fao-manual, fish, fish-stocks
- Language: R
- Size: 20.2 MB
- Stars: 22
- Watchers: 12
- Forks: 16
- Open Issues: 13
- Releases: 11
-
Metadata Files:
- Readme: README.md
README.md
TropFishR 🎣
Package description
TropFishR is a collection of fisheries models based on the FAO Manual
"Introduction to tropical fish stock assessment" by Sparre and Venema
(1998, 1999). Not only scientists working in the tropics will benefit
from this new toolbox. The methods work with age-based or
length-frequency data and assist in the assessment of data poor fish
stocks. Overall, the package comes with 30 functions, 19 data sets and
10 s3 methods. All objects are documented and provide examples that
allow reproducing the examples from the FAO manual.
News
You can find detailed descriptions of new features, bug fixes, other changes of
specific package versions here.
Installation
Download the released version of TropFishR from CRAN:
install.packages("TropFishR")
Or the development version from GitHub:
# install.packages("remotes")
remotes::install_github("tokami/TropFishR")
Citation
Please use the R command citation("TropFishR") to receive information on
how to cite this package.
Documentation
The
tutorial
demonstrates the use of the main functions of TropFishR for a
single-species stock assessment with length-frequency data. The
lfqDataTutorial
gives a brief description of LFQ data and illustrates how files with
raw length measurements (e.g. excel files) can be imported into R and
trimmed for the use with TropFishR. The
ELEFANTutorial
demonstrates the ELEFAN functions available in TropFishR in detail and
discusses best practices.
Questions / Issues
In case you have questions or find bugs, please write an email to
Tobias Mildenberger or post on
TropFishR/issues.
References
- Sparre, P., Venema, S.C., 1998. Introduction to tropical fish stock assessment. Part 1. Manual. FAO Fisheries Technical Paper, (306.1, Rev. 2). 407p. link
- Sparre, P., Venema, S.C., 1999. Introduction to tropical fish stock assessment. Part 2. Excercises. FAO Fisheries Technical Paper, (306.2, Rev. 2). 94p. link
- Mildenberger, T. K., Taylor, M. H. and Wolff, M., 2017. TropFishR: an R package for fisheries analysis with length-frequency data. Methods in Ecology and Evolution, 8: 1520-1527. doi:10.1111/2041-210X.12791 link
- Taylor, M. H., and Mildenberger, T. K., 2017. Extending electronic length frequency analysis in R. Fisheries Management and Ecology, 24:330-338. doi:10.1111/fme.12232 link
Owner metadata
- Name: Tobias Mildenberger
- Login: tokami
- Email:
- Kind: user
- Description: I am interested in the processes governing the stability, diversity and productivity of marine fish communities and their implication on sustainable management.
- Website: tobiasmildenberger.com
- Location: Seattle
- Twitter:
- Company: University of Washington
- Icon url: https://avatars.githubusercontent.com/u/14937508?u=f0135015326cb320e28df947b8f9caeae8d9f435&v=4
- Repositories: 30
- Last ynced at: 2023-08-04T11:54:53.009Z
- Profile URL: https://github.com/tokami
GitHub Events
Total
- Watch event: 1
- Push event: 1
Last Year
- Watch event: 1
- Push event: 1
Committers metadata
Last synced: over 1 year ago
Total Commits: 672
Total Committers: 10
Avg Commits per committer: 67.2
Development Distribution Score (DDS): 0.326
Commits in past year: 0
Committers in past year: 0
Avg Commits per committer in past year: 0.0
Development Distribution Score (DDS) in past year: 0.0
| Name | Commits | |
|---|---|---|
| tokami | t****r@y****e | 453 |
| marchtaylor | m****r@g****m | 80 |
| tokami | t****m@a****k | 56 |
| tokami | j****s@w****e | 55 |
| marchtaylor | m****r@t****e | 10 |
| Tobias Mildenberger | t****r@T****n | 7 |
| Tobias Mildenberger | t****r@T****l | 4 |
| Alexandros Kokkalis | a****o@a****k | 3 |
| Tobias Mildenberger | t****r@t****k | 3 |
| tokami | t****r@g****m | 1 |
Committer domains:
Issue and Pull Request metadata
Last synced: 23 days ago
Total issues: 47
Total pull requests: 6
Average time to close issues: 6 months
Average time to close pull requests: 6 months
Total issue authors: 25
Total pull request authors: 3
Average comments per issue: 1.36
Average comments per pull request: 0.0
Merged pull request: 4
Bot issues: 0
Bot pull requests: 0
Past year issues: 2
Past year pull requests: 0
Past year average time to close issues: N/A
Past year average time to close pull requests: N/A
Past year issue authors: 2
Past year pull request authors: 0
Past year average comments per issue: 0.5
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- tokami (15)
- marchtaylor (4)
- jethroppaPH (4)
- Hanqingpeng (2)
- ppagliosa (2)
- FISSSSS (1)
- Isabella84 (1)
- mohammad4458 (1)
- NRagavan (1)
- MeriSoto (1)
- xiphiasTR (1)
- freddycus (1)
- quangvanvo (1)
- Ibrahim05-05 (1)
- SimonDedman (1)
Top Pull Request Authors
- cedricbriandgithub (2)
- alko989 (2)
- tokami (2)
Top Issue Labels
- bug (4)
Top Pull Request Labels
Package metadata
- Total packages: 1
-
Total downloads:
- cran: 972 last-month
- Total dependent packages: 0
- Total dependent repositories: 2
- Total versions: 14
- Total maintainers: 1
cran.r-project.org: TropFishR
Tropical Fisheries Analysis
- Homepage: https://github.com/tokami/TropFishR
- Documentation: http://cran.r-project.org/web/packages/TropFishR/TropFishR.pdf
- Licenses: GPL-3
- Latest release: 1.6.5 (published 6 months ago)
- Last Synced: 2025-04-06T07:18:40.408Z (23 days ago)
- Versions: 14
- Dependent Packages: 0
- Dependent Repositories: 2
- Downloads: 972 Last month
-
Rankings:
- Forks count: 4.853%
- Downloads: 9.273%
- Stargazers count: 11.875%
- Average: 14.68%
- Dependent repos count: 19.546%
- Dependent packages count: 27.852%
- Maintainers (1)
Dependencies
- R >= 3.0.0 depends
- GA * imports
- GenSA * imports
- Hmisc * imports
- MASS * imports
- Matrix * imports
- doParallel * imports
- msm * imports
- parallel * imports
- propagate * imports
- reshape2 * imports
- stats * imports
- utils * imports
- grDevices * suggests
- graphics * suggests
- knitr * suggests
- plyr * suggests
- rmarkdown * suggests
Score: 12.740370625481306