OSMOSE
A multispecies and individual-based model which focuses on fish species.
https://github.com/osmose-model/osmose
Category: Biosphere
Sub Category: Marine Life and Fishery
Last synced: about 13 hours ago
JSON representation
Repository metadata
OSMOSE: Modelling Marine Exploited Ecosystems
- Host: GitHub
- URL: https://github.com/osmose-model/osmose
- Owner: osmose-model
- License: gpl-3.0
- Created: 2015-12-19T20:28:34.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2026-03-31T07:34:21.000Z (about 1 month ago)
- Last Synced: 2026-04-27T12:05:57.243Z (16 days ago)
- Language: Java
- Homepage: http://www.osmose-model.org/
- Size: 355 MB
- Stars: 25
- Watchers: 8
- Forks: 7
- Open Issues: 24
- Releases: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
README.md
OSMOSE: Modelling Marine Exploited Ecosystems
Overview
OSMOSE is a multispecies and Individual-based model (IBM) which focuses on fish species. This model assumes opportunistic predation based on spatial co-occurrence and size adequacy between a predator and its prey (size-based opportunistic predation). It represents fish individuals grouped into schools, which are characterized by their size, weight, age, taxonomy and geographical location (2D model), and which undergo major processes of fish life cycle (growth, explicit predation, natural and starvation mortalities, reproduction and migration) and fishing exploitation. The model needs basic biological parameters that are often available for a wide range of species, and which can be found in FishBase for instance, and fish spatial distribution data. This package provides tools to build a model and run simulations using the OSMOSE model. See http://www.osmose-model.org/ for more details.
Installation
# The easiest way to get osmose is from CRAN:
install.packages("osmose")
# Or the development version from GitHub:
# install.packages("devtools")
devtools::install_github("osmose-model/osmose")
Documentation and usage
osmose includes several ways to get help and test his functions: demo scripts, vignettes and help files.
Help files
In order to get information about any function, the user just have to ask it by ? command:
# Help file of read_osmose function
?read_osmose
# Help file of available plot methods
?plot.osmose
Demo scripts
The users can test the main functions by using demo scripts (embedded on the package root). In order to access to them, they need to run the demo command:
# Check all the available topics
demo(package = "osmose")
# Select and run one of the topics (e.g. osmose.config_class)
demo(package = "osmose", topic = "osmose.config_class")
Vignettes
Vignettes can be a good simple way to review all the main functions, because they will be showed as a html. The commands to call are pretty similar to demo scripts:
# Check all the available topics
vignette(package = "osmose")
# Select and run one of the topics (e.g. osmose.config_class)
vignette(package = "osmose", topic = "create_run_read")
References
Official website of the model, including info about the development of the project as well as references.
Documentation website with information of parameters of java model (the core).
Github site where the development code is placed.
Using documentation plugins
Some documentation tools (Javadoc, PlantUML diagrams) can be generated using Maven plugins, which are defined in the pom.xml file.
Building Javadoc
mvn javadoc:javadoc
The Javadoc will be stored on the doc/_static/javadoc/apidocs/ folder.
Generate PlantUML diagrams
To generate PlantUML diagrams for the full Osmose project:
mvn plantuml-generator:generate@osmose-full
The PlantUML diagram will be stored on doc/_static/puml
To convert the resulting diagram in an image format (SVG for instance), the PlantUML tool is required. When
the diagram has been generated, type:
plantuml -tsvg doc/_static/puml/osmose-full.puml
Acknowledgements
Citation (CITATION.cff)
cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Barrier
given-names: Nicolas
orcid: https://orcid.org/0000-0002-1693-4719
- family-names: Oliveros-Ramos
given-names: Ricardo
orcid: https://orcid.org/0000-0002-8069-2101
- family-names: Verley
given-names: Philippe
orcid: https://orcid.org/0000-0002-5686-2764
- family-names: Ernande
given-names: Bruno
orcid: https://orcid.org/0000-0002-0727-5774
- family-names: Lau-Medrano
given-names: Wencheng
orcid: https://orcid.org/0000-0002-7979-9710
- family-names: Luján
given-names: Criscely
orcid: https://orcid.org/0000-0003-2658-7340
- family-names: Morell
given-names: Alaia
orcid: https://orcid.org/0000-0003-3719-4462
- family-names: Travers-Trolet
given-names: Morgane
orcid: https://orcid.org/0000-0003-1493-662X
- family-names: Velez
given-names: Laure
orcid: https://orcid.org/0000-0001-9555-6770
- family-names: Shin
given-names: Yunne-Jai
orcid: https://orcid.org/0000-0002-7259-9265
title: Object-oriented Simulator of Marine ecOSystEms (OSMOSE)
version: 4.3.3
date-released: 2023-02-10
doi: 10.5281/zenodo.7629326
Owner metadata
- Name: OSMOSE: Modelling Marine Exploited Ecosystems
- Login: osmose-model
- Email:
- Kind: organization
- Description:
- Website: http://www.osmose-model.org
- Location:
- Twitter:
- Company:
- Icon url: https://avatars.githubusercontent.com/u/16767770?v=4
- Repositories: 18
- Last ynced at: 2024-10-31T05:34:03.907Z
- Profile URL: https://github.com/osmose-model
GitHub Events
Total
- Issues event: 5
- Watch event: 4
- Issue comment event: 5
- Gollum event: 86
- Create event: 1
Last Year
- Issues event: 3
- Watch event: 3
- Issue comment event: 3
- Gollum event: 28
- Create event: 1
Committers metadata
Last synced: about 2 months ago
Total Commits: 2,846
Total Committers: 16
Avg Commits per committer: 177.875
Development Distribution Score (DDS): 0.501
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 | |
|---|---|---|
| barriern | n****r@i****r | 1419 |
| pverley | p****y@4****a | 710 |
| barrier.n | b****n@4****a | 245 |
| CriscelyLP | c****n@g****m | 157 |
| roliveros-ramos | r****s@g****m | 128 |
| barrier | b****r@4****a | 43 |
| amorell | a****l@4****a | 39 |
| albouy | a****y@4****a | 26 |
| Wencheng Lau-Medrano | l****m@g****m | 23 |
| morgane | m****e@4****a | 19 |
| alaiam | a****l@i****r | 12 |
| yjshin | y****n@4****a | 7 |
| fraile | f****e@4****a | 7 |
| Morell | a****l@i****r | 7 |
| MichaelMobius | m****7@g****m | 3 |
| Hanna Schenk | h****k@i****e | 1 |
Committer domains:
- ifremer.fr: 2
- idiv.de: 1
- ird.fr: 1
Issue and Pull Request metadata
Last synced: 3 months ago
Total issues: 28
Total pull requests: 2
Average time to close issues: over 1 year
Average time to close pull requests: 5 minutes
Total issue authors: 11
Total pull request authors: 2
Average comments per issue: 0.89
Average comments per pull request: 0.0
Merged pull request: 0
Bot issues: 0
Bot pull requests: 1
Past year issues: 3
Past year pull requests: 1
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: 1
Past year average comments per issue: 0.0
Past year average comments per pull request: 0.0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 1
Top Issue Authors
- barriern (8)
- roliveros-ramos (6)
- yunneshin (3)
- Boylad (3)
- Dengwenbo1997 (2)
- MarcVJ (1)
- ekinakoglu (1)
- Jose-Rubilar (1)
- cleaab (1)
- GhassenH (1)
- LeiXing0726 (1)
Top Pull Request Authors
- CriscelyLP (1)
- dependabot[bot] (1)
Top Issue Labels
- enhancement (7)
- bug (2)
Top Pull Request Labels
- dependencies (1)
- java (1)
Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/setup-java v1 composite
- actions/cache v2 composite
- actions/checkout v2 composite
- r-lib/actions/setup-r v2 composite
- R >= 3.5.0 depends
- R.utils * imports
- calibrar * imports
- fields * imports
- grDevices * imports
- graphics * imports
- knitr * imports
- mgcv * imports
- ncdf4 * imports
- rlist * imports
- rmarkdown * imports
- stats * imports
- stringr * imports
- utils * imports
- au.com.bytecode:opencsv 2.4
- de.elnarion.util:plantuml-generator-util 1.5.4
- edu.ucar:netcdfAll 5.5.2
- ml.options:options 1.0.0
- org.apache.commons:commons-lang3 3.12.0
- org.apache.commons:commons-math3 3.6.1
- org.junit.jupiter:junit-jupiter-api 5.9.1 test
- org.junit.jupiter:junit-jupiter-engine 5.9.1 test
Score: 6.664409020350408