Onboarding Request: phylosem

James-Thorson-NOAA commented 1 year ago

Active Development

Yes

Tool name

phylosem

Tool abbreviation

phylosem

Author(s)

James Thorson and Wouter van der Bijl

NOAA Internal

Yes

Maintainer Name

James Thorson

Maintainer Email

James.Thorson@noaa.gov

Background Text

phylosem is a user-friendly and minimal R-package for phylogenetic structural equation models (PSEM). PSEM generalizes a wide range of methods including phylogenetic generalized linear models, phylologenetic trait imputation, and structural equation models. PSEM can be used to estimate continuous and categorical traits (e.g., demographic parameters, ecological role, mophometric measurements) for species based on evolutionary trade-offs and measurements for related taxa. Package phylosem is intended as a simplified alternative to R-package FishLife.

Citation

Thorson, J. T., & van der Bijl, W. (In review). phylosem: A fast and simple R package for phylogenetic inference and trait imputation using phylogenetic structural equation models. Journal of Evolutionary Biology.

References

Thorson, J. T., & van der Bijl, W. (In review). phylosem: A fast and simple R package for phylogenetic inference and trait imputation using phylogenetic structural equation models. Journal of Evolutionary Biology.

Thorson, J. T., Maureaud, A. A., Frelat, R., Mérigot, B., Bigman, J. S., Friedman, S. T., Palomares, M. L. D., Pinsky, M. L., Price, S. A., & Wainwright, P. (2023). Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models. Methods in Ecology and Evolution, 14(5), 1259–1275. https://doi.org/10.1111/2041-210X.14076

Associated Tools

FishLife https://github.com/James-Thorson-NOAA/FishLife

User Organizations

Alaska Fisheries Science Center

Online App Link

NA

Executable Link

install.packages("phylosem")

PDF Download Link

NA

Software Badges

No response

Toolbox Drawers

[ ] Ecosystems
[X] Fish and Fisheries
[ ] Human Dimensions
[ ] Protected Species
[X] General Modeling and Productivity Tools

Keywords

[ ] ADMB
[ ] Age Structured Model
[ ] Bayesian Modeling
[ ] Bycatch
[ ] C++
[ ] Calculator
[ ] Data Exploration
[ ] Data Limited Method
[ ] Data Visualization
[ ] Decision Support Tool
[ ] Developer Utilities
[ ] Economics
[ ] Ecosystem
[ ] Ensemble Modeling
[ ] Fish Biology
[ ] Fisheries
[ ] Gradient Solver
[ ] Guided User Interface
[ ] Individual Based Model
[ ] Legacy Tool
[ ] Length Structured Model
[ ] Management Strategy Evaluation
[ ] Marine Mammals
[ ] Maximum Likelihood Estimation
[ ] Model Builder
[ ] Model Comparision
[ ] Multispecies Model
[X] Natural Mortality Model
[ ] NOAA Branding
[ ] North Pacific
[ ] Output Visualization
[ ] Projection Modeling
[X] R Package
[ ] Reference Points Model
[ ] Risk Assessment Tool
[ ] Salmon
[ ] Sampling Decision Tool
[ ] Shiny
[ ] Simulation
[ ] Size Spectra Model
[ ] Size Structured Model
[ ] Socioeconomics
[ ] Spatial Model
[ ] Species Distribution Model
[ ] Standardized Reporting
[ ] Stock Assessment Model
[ ] Stock Assessment Projections
[ ] Stock Assessment Tool
[ ] Surplus Production Model
[ ] Tag Data Model
[ ] Teaching Tool
[ ] Time Series
[X] TMB
[ ] User Utilities
[ ] Virtual Population Analysis
[ ] Visualization
[ ] Web App

Uses Github Releases

Yes

Static version number

No response

Comments

Thanks for developing a helpful and efficient process!

Code of Conduct

[X] I agree to follow the FIT's Code of Conduct

k-doering-NOAA commented 1 year ago

Automatically generated JSON for the onboarding request:

{
  "active_development": true,
  "tool_name": "phylosem",
  "tool_abbreviation": "phylosem",
  "authors": "James Thorson and Wouter van der Bijl",
  "noaa_internal": true,
  "maintainer_name": "James Thorson",
  "maintainer_email": "James.Thorson@noaa.gov",
  "background_text": "phylosem is a user-friendly and minimal R-package for phylogenetic structural equation models (PSEM).  PSEM generalizes a wide range of methods including phylogenetic generalized linear models, phylologenetic trait imputation, and structural equation models.  PSEM can be used to estimate continuous and categorical traits (e.g., demographic parameters, ecological role, mophometric measurements) for species based on evolutionary trade-offs and measurements for related taxa.  Package phylosem is intended as a simplified alternative to R-package FishLife. ",
  "citation": "Thorson, J. T., & van der Bijl, W. (In review). phylosem: A fast and simple R package for phylogenetic inference and trait imputation using phylogenetic structural equation models. Journal of Evolutionary Biology.",
  "references": ["Thorson, J. T., & van der Bijl, W. (In review). phylosem: A fast and simple R package for phylogenetic inference and trait imputation using phylogenetic structural equation models. Journal of Evolutionary Biology."],
  "associated_tools": [
    {
      "name": "FishLife",
      "link": "https://github.com/James-Thorson-NOAA/FishLife"
    }
  ],
  "user_organizations": ["Alaska Fisheries Science Center"],
  "online_app_link": "NA",
  "executable_link": "install.packages(\"phylosem\")",
  "website_link": "https://cran.r-project.org/web/packages/phylosem/index.html",
  "documentation_link": "https://github.com/James-Thorson-NOAA/phylosem/tree/main/vignettes",
  "source_code_link": "https://github.com/James-Thorson-NOAA/phylosem/",
  "pdf_download_link": "NA",
  "toolbox_drawers": ["Fish and Fisheries", "General Modeling and Productivity Tools"],
  "keywords": ["Natural Mortality Model", "R Package", "TMB"],
  "uses_github_releases": true
}

k-doering-NOAA commented 1 year ago

Thanks so much! Does this preview of the phylosem page look ok? Let me know if there is anything that needs to be fixed.

I also added a link to phylosem from the FishLife toolbox page. (note the link does not currently work, but will when I push the changes to the production site)

If it looks ok, I'll push the changes to production so that phylosem appears on the main toolbox page!

James-Thorson-NOAA commented 1 year ago

Thanks! looks great :)

k-doering-NOAA commented 1 year ago

Thanks, I pushed the changes, so it is live! https://noaa-fisheries-integrated-toolbox.github.io/phylosem

James-Thorson-NOAA commented 1 year ago

awesome thanks again!

noaa-fisheries-integrated-toolbox / onboard-and-update