Closed James-Thorson-NOAA closed 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
}
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!
Thanks! looks great :)
Thanks, I pushed the changes, so it is live! https://noaa-fisheries-integrated-toolbox.github.io/phylosem
awesome thanks again!
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")
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
Software Badges
No response
Toolbox Drawers
Keywords
Uses Github Releases
Yes
Static version number
No response
Comments
Thanks for developing a helpful and efficient process!
Code of Conduct