Science Score: 26.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary
Repository
Phylogenetic structural equation models
Basic Info
- Host: GitHub
- Owner: James-Thorson-NOAA
- Language: R
- Default Branch: main
- Homepage: https://james-thorson-noaa.github.io/phylosem/
- Size: 14.4 MB
Statistics
- Stars: 1
- Watchers: 4
- Forks: 0
- Open Issues: 0
- Releases: 7
Metadata Files
README.md
Phylogenetic structural equation models
Package phylosem combines features from structural equation models (SEM), phylogenetic comparative methods (PCM), and generalized linear mixed models (GLMM). By doing so, it incorporates a broad feature-set:
- Comparing multiple evolutionary models similar to phylopath
- Estimating trade-offs among multiple traits similar to phylolm
- Predicting missing trait values (and associated standard errors) similar to Rphylopars
- Estimating tradeoffs including recursive (cyclic) dependencies similar to package sem
- Applying ordination to multiple traits, similar to phylogenetic factor analysis in package FishLife
phylosem is specifically intended as a minimal implementation, and uses standard packages for input/output formatting:
- Input: phylogenetic relatedness defined using class phylo in package ape
- Input: structural trade-offs specified using syntax defined by package sem
- Output: visualizing trade-offs using semPlot, diagrammeR, and ggraph
- Output: assembling trait predictions and standard errors using phylobase
- Output: plotting trait predictions using phylosignal
Please see package vignettes for more details regarding syntax and features.
NOAA Enterprise GitHub disclaimer
This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
Owner
- Name: Jim Thorson
- Login: James-Thorson-NOAA
- Kind: user
- Location: Seattle
- Website: https://sites.google.com/site/thorsonresearch/
- Repositories: 7
- Profile: https://github.com/James-Thorson-NOAA
GitHub Events
Total
- Issues event: 2
- Delete event: 1
- Issue comment event: 3
- Member event: 1
- Push event: 15
- Pull request event: 2
- Create event: 1
Last Year
- Issues event: 2
- Delete event: 1
- Issue comment event: 3
- Member event: 1
- Push event: 15
- Pull request event: 2
- Create event: 1
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 4
- Total pull requests: 9
- Average time to close issues: 6 days
- Average time to close pull requests: 1 day
- Total issue authors: 4
- Total pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: 3 days
- Average time to close pull requests: about 1 hour
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kaskr (1)
- JWOyston (1)
- James-Thorson-NOAA (1)
- Ax3man (1)
Pull Request Authors
- James-Thorson-NOAA (13)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 273 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 8
- Total maintainers: 1
cran.r-project.org: phylosem
Phylogenetic Structural Equation Model
- Homepage: https://james-thorson-noaa.github.io/phylosem/
- Documentation: http://cran.r-project.org/web/packages/phylosem/phylosem.pdf
- License: GPL-3
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Latest release: 1.1.4
published over 2 years ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- R >= 4.0.0 depends
- TMB * depends
- ape * imports
- phylobase * imports
- phylopath * imports
- sem * imports
- DiagrammeR * suggests
- Rphylopars * suggests
- TreeTools * suggests
- ggplot2 * suggests
- knitr * suggests
- phylolm * suggests
- phylosignal * suggests
- phyr * suggests
- phytools * suggests
- rmarkdown * suggests
- semPlot * suggests
- testthat * suggests