Package: phylosem 1.1.4
phylosem: Phylogenetic Structural Equation Model
Applies phylogenetic comparative methods (PCM) and phylogenetic trait imputation using structural equation models (SEM), extending methods from Thorson et al. (2023) <doi:10.1111/2041-210X.14076>. This implementation includes a minimal set of features, to allow users to easily read all of the documentation and source code. PCM using SEM includes phylogenetic linear models and structural equation models as nested submodels, but also allows imputation of missing values. Features and comparison with other packages are described in Thorson and van der Bijl (2023) <doi:10.1111/jeb.14234>.
Authors:
phylosem_1.1.4.tar.gz
phylosem_1.1.4.zip(r-4.5)phylosem_1.1.4.zip(r-4.4)phylosem_1.1.4.zip(r-4.3)
phylosem_1.1.4.tgz(r-4.4-x86_64)phylosem_1.1.4.tgz(r-4.4-arm64)phylosem_1.1.4.tgz(r-4.3-x86_64)phylosem_1.1.4.tgz(r-4.3-arm64)
phylosem_1.1.4.tar.gz(r-4.5-noble)phylosem_1.1.4.tar.gz(r-4.4-noble)
phylosem.pdf |phylosem.html✨
phylosem/json (API)
NEWS
| # Install 'phylosem' in R: |
| install.packages('phylosem', repos = c('https://james-thorson-noaa.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/james-thorson-noaa/phylosem/issues
- Mlifehist_ver1_0 - Fisheries natural mortality example
Last updated 13 days agofrom:5ac1104dbc. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 09 2024 |
| R-4.5-win-x86_64 | OK | Nov 09 2024 |
| R-4.5-linux-x86_64 | OK | Nov 09 2024 |
| R-4.4-win-x86_64 | OK | Nov 09 2024 |
| R-4.4-mac-x86_64 | OK | Nov 09 2024 |
| R-4.4-mac-aarch64 | OK | Nov 09 2024 |
| R-4.3-win-x86_64 | OK | Nov 09 2024 |
| R-4.3-mac-x86_64 | OK | Nov 09 2024 |
| R-4.3-mac-aarch64 | OK | Nov 09 2024 |
Exports:as_fitted_DAGas_phylo4das_semaveragebestchoicecompare_phylosemlist_parametersphylosemphylosem_control
Dependencies:abindade4apearmaskpassBiocGenericsBiocManagerbootcachemclicodacodetoolscolorspacecpp11crayoncurldigestdplyrfansifarverfastmapfuturefuture.applygenericsggforceggmggplot2ggraphggrepelglobalsgluegraphgraphlayoutsgridExtragtablehmshttrigraphisobandjsonlitelabelinglatticelifecyclelistenvlme4magrittrMASSMatrixmemoisemgcvmimimeminqamunsellnlmenloptropensslparallellyphylobasephylolmphylopathpillarpixmappkgconfigplyrpolyclipprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangrnclRNeXMLscalessemspstringistringrsyssystemfontstibbletidygraphtidyrtidyselectTMBtweenrutf8uuidvctrsviridisviridisLitewithrXMLxml2
Comparison with other packages
Rendered fromcomparison.Rmdusingknitr::rmarkdownon Nov 09 2024.Last update: 2024-02-01
Started: 2023-01-27
Demonstration of selected features
Rendered fromdemonstration.Rmdusingknitr::rmarkdownon Nov 09 2024.Last update: 2024-02-01
Started: 2023-06-13
Detailed comparison with phylopath
Rendered fromphylopath.Rmdusingknitr::rmarkdownon Nov 09 2024.Last update: 2024-02-01
Started: 2023-02-03
Phylogenetic comparative methods in fisheries science
Rendered fromfisheries.Rmdusingknitr::rmarkdownon Nov 09 2024.Last update: 2024-02-01
Started: 2023-10-07
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert phylosem to phylopath output | as_fitted_DAG |
| Convert phylosem to phylo4d | as_phylo4d |
| Convert phylosem to sem output | as_sem |
| Choose model | average |
| Choose model | average.compare_phylosem |
| Extract best fitted model | best |
| Extract best fitted model | best.compare_phylosem |
| Choose model | choice |
| Choose model | choice.compare_phylosem |
| Extract path coefficients | coef.phylosem |
| Compare phylogenetic structural equation models | compare_phylosem |
| List fixed and random effects | list_parameters |
| Fisheries natural mortality example | Mlifehist_ver1_0 |
| Parse path | parse_path |
| Fit phylogenetic structural equation model | phylosem |
| Detailed control for phylosem structure | phylosem_control |
| Print parameter estimates and standard errors. | print.phylosem |
| summarize phylosem | summary.phylosem |
| Extract Variance-Covariance Matrix | vcov.phylosem |
