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 (In press).
| Version: | 1.1.1 |
| Depends: | TMB (≥ 1.9.7), R (≥ 4.0.0) |
| Imports: | sem, ape, phylobase, phylopath |
| LinkingTo: | RcppEigen, TMB |
| Suggests: | semPlot, TreeTools, Rphylopars, phylolm, fishtree, phyr, knitr, rmarkdown, ggplot2, testthat, phylosignal |
| Enhances: | phytools, DiagrammeR |
| Published: | 2023-11-26 |
| Author: | James Thorson 
[aut, cre],
Wouter van der Bijl
[ctb] |
| Maintainer: | James Thorson <James.Thorson at noaa.gov> |
| License: | GPL-3 |
| NeedsCompilation: | yes |
| Citation: | phylosem citation info |
| Materials: | README NEWS |
| CRAN checks: | phylosem results |
Documentation:
| Reference manual: | phylosem.pdf |
| Vignettes: |
Comparison with other packages Demonstration of selected features PCM in fisheries Detailed comparison with 'phylopath' |
Downloads:
| Package source: | phylosem_1.1.1.tar.gz |
| Windows binaries: | r-devel: phylosem_1.1.1.zip, r-release: phylosem_1.1.1.zip, r-oldrel: phylosem_1.1.1.zip |
| macOS binaries: | r-release (arm64): phylosem_1.1.1.tgz, r-oldrel (arm64): phylosem_1.1.1.tgz, r-release (x86_64): phylosem_1.1.1.tgz, r-oldrel (x86_64): phylosem_1.1.0.tgz |
| Old sources: | phylosem archive |
Linking:
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