Package index

Specification and fitting

Core tools for model fitting and diagnostics.

phylosem()

Fit phylogenetic structural equation model

phylosem_control()

Detailed control for phylosem structure

beverton_holt()

Organize stock-recruit time series

Families

Additional families beyond the standard R families.

fixed()

Family for data that are known without error

categorical()

Family for categorical data

Interpret output

Tools for interpreting output.

summary(<phylosem>)

summarize phylosem

plot(<phylosem>)

Plot phylosem

vcov(<phylosem>)

Extract Variance-Covariance Matrix

print(<phylosem>)

Print parameter estimates and standard errors.

coef(<phylosem>)

Extract path coefficients

as_fitted_DAG()

Convert phylosem to phylopath output

as_phylo4d()

Convert phylosem to phylo4d

as_sem()

Convert phylosem to sem output

logLik(<phylosem>)

Extract the (marginal) log-likelihood of a phylosem model

Model comparison

Tools for selecting and comparing models (based on phylopath)

average()

Choose model

choice()

Choose model

best()

Extract best fitted model

compare_phylosem()

Compare phylogenetic structural equation models

best(<compare_phylosem>)

Extract best fitted model

average(<compare_phylosem>)

Choose model

choice(<compare_phylosem>)

Choose model

Data sets

Data sets used for illustration and testing.

Mlifehist_ver1_0

Fisheries natural mortality example