Package index

Top level functions

Use these functions to describe, fit, select and average your models.

define_model_set()

Define a model set.

DAG()

Directed acyclic graphs (DAGs)

phylo_path()

Compare causal models in a phylogenetic context.

average()

Extract and average the best supported models from a phylogenetic path analysis.

best()

Extract and estimate the best supported model from a phylogenetic path analysis.

choice()

Extract and estimate an arbitrary model from a phylogenetic path analysis.

show_warnings()

Print out warnings from a phylopath analysis.

Plotting

plot(<DAG>)

Plot a directed acyclic graph.

plot(<fitted_DAG>)

Plot a directed acyclic graph with path coefficients.

plot(<phylopath_summary>)

Plot the comparison of a set of causal models.

plot_model_set()

Plot several causal hypothesis at once.

coef_plot()

Plot path coefficients and their confidence intervals or standard errors.

Extracting coefficients

as.data.frame(<fitted_DAG>)

Extract the paths of a fitted causal model.

coef(<fitted_DAG>) confint(<fitted_DAG>)

Extract the coefficients and confidence intervals of a fitted causal model.

Low level functions

Use these functions for finer control. These are mostly for internal use.

est_DAG()

Estimate path coefficients for a DAG.

average_DAGs()

Perform model averaging on a list of DAGs.

Included datasets

rhino

Rhinogrades traits.

rhino_tree

Rhinogrades phylogeny.

cichlids

Cichlid traits and the evolution of cooperative breeding.

cichlids_tree

Cichlid phylogeny.

red_list

Data on brain size, life history and vulnerability to extinction

red_list_tree

Mammalian phylogeny