DAG: Directed acyclic graphs (DAGs)

In phylopath: Perform Phylogenetic Path Analysis

Directed acyclic graphs (DAGs)

Description

This function is a simple wrapper around the function from the ggm package with the same name. The only differences are that the order argument defaults to TRUE and that it adds a DAG class for easy plotting. Typically, one would use define_model_set() to create models for use with the phylopath package.

Usage

DAG(..., order = TRUE)

Arguments

...	a sequence of model formulae
order	logical, defaulting to TRUE. If TRUE the nodes of the DAG are permuted according to the topological order. If FALSE the nodes are in the order they first appear in the model formulae (from left to right). For use in the phylopath package, this should always be kept to TRUE, but the argument is available to avoid potential problems with masking the function from other packages.

Details

Supply a formulas for the model as arguments. Formulas should be of the form ⁠child ~ parent`` and describe each path in your model. Multiple children of a single parent can be combined into a single formula: ⁠child ~ parent1 + parent2⁠. Finally, an isolate (unconnected variable) can be included as being connected to itself: ⁠isolate ~ isolate'.

Value

An object of classes matrix and DAG

Examples

  # Use formula notation to create DAGs:
  plot(DAG(A~B, B~C))
  # Use + to easily add multiple parents to a node:
  plot(DAG(A~B+C))
  # Add a node as it's own parent to create an isolate:
  plot(DAG(A~B+C, D~D))

phylopath documentation built on June 22, 2024, 10:31 a.m.