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Saturate or prune an existing DAG

Source: R/saturate_and_prune.R
dag_saturate.Rd

dag_saturate() takes a tidy DAG object and, optionally using existing coordinates, saturates the DAG based on time ordering of the nodes. To create a saturated DAG from scratch, see as_tidy_dagitty.list(). dag_prune() takes an existing DAG and removes edges. This is most useful when used together with saturated DAG.

Usage

dag_saturate(
  .tdy_dag,
  use_existing_coords = FALSE,
  layout = "time_ordered",
  seed = NULL,
  ...
)

dag_prune(.tdy_dag, edges)

Arguments

.tdy_dag

A tidy_dagitty or dagitty object

use_existing_coords

Logical, indicating whether to use existing node coordinates.

layout

a layout available in ggraph. See ggraph::create_layout() for details. Alternatively, "time_ordered" will use time_ordered_coords() to algorithmically sort the graph by time. You can also pass the result of time_ordered_coords() directly: either the function returned when called with no arguments, or the coordinate tibble returned when called with arguments.

seed

a numeric seed for reproducible layout generation

...

optional arguments passed to ggraph::create_layout()

edges

The edges to remove, in either of two forms. A named character vector where the name is the starting node and the value is the end node, e.g. c("x" = "y") removes the edge going from x to y. Or a data frame with a name and a to column, which says the same thing, and an optional direction column of "->", "<->", or "--", which names one of the edges a pair of nodes holds.

Value

A tidy_dagitty object

Details

Bidirected edges carry no time-ordering information, so dag_saturate() assigns time order from the directed edges alone and then passes the input's bidirected edges through to the saturated DAG unchanged. A saturated model therefore never implies an independence that the input denies.

dag_prune() errors if edges is empty, and if it names an edge the DAG does not contain, including an edge written in the reverse direction. A node whose every edge is pruned is kept as an isolated node.

A pair of nodes can hold a directed edge and a bidirected edge at the same time, and endpoints alone name both of them. dag_prune() errors on such a pair rather than pruning both; name the direction as well, with the data frame form of edges, to prune one of them.

See also

as_tidy_dagitty.list()

Examples

# Example usage:
dag <- dagify(y ~ x, x ~ z)
saturated_dag <- dag_saturate(dag)

saturated_dag |>
  ggdag(edge_type = "arc")


saturated_dag |>
  dag_prune(c("x" = "y")) |>
  ggdag(edge_type = "arc")