Find Open Paths Between Variables

dag_paths finds open paths between a given exposure and outcome. ggdag_paths and ggdag_paths_fan plot all open paths. See dagitty::paths() for details.

Usage

dag_paths(
  .dag,
  from = NULL,
  to = NULL,
  adjust_for = NULL,
  limit = 100,
  directed = FALSE,
  paths_only = FALSE,
  ...
)

ggdag_paths(
  .tdy_dag,
  from = NULL,
  to = NULL,
  adjust_for = NULL,
  limit = 100,
  directed = FALSE,
  shadow = TRUE,
  ...,
  size = 1,
  edge_type = c("link_arc", "link", "arc", "diagonal"),
  node_size = 16,
  text_size = 3.88,
  label_size = text_size,
  text_col = "white",
  label_col = "black",
  edge_width = 0.6,
  edge_cap = 8,
  arrow_length = 5,
  use_edges = TRUE,
  use_nodes = TRUE,
  use_stylized = FALSE,
  use_text = TRUE,
  use_labels = FALSE,
  text = NULL,
  label = NULL,
  node = deprecated(),
  stylized = deprecated()
)

ggdag_paths_fan(
  .tdy_dag,
  from = NULL,
  to = NULL,
  adjust_for = NULL,
  limit = 100,
  directed = FALSE,
  ...,
  shadow = TRUE,
  spread = 0.7,
  size = 1,
  node_size = 16,
  text_size = 3.88,
  label_size = text_size,
  text_col = "white",
  label_col = "black",
  edge_width = 0.6,
  edge_cap = 8,
  arrow_length = 5,
  use_edges = TRUE,
  use_nodes = TRUE,
  use_stylized = FALSE,
  use_text = TRUE,
  use_labels = FALSE,
  text = NULL,
  label = NULL,
  node = deprecated(),
  stylized = deprecated()
)

Arguments

.dag, .tdy_dag: input graph, an object of class tidy_dagitty or dagitty
from: character vector of length 1, name of exposure variable. Default is NULL, in which case it will check the input DAG for exposure.
to: character vector of length 1, name of exposure variable. Default is NULL, in which case it will check the input DAG for exposure.
adjust_for: character vector, a set of variables to control for. Default is NULL.
limit: maximum amount of paths to show. In general, the number of paths grows exponentially with the number of variables in the graph, such that path inspection is not useful except for the most simple models.
directed: logical. Should only directed paths be shown?
paths_only: logical. Should only open paths be returned? Default is FALSE, which includes every variable and edge in the DAG regardless if they are part of the path.
...: additional arguments passed to tidy_dagitty()
shadow: logical. Show edges which are not on an open path?
size: A numeric value scaling the size of all elements in the DAG. This allows you to change the scale of the DAG without changing the proportions.
edge_type: The type of edge, one of "link_arc", "link", "arc", "diagonal".
node_size: The size of the nodes.
text_size: The size of the text.
label_size: The size of the labels.
text_col: The color of the text.
label_col: The color of the labels.
edge_width: The width of the edges.
edge_cap: The size of edge caps (the distance between the arrowheads and the node borders).
arrow_length: The length of arrows on edges.
use_edges: A logical value. Include a geom_dag_edges*() function? If TRUE, which is determined by edge_type.
use_nodes: A logical value. Include geom_dag_point()?
use_stylized: A logical value. Include geom_dag_node()?
use_text: A logical value. Include geom_dag_text()?
use_labels: A logical value. Include geom_dag_label_repel()?
text: The bare name of a column to use for geom_dag_text(). If use_text = TRUE, the default is to use name.
label: The bare name of a column to use for geom_dag_label_repel(). If use_labels = TRUE, the default is to use label.
node: Deprecated.
stylized: Deprecated.
spread: the width of the fan spread

Value

a tidy_dagitty with a path column for path variables and a set grouping column or a ggplot.

Examples

confounder_triangle(x_y_associated = TRUE) %>%
  dag_paths(from = "x", to = "y")
#> # A DAG with 3 nodes and 6 edges
#> #
#> # Exposure: x
#> # Outcome: y
#> #
#> # A tibble: 9 × 10
#>   set   name      x     y direction to     xend  yend circular path     
#>   <chr> <chr> <int> <int> <fct>     <chr> <int> <int> <lgl>    <chr>    
#> 1 1     x         0     0 ->        y         2     0 FALSE    open path
#> 2 1     y         2     0 NA        NA       NA    NA FALSE    open path
#> 3 1     z         1     1 ->        x         0     0 FALSE    NA       
#> 4 1     z         1     1 ->        y         2     0 FALSE    NA       
#> 5 2     x         0     0 ->        y         2     0 FALSE    NA       
#> 6 2     y         2     0 NA        NA       NA    NA FALSE    open path
#> 7 2     z         1     1 ->        x         0     0 FALSE    open path
#> 8 2     z         1     1 ->        y         2     0 FALSE    open path
#> 9 2     x         0     0 NA        NA        2     0 FALSE    open path

confounder_triangle(x_y_associated = TRUE) %>%
  ggdag_paths(from = "x", to = "y")


butterfly_bias(x_y_associated = TRUE) %>%
  ggdag_paths_fan(shadow = TRUE)