drawdag: Plot Directed Acyclic Graphs (dagitty)

In rmcelreath/rethinking: Statistical Rethinking book package

Plot Directed Acyclic Graphs (dagitty)

Description

A fancier version of dagitty's plot function, as well as a way to show open paths given a conditioning set.

Usage

drawdag( x , col_arrow="black" , col_segment="black" , col_labels="black" , cex=1 , 
  lwd=1.5 , goodarrow=TRUE , xlim , ylim , shapes , col_shapes , radius=3 , 
  add=FALSE , ... )

drawopenpaths( x , Z=list() , col_arrow="red" , ... )

Arguments

x	A dagitty graph
col_arrow	Color or vector of colors for the graph arrows
col_segment	Color or vector of colors for the graph segments
col_labels	Color or vector of colors for the graph text labels
cex	Size of text labels
lwd	Width of arrow lines
goodarrow	Use Arrow from shape package to draw arrows
xlim	Optional plot limits
ylim	Optional plot limits
shapes	A named list of variables with one of "c" for an open circle or "fc" for a filled circle
col_shapes	A named list of colors to correspond to the shapes list
radius	Radius of shapes circles
add	If TRUE, draw over existing DAG in active plot
Z	List of variables to condition on when computing open paths
...	Optional arguments to pass to other functions

Details

drawdag is a modified version of plot.dagitty but with additional stylistic options. By default, it draws arrows in black and with thicker line width. It also uses the nicer arrows drawn by Arrows in the shape package. If the DAG doesn't already have coordinates, then graphLayout is called to provide them.

drawopenpaths uses dagitty::paths to compute and then overdraw open paths, given an exposure and outcome variable. It uses drawdag to perform the drawing. Requires that the DAG already be displayed. Only open paths are drawn in the overlay color.

Author(s)

Richard McElreath

Examples

## Not run: 

ex1 <- dagitty("dag {
    X [exposure]
    Y [outcome]
    U [unobserved]
    Z -> X -> Y
    X <- U -> Y
}")
coordinates(ex1) <- list( x=c(Z=0,X=1,Y=1,U=0) , y=c(Z=0,U=0.5,X=0,Y=1) )
drawdag( ex1 )

# example of drawing open paths
drawdag( ex1 )
drawopenpaths( ex1 ) # open backdoor

drawdag( ex1 , col_arrow="gray" )
drawopenpaths( ex1 , Z=list("U") ) # closed backdoor

## End(Not run)

rmcelreath/rethinking documentation built on Aug. 26, 2024, 5:54 p.m.