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Get the Attribute Values of Selected Edges

Source: R/get_edge_attribute.R
get_edge_attribute.Rd

Get the values of an arbitrary attribute of selected edges.

Usage

get_edge_attribute(
  semPaths_plot,
  edges = NULL,
  attribute_name = NULL,
  check_direction = TRUE
)

Arguments

semPaths_plot

A qgraph::qgraph object generated by semPlot::semPaths, or a similar qgraph object modified by other semptools functions. Unlike some other functions, this function does not support a list of qgraph::qgraph objects. If semPaths_plot is a list of qgraph::qgraph objects, only the first object will be processed. Use functions such as lapply() manually to get the attribute values from a list of qgraph::qgraph objects.

edges

A character vector of the edges. Each edge is denoted by lavaan model syntax, such as y ~ x or x1 ~~ x2. If NULL, then the values of all edges will be retrieved.

attribute_name

The name of the attribute from which the values will be retrieved.

check_direction

If FALSE, the direction of an edge is ignored. For example, both y ~ x and x ~ y will affect y ~ x, x ~ y, and y ~~ x. Useful when we want to identify an edge regardless of its direction and whether it is directional.

Value

A named vector of the values.

Details

From a qgraph::qgraph() object generated by semPlot::semPaths(), get the values of an attribute of selected edges.

This function is designed to be a general one that gets the values of the attributes named by the user.

Setting the value of values

This argument can be set in three ways.

For a named vector, the name of an element should be the path as specified by lavaan::model.syntax or as appeared in lavaan::parameterEstimates().

For example, if the attributes to be changed are the colors of selected edges, to change the color of the path regressing y on x, the name should be "y ~ x". To change the color of the covariance between x1 and x2, the name should be "x1 ~~ x2". Therefore, c("y ~ x1" = "red", "x1 ~~ x2" = "blue") changes the colors of the path from x1 to y and the covariance between x1 and x2 to "red" and "blue", respectively.

The order of the two nodes may matter for covariances. Therefore, if the attribute of a covariance is not changed, try switching the order of the two nodes.

For a list of named lists, each named list should have three named values: from, to, and new_value. The attribute of the edge from from to to will be set to new_value.

The second approach is no longer recommended, though kept for backward compatibility.

The last approach is setting values to a one-element vector with no name. All edges in plot will then have the selected attributes set to this value.

Examples

mod_pa <-
  'x1 ~~ x2
   x3 ~  x1 + x2
   x4 ~  x1 + x3
  '
fit_pa <- lavaan::sem(mod_pa, pa_example)
lavaan::parameterEstimates(fit_pa)[, c("lhs", "op", "rhs", "est", "pvalue")]
#>   lhs op rhs   est pvalue
#> 1  x1 ~~  x2 0.005  0.957
#> 2  x3  ~  x1 0.537  0.000
#> 3  x3  ~  x2 0.376  0.000
#> 4  x4  ~  x1 0.111  0.382
#> 5  x4  ~  x3 0.629  0.000
#> 6  x3 ~~  x3 0.874  0.000
#> 7  x4 ~~  x4 1.194  0.000
#> 8  x1 ~~  x1 0.933  0.000
#> 9  x2 ~~  x2 1.017  0.000
m <- matrix(c("x1",   NA,   NA,
                NA, "x3", "x4",
              "x2",   NA,   NA), byrow = TRUE, 3, 3)
p_pa <- semPlot::semPaths(fit_pa, whatLabels="est",
            style = "ram",
            nCharNodes = 0, nCharEdges = 0,
            layout = m)


get_edge_attribute(
   p_pa,
   edges = c("x2 ~~ x1", "x4 ~ x1"),
   attribute_name = "labels")
#> x2 ~~ x1  x4 ~ x1 
#>   "0.01"   "0.11" 

get_edge_attribute(
   p_pa,
   edges = c("x2 ~~ x1", "x4 ~ x1"),
   attribute_name = "color")
#>    x2 ~~ x1     x4 ~ x1 
#> "#808080FF" "#808080FF"