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Enumerate All Indirect Effects in a Model

Source: R/all_indirect_paths.R
all_indirect_paths.Rd

Check all indirect paths in a model and return them as a list of arguments of x, y, and m, to be used by indirect_effect().

Usage

all_indirect_paths(fit = NULL, exclude = NULL, x = NULL, y = NULL)

all_paths_to_df(all_paths)

Arguments

fit

A fit object. Either the output of lavaan::lavaan() or its wrapper such as lavaan::sem(), or a list of the output of lm() or the output of lm2list().

exclude

A character vector of variables to be excluded in the search, such as control variables.

x

A character vector of variables that will be included as the x variables. If supplied, only paths that start from these variables will be included in the search. If NULL, the default, then all variables that are one of the predictors in at least one regression equation will be included in the search.

y

A character vector of variables that will be included as the y variables. If supplied, only paths that start from these variables will be included in the search. If NULL, the default, then all variables that are the outcome variables in at least one regression equation will be included in the search.

all_paths

An all_paths-class object. For example, the output of all_indirect_paths().

Value

all_indirect_paths() returns a list of the class all_paths. Each argument is a list of three character vectors, x, the name of the predictor that starts a path, y, the name of the outcome that ends a path, and m, a character vector of one or more names of the mediators, from x to y. This class has a print method.

all_paths_to_df() returns a data frame with three columns, x, y, and m, which can be used by functions such as indirect_effect().

Details

It makes use of igraph::all_simple_paths() to identify paths in a model.

Functions

  • all_indirect_paths(): Enumerate all indirect paths.

  • all_paths_to_df(): Convert the output of all_indirect_paths() to a data frame with three columns: x, y, and m.

See also

indirect_effect(), lm2list(). many_indirect_effects()

Author

Shu Fai Cheung https://orcid.org/0000-0002-9871-9448

Examples

library(lavaan)
#> This is lavaan 0.6-15
#> lavaan is FREE software! Please report any bugs.
data(data_serial_parallel)
mod <-
"
m11 ~ x + c1 + c2
m12 ~ m11 + x + c1 + c2
m2 ~ x + c1 + c2
y ~ m12 + m2 + m11 + x + c1 + c2
"
fit <- sem(mod, data_serial_parallel,
           fixed.x = FALSE)
# All indirect paths
out1 <- all_indirect_paths(fit)
out1
#> Call: 
#> all_indirect_paths(fit = fit)
#> Path(s): 
#>    path                 
#> 1  m11 -> m12 -> y      
#> 2  x -> m11 -> m12      
#> 3  x -> m11 -> m12 -> y 
#> 4  x -> m11 -> y        
#> 5  x -> m12 -> y        
#> 6  x -> m2 -> y         
#> 7  c1 -> m11 -> m12     
#> 8  c1 -> m11 -> m12 -> y
#> 9  c1 -> m11 -> y       
#> 10 c1 -> m12 -> y       
#> 11 c1 -> m2 -> y        
#> 12 c2 -> m11 -> m12     
#> 13 c2 -> m11 -> m12 -> y
#> 14 c2 -> m11 -> y       
#> 15 c2 -> m12 -> y       
#> 16 c2 -> m2 -> y        
names(out1)
#>  [1] "m11 -> m12 -> y"       "x -> m11 -> m12"       "x -> m11 -> m12 -> y" 
#>  [4] "x -> m11 -> y"         "x -> m12 -> y"         "x -> m2 -> y"         
#>  [7] "c1 -> m11 -> m12"      "c1 -> m11 -> m12 -> y" "c1 -> m11 -> y"       
#> [10] "c1 -> m12 -> y"        "c1 -> m2 -> y"         "c2 -> m11 -> m12"     
#> [13] "c2 -> m11 -> m12 -> y" "c2 -> m11 -> y"        "c2 -> m12 -> y"       
#> [16] "c2 -> m2 -> y"        

# Exclude c1 and c2 in the search
out2 <- all_indirect_paths(fit, exclude = c("c1", "c2"))
out2
#> Call: 
#> all_indirect_paths(fit = fit, exclude = c("c1", "c2"))
#> Path(s): 
#>   path                
#> 1 m11 -> m12 -> y     
#> 2 x -> m11 -> m12     
#> 3 x -> m11 -> m12 -> y
#> 4 x -> m11 -> y       
#> 5 x -> m12 -> y       
#> 6 x -> m2 -> y        
names(out2)
#> [1] "m11 -> m12 -> y"      "x -> m11 -> m12"      "x -> m11 -> m12 -> y"
#> [4] "x -> m11 -> y"        "x -> m12 -> y"        "x -> m2 -> y"        

# Exclude c1 and c2, and only consider paths start
# from x and end at y
out3 <- all_indirect_paths(fit, exclude = c("c1", "c2"),
                           x = "x",
                           y = "y")
out3
#> Call: 
#> all_indirect_paths(fit = fit, exclude = c("c1", "c2"), x = "x", 
#>     y = "y")
#> Path(s): 
#>   path                
#> 1 x -> m11 -> m12 -> y
#> 2 x -> m11 -> y       
#> 3 x -> m12 -> y       
#> 4 x -> m2 -> y        
names(out3)
#> [1] "x -> m11 -> m12 -> y" "x -> m11 -> y"        "x -> m12 -> y"       
#> [4] "x -> m2 -> y"