The Initial semPaths Graph
Let us consider an SEM model. We will use sem_example, a
sample CFA dataset from semptools with 14 variables for
illustration.
library(semptools)
head(round(sem_example, 3), 3)
#> x01 x02 x03 x04 x05 x06 x07 x08 x09 x10 x11
#> 1 2.861 2.289 3.381 0.191 0.095 -0.395 -0.060 1.320 2.807 2.330 2.069
#> 2 -0.246 -1.299 -0.371 2.232 -0.419 -0.565 -0.162 3.050 1.513 1.777 2.991
#> 3 0.079 0.067 0.323 -3.043 -1.093 -0.626 -1.961 -4.908 -2.048 -3.190 1.403
#> x12 x13 x14
#> 1 0.569 -0.808 1.989
#> 2 2.125 0.767 1.539
#> 3 1.888 1.356 1.107
This is the SEM model to be fitted:
mod <-
'f1 =~ x01 + x02 + x03
f2 =~ x04 + x05 + x06 + x07
f3 =~ x08 + x09 + x10
f4 =~ x11 + x12 + x13 + x14
f3 ~ f1 + f2
f4 ~ f1 + f3
'
Fitting the model using lavaan::sem():
library(lavaan)
fit <- lavaan::sem(mod, cfa_example)
This is the plot from semPaths:
library(semPlot)
p <- semPaths(fit, whatLabels="est",
sizeMan = 5,
node.width = 1,
edge.label.cex = .75,
style = "ram",
mar = c(5, 5, 5, 5))
We will see how set_sem_layout() can be used to do the
following tasks to post-process the graph:
Change the order of the indicators.
Assign factors to indicators manually.
Specify how to set the approximate positions of the
factors.
Specify how to place the indicators of a factor.
Adjust the placement of the indicators relative to their
corresponding factors.
Move the loadings along the paths from factors to
indicators.
Assign Indicators to Factors
This section describes how to set the order of the indicators, assign
them to factors, and specify the approximate positions of the
factors.
Suppose we want to do this:
To do this, we create two vectors, one for the argument
indicator_order and the other for the argument
indicator_factor.
indicator_order is a string vector with length equal to
the number of indicators, with the desired order if the indicators are
placed above the corresponding factors. In this example, it
will be like this:
indicator_order <- c("x04", "x05", "x06", "x07",
"x01", "x02", "x03",
"x11", "x12", "x13", "x14",
"x08", "x09", "x10")
indicator_factor is a string vector with length equal
to the number of indicators. The elements are the names of the latent
factors, denoting which factor each indicator will be assigned to:
indicator_factor <- c( "f2", "f2", "f2", "f2",
"f1", "f1", "f1",
"f4", "f4", "f4", "f4",
"f3", "f3", "f3")
To specify the locations of the factors, we need two more arguments,
factor_layout and factor_point_to.
factor_layout is a matrix of arbitrary size, with either
NA or the name of a factor. For example:
factor_layout <- matrix(c("f1", NA, NA,
NA, "f3", "f4",
"f2", NA, NA), byrow = TRUE, 3, 3)
This sets up a 3-by-3 grid, with f1 on the top left,
f2 on the bottom left, f3 in the center, and
f4 on the right of f3. Each factor must be in
one and only one cell of this matrix.
Note that a column or row can contain only NA, to
increase the vertical or horizontal distance between factors.
The helper function layout_matrix() can also be used to
create the matrix to be used in factor_layout (see
vignette("layout_matrix") on how to use
layout_matrix()):
factor_layout <- layout_matrix(f1 = c(1, 1),
f2 = c(3, 1),
f3 = c(2, 2),
f4 = c(2, 3))
factor_layout
#> [,1] [,2] [,3]
#> [1,] "f1" NA NA
#> [2,] NA "f3" "f4"
#> [3,] "f2" NA NA
factor_point_to is a matrix of the size as
factor_layout, with either NA or one of these:
“down”, “left”, “up”, or “right”, to indicate the direction that a
factor “points to” its indicator. For example:
factor_point_to <- matrix(c("left", NA, NA,
NA, "down", "down",
"left", NA, NA), byrow = TRUE, 3, 3)
f1 and f2 will point to the left (i.e.,
indicators on the left), f3 and f4 will point
downwards.
layout_matrix() can also be used to create this
matrix:
factor_point_to <- layout_matrix(left = c(1, 1),
left = c(3, 1),
down = c(2, 2),
down = c(2, 3))
factor_point_to
#> [,1] [,2] [,3]
#> [1,] "left" NA NA
#> [2,] NA "down" "down"
#> [3,] "left" NA NA
In sum, the set_sem_layout() function needs at least
these arguments:
semPaths_plot: The semPaths
plot.
indicator_order: The vector for the order of
indicators.
indicator_factor: The vector for assigning
indicators to latent factors.
factor_layout: The position of the factors on a
grid.
factor_point_to: The placement of the
indicators.
They do not have to be named if they are in this order.
We now use set_sem_layout() to post-process the
graph:
p2 <- set_sem_layout(p,
indicator_order = indicator_order,
indicator_factor = indicator_factor,
factor_layout = factor_layout,
factor_point_to = factor_point_to)
plot(p2)
Move the Loadings
We can move the loadings of indicators along the paths by the
argument loading_position. If we supply one single number,
from 0 to 1, this number will be used for the position of all loadings.
A value of .5 place the loadings on the middle of the paths. Larger the
value, closer the loadings to the indicators. Smaller the value, closer
the loadings to the factors.
We can also use a named vector to specify the positions of indicators
for each factor.In each element, the name if the factor whose loadings
will be moved. The value is the positions of its loadings. The default
is .50. We only need to specify the positions for factors to be changed
from .50 to other values. For example:
loading_position <- c(f2 = .7,
f3 = .8,
f4 = .8)
p2 <- set_sem_layout(p,
indicator_order = indicator_order,
indicator_factor = indicator_factor,
factor_layout = factor_layout,
factor_point_to = factor_point_to,
indicator_push = indicator_push,
indicator_spread = indicator_spread,
loading_position = loading_position)
plot(p2)
