quick_sem_plot: Quick Plots of Common Models

In sfcheung/semptools: Customizing Structural Equation Modelling Plots

Quick Plots of Common Models

Description

Simple-to-use functions for generating plots of common models.

Usage

quick_parallel_mediation(
  object,
  x,
  m,
  y,
  mediators_position = c("center", "top", "bottom"),
  what = "path",
  whatLabels = "est",
  style = c("lisrel", "ram"),
  nCharNodes = 0,
  nCharEdges = 0,
  sizeMan = NULL,
  sizeLat = NULL,
  edge.label.cex = NULL,
  ...,
  plot_now = TRUE,
  do_mark_se = TRUE,
  do_mark_sig = TRUE,
  do_rotate_resid = TRUE,
  do_add_rsq = TRUE,
  add_notes = FALSE,
  notes = NULL
)

q_parallel(
  object,
  x,
  m,
  y,
  mediators_position = c("center", "top", "bottom"),
  what = "path",
  whatLabels = "est",
  style = c("lisrel", "ram"),
  nCharNodes = 0,
  nCharEdges = 0,
  sizeMan = NULL,
  sizeLat = NULL,
  edge.label.cex = NULL,
  ...,
  plot_now = TRUE,
  do_mark_se = TRUE,
  do_mark_sig = TRUE,
  do_rotate_resid = TRUE,
  do_add_rsq = TRUE,
  add_notes = FALSE,
  notes = NULL
)

quick_serial_mediation(
  object,
  x,
  m,
  y,
  mediators_position = c("top", "bottom"),
  what = "path",
  whatLabels = "est",
  style = c("lisrel", "ram"),
  nCharNodes = 0,
  nCharEdges = 0,
  sizeMan = NULL,
  sizeLat = NULL,
  edge.label.cex = NULL,
  ...,
  plot_now = TRUE,
  do_mark_se = TRUE,
  do_mark_sig = TRUE,
  do_rotate_resid = TRUE,
  do_add_rsq = TRUE,
  add_notes = FALSE,
  notes = NULL
)

q_serial(
  object,
  x,
  m,
  y,
  mediators_position = c("top", "bottom"),
  what = "path",
  whatLabels = "est",
  style = c("lisrel", "ram"),
  nCharNodes = 0,
  nCharEdges = 0,
  sizeMan = NULL,
  sizeLat = NULL,
  edge.label.cex = NULL,
  ...,
  plot_now = TRUE,
  do_mark_se = TRUE,
  do_mark_sig = TRUE,
  do_rotate_resid = TRUE,
  do_add_rsq = TRUE,
  add_notes = FALSE,
  notes = NULL
)

quick_simple_mediation(
  object,
  x,
  m,
  y,
  mediators_position = c("top", "bottom"),
  what = "path",
  whatLabels = "est",
  style = c("lisrel", "ram"),
  nCharNodes = 0,
  nCharEdges = 0,
  sizeMan = NULL,
  sizeLat = NULL,
  edge.label.cex = NULL,
  ...,
  plot_now = TRUE,
  do_mark_se = TRUE,
  do_mark_sig = TRUE,
  do_rotate_resid = TRUE,
  do_add_rsq = TRUE,
  add_notes = FALSE,
  notes = NULL
)

q_simple(
  object,
  x,
  m,
  y,
  mediators_position = c("top", "bottom"),
  what = "path",
  whatLabels = "est",
  style = c("lisrel", "ram"),
  nCharNodes = 0,
  nCharEdges = 0,
  sizeMan = NULL,
  sizeLat = NULL,
  edge.label.cex = NULL,
  ...,
  plot_now = TRUE,
  do_mark_se = TRUE,
  do_mark_sig = TRUE,
  do_rotate_resid = TRUE,
  do_add_rsq = TRUE,
  add_notes = FALSE,
  notes = NULL
)

Arguments

object	A lavaan object, such as the output of lavaan::sem().
x	The name of the x variable. Must have exactly one x variable.
m	The name(s) of the m variable(s). The allowed number of m variable(s) depends of the model to be drawn.
y	The name of the y variable. Must have exactly one y variable.
mediators_position	For a simple mediation model, it can be either "top" or "bottom". For a parallel or serial mediation model, it can be "top", "bottom", or "center".
what	The same argument of semPlot::semPaths(). What the edges (arrows) denote. Default is "path", the paths drawn with equal width.
whatLabels	The same argument of semPlot::semPaths(). What the edge labels represent. Default is "est", the parameter estimates. Can be set to "std" to print standardized coefficients.
style	The same argument of semPlot::semPaths(). How residual variances are drawn. Can be "lisrel", the default, or "ram".
nCharNodes	The same argument of semPlot::semPaths(). Default is 0, to disable abbreviation of the variable names.
nCharEdges	The same argument of semPlot::semPaths(). Default is 0, to disable abbreviation of the edge labels.
sizeMan	The same argument of semPlot::semPaths(). The size of the observed variables. Default is NULL and the actual size determined internally based on the number of mediators.
sizeLat	The same argument of semPlot::semPaths(). The size of the latent variables. Default is NULL and the actual size determined internally based on the number of mediators.
edge.label.cex	The same argument of semPlot::semPaths(). The size of the edge labels (parameter estimates). Default is NULL and the actual size determined internally based on the number of mediators.
...	Other arguments to be passed to to semPlot::semPaths().
plot_now	Logical. If TRUE, the default, the plot will be plotted immediately. Set it to FALSE if the plot will be further processed before being plotted.
do_mark_se	Logical. If TRUE, the default, standard errors will be added by mark_se(). The lavaan standard errors will be used if the standardized coefficients are requested (whatLabels set to std).
do_mark_sig	Logical. If TRUE, the default, significance test results will be marked by asterisks using mark_sig().
do_rotate_resid	Logical. If TRUE, the default, Error variances, or R-squares if do_add_rsq is TRUE, will be rotated based on the layout.
do_add_rsq	Logical. If TRUE, the default, Error variances will be replaced by R-squares, added by add_rsq().
add_notes	Logical. If TRUE and plot_now is also TRUE, a note will be added by text(), using notes. Customization is limited. Do not use for now. Commonly used notes will be added in the future.
notes	A string, the notes to be printed if add_notes is TRUE.

Details

A collection of functions for generating the plots of common models. They are designed to need as few arguments as possible to have a plot that should need minimal postprocessing.

Currently, functions are available for these plots:

• Simple mediation models (a model with only one mediator): q_simple() or quick_simple_mediation().

• Parallel mediation models (a model with one or more paths between two variables, each path with only one mediator): q_parallel() or quick_parallel_mediation().

• Serial mediation models (a model with one main path between two variables, withe one or more mediators along the path): q_serial() or quick_serial_mediation().

For these three functions, if the default settings are desired, users only need to supply the lavaan output, and specify:

• The x variable (predictor) to be included.

• The m variable(s) to be included, which is a character vector if the model has more than one mediator.

• The y variable to be included.

These variables can be observed variables or latent factors. Indicators of latent variables will not be drawn (unless they are listed in x, m, or y).

The layout is determined by the argument mediators_position, with two or more preset layouts for each model.

By default, the following will be added to the plot:

• Asterisks included to denote the significance test results (implemented by mark_sig()).

• Standard errors included for free parameters (implemented by mark_se()).

• R-squares are drawn in place of error variances for the m variable(s) and y variable (implemented by add_rsq()).

These options can be turned off if so desired.

Unlike other function in semptools, these functions are usually used to plot a model immediately. Therefore, the resulting plot will be plotted by default. Turned this off by setting plot_now to FALSE (analogous to setting DoNotPlot to FALSE when calling semPlot::semPaths()).

Although the plot is designed to be ready-to-plot, it can be further processed by other semptools functions if necessary, just like the plot of semPlot::semPaths().

Variables to be drawn

For readability, it is common for researchers to omit some variables when drawing a model.

For example:

m ~ x + c1 + c2

y ~ m + x + c1 + c2

If c1 and c2 are control variables, researchers want to draw only these\ paths

m ~ x

y ~ m + x

The quick plot functions can be used for this purpose. Only selected variables will be included in the plots.

Researchers may also want to draw several plots, one for each pair of the predictor (the x-variable) and the outcome variable (the y-variable).

For example,

m ~ x + c1 + c2

y1 ~ m + x + c1 + c2

y2 ~ m + x + c1 + c2

For this model, in addition to excluding the control variables, researchers may want to generate two diagrams, one for y1:

m ~ x

y1 ~ m + x

and the other for y2:

m ~ x

y2 ~ m + x

Note that all the functions will not check the models. The specification of x, m, and y are assumed to be valid for the fitted models.

Value

A qgraph::qgraph generated by semPlot::semPaths() and customized by other semptools functions is returned invisibly. Called for its side effect.

Examples

library(lavaan)
library(semPlot)

# ---- Parallel Mediation Model

mod_parallel <-
 'x04 ~ x01
  x05 ~ x01
  x06 ~ x01
  x07 ~ x01
  x10 ~ x04 + x05 + x06 + x07 + x01'

fit_parallel <- lavaan::sem(mod_parallel,
                            sem_example)

q_parallel(fit_parallel,
           x = "x01",
           m = c("x04", "x05", "x06", "x07"),
           y = "x10")

q_parallel(fit_parallel,
           x = "x01",
           m = c("x04", "x05", "x06", "x07"),
           y = "x10",
           mediators_position = "top")

q_parallel(fit_parallel,
           x = "x01",
           m = c("x04", "x05", "x06", "x07"),
           y = "x10",
           mediators_position = "bottom")

# Suppress some elements for readability

q_parallel(fit_parallel,
           x = "x01",
           m = c("x04", "x05", "x06", "x07"),
           y = "x10",
           mediators_position = "bottom",
           do_mark_se = FALSE)

# ---- Serial Mediation Model

mod_serial <-
 'x04 ~ x01
  x05 ~ x04 + x01
  x06 ~ x04 + x05 + x01
  x07 ~ x04 + x05 + x06 + x01
  x08 ~ x04 + x05 + x06 + x07 + x01'
fit_serial <- lavaan::sem(mod_serial,
                          sem_example)
q_serial(fit_serial,
         x = "x01",
         m = c("x04", "x05", "x06", "x07"),
         y = "x08")

q_serial(fit_serial,
         x = "x01",
         m = c("x04", "x05", "x06", "x07"),
         y = "x08",
         mediators_position = "bottom")

# Suppress some elements for readability

q_serial(fit_serial,
         x = "x01",
         m = c("x04", "x05", "x06", "x07"),
         y = "x08",
         mediators_position = "bottom",
         do_mark_se = FALSE)

# ---- Simple Mediation Model: With Control Variables

mod_pa <-
'x3 ~  x1 + x2
 x4 ~  x3 + x1 + x2'
fit_pa <- lavaan::sem(mod_pa,
                      pa_example)

mod_sem <-
'f1 =~ x01 + x02 + x03
 f2 =~ x04 + x05 + x06 + x07
 f3 =~ x08 + x09 + x10
 f4 =~ x11 + x12 + x13 + x14
 f3 ~  f1 + f2
 f4 ~  f1 + f3'
fit_sem <- lavaan::sem(mod_sem,
                       sem_example)
q_simple(fit_pa,
         x = "x1",
         m = "x3",
         y = "x4")

# Drawing latent factors only

q_simple(fit_sem,
         x = "f1",
         m = "f3",
         y = "f4",
         whatLabels = "std",
         mediators_position = "bottom")

sfcheung/semptools documentation built on Jan. 16, 2025, 3:09 a.m.