mark_se: Add Standard Error Estimates to Parameter Estimates (Edge...

View source: R/mark_se.R

mark_seR Documentation

Add Standard Error Estimates to Parameter Estimates (Edge Labels)


Add standard error estimates, in parentheses, to parameter estimates (edge labels) in a qgraph::qgraph object.


mark_se(semPaths_plot, object, sep = " ", digits = 2L, ests = NULL)



A qgraph object generated by semPaths, or a similar qgraph object modified by other semptools functions.


The object used by semPaths to generate the plot. Use the same argument name used in semPaths to make the meaning of this argument obvious. Currently only object of class lavaan is supported.


A character string to separate the coefficient and the standard error (in parentheses). Default to " " (one space). Use "\n" to enforce a line break.


Integer indicating number of decimal places for the appended standard errors. Default is 2L.


A data.frame from the parameterEstimates function. Only used when object is not specified.


Modify a qgraph::qgraph object generated by semPaths (currently in parentheses) to the labels. Require the original object used in the semPaths call.

Currently supports only plots based on lavaan output.

This function is a variant of, and can be combined with, the mark_sig function.


If the input is a qgraph::qgraph object, the function returns a qgraph based on the original one, with standard error estimates appended. If the input is a list of qgraph objects, the function returns a list of the same length.


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", "se")]
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)
p_pa2 <- mark_se(p_pa, fit_pa)

mod_cfa <-
 'f1 =~ x01 + x02 + x03
  f2 =~ x04 + x05 + x06 + x07
  f3 =~ x08 + x09 + x10
  f4 =~ x11 + x12 + x13 + x14
fit_cfa <- lavaan::sem(mod_cfa, cfa_example)
lavaan::parameterEstimates(fit_cfa)[ , c("lhs", "op", "rhs",
                                        "est", "pvalue", "se")]
p_cfa <- semPlot::semPaths(fit_cfa, whatLabels = "est",
                          style = "ram",
                          nCharNodes = 0, nCharEdges = 0)
# Place standard errors on a new line
p_cfa2 <- mark_se(p_cfa, fit_cfa, sep = "\n")

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)
lavaan::parameterEstimates(fit_sem)[ , c("lhs", "op", "rhs",
                                        "est", "pvalue", "se")]
p_sem <- semPlot::semPaths(fit_sem, whatLabels = "est",
                          style = "ram",
                          nCharNodes = 0, nCharEdges = 0)
# Mark significance, and then add standard errors
p_sem2 <- mark_sig(p_sem, fit_sem)
p_sem3 <- mark_se(p_sem2, fit_sem, sep = "\n")

semptools documentation built on Oct. 15, 2023, 5:07 p.m.