Mark parameter estimates (edge labels) based on p-value.

mark_sig(
  semPaths_plot,
  object,
  alphas = c(`*` = 0.05, `**` = 0.01, `***` = 0.001)
)

Arguments

semPaths_plot

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

object

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.

alphas

A named numeric vector. Each element is the cutoff (level of significance), and the name of it is the symbol to be used if p-value is less than this cutoff. The default is c("" = .05, "" = .01, "" = .001).

Value

A qgraph::qgraph based on the original one, with marks appended to edge labels based on their p-values.

Details

Modify a qgraph::qgraph object generated by semPaths and add marks (currently asterisk, "*") to the labels based on their p-values. Require the original object used in the semPaths call.

Currently supports only plots based on lavaan output.

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)

p_pa2 <- mark_sig(p_pa, fit_pa)
plot(p_pa2)


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")]
#>    lhs op rhs    est pvalue
#> 1   f1 =~ x01  1.000     NA
#> 2   f1 =~ x02  1.097  0.000
#> 3   f1 =~ x03  1.247  0.000
#> 4   f2 =~ x04  1.000     NA
#> 5   f2 =~ x05 -0.040  0.587
#> 6   f2 =~ x06  1.098  0.000
#> 7   f2 =~ x07  0.771  0.000
#> 8   f3 =~ x08  1.000     NA
#> 9   f3 =~ x09  0.937  0.000
#> 10  f3 =~ x10  1.785  0.000
#> 11  f4 =~ x11  1.000     NA
#> 12  f4 =~ x12  0.949  0.000
#> 13  f4 =~ x13 -0.077  0.356
#> 14  f4 =~ x14  1.184  0.000
#> 15 x01 ~~ x01  0.969  0.000
#> 16 x02 ~~ x02  0.853  0.000
#> 17 x03 ~~ x03  0.976  0.000
#> 18 x04 ~~ x04  0.725  0.000
#> 19 x05 ~~ x05  0.954  0.000
#> 20 x06 ~~ x06  1.161  0.000
#> 21 x07 ~~ x07  0.903  0.000
#> 22 x08 ~~ x08  1.026  0.000
#> 23 x09 ~~ x09  1.119  0.000
#> 24 x10 ~~ x10  0.566  0.009
#> 25 x11 ~~ x11  1.231  0.000
#> 26 x12 ~~ x12  1.032  0.000
#> 27 x13 ~~ x13  0.990  0.000
#> 28 x14 ~~ x14  0.985  0.000
#> 29  f1 ~~  f1  0.855  0.000
#> 30  f2 ~~  f2  1.119  0.000
#> 31  f3 ~~  f3  0.585  0.000
#> 32  f4 ~~  f4  0.943  0.000
#> 33  f1 ~~  f2 -0.173  0.059
#> 34  f1 ~~  f3  0.387  0.000
#> 35  f1 ~~  f4 -0.178  0.041
#> 36  f2 ~~  f3 -0.112  0.132
#> 37  f2 ~~  f4  0.593  0.000
#> 38  f3 ~~  f4 -0.181  0.014
p_cfa <- semPlot::semPaths(fit_cfa, whatLabels="est",
           style = "ram",
           nCharNodes = 0, nCharEdges = 0)

p_cfa2 <- mark_sig(p_cfa, fit_cfa)
plot(p_cfa2)


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")]
#>    lhs op rhs    est pvalue
#> 1   f1 =~ x01  1.000     NA
#> 2   f1 =~ x02  1.124  0.000
#> 3   f1 =~ x03  1.310  0.000
#> 4   f2 =~ x04  1.000     NA
#> 5   f2 =~ x05  0.079  0.205
#> 6   f2 =~ x06  1.120  0.000
#> 7   f2 =~ x07  0.736  0.000
#> 8   f3 =~ x08  1.000     NA
#> 9   f3 =~ x09  0.819  0.000
#> 10  f3 =~ x10  1.230  0.000
#> 11  f4 =~ x11  1.000     NA
#> 12  f4 =~ x12  0.773  0.000
#> 13  f4 =~ x13  0.064  0.160
#> 14  f4 =~ x14  0.928  0.000
#> 15  f3  ~  f1  0.612  0.000
#> 16  f3  ~  f2  0.584  0.000
#> 17  f4  ~  f1 -0.542  0.001
#> 18  f4  ~  f3  0.980  0.000
#> 19 x01 ~~ x01  1.055  0.000
#> 20 x02 ~~ x02  1.015  0.000
#> 21 x03 ~~ x03  1.028  0.000
#> 22 x04 ~~ x04  0.933  0.000
#> 23 x05 ~~ x05  0.795  0.000
#> 24 x06 ~~ x06  0.771  0.000
#> 25 x07 ~~ x07  1.071  0.000
#> 26 x08 ~~ x08  0.976  0.000
#> 27 x09 ~~ x09  0.937  0.000
#> 28 x10 ~~ x10  1.164  0.000
#> 29 x11 ~~ x11  1.008  0.000
#> 30 x12 ~~ x12  1.033  0.000
#> 31 x13 ~~ x13  0.846  0.000
#> 32 x14 ~~ x14  0.807  0.000
#> 33  f1 ~~  f1  0.714  0.000
#> 34  f2 ~~  f2  1.277  0.000
#> 35  f3 ~~  f3  0.759  0.000
#> 36  f4 ~~  f4  1.188  0.000
#> 37  f1 ~~  f2  0.016  0.856
p_sem <- semPlot::semPaths(fit_sem, whatLabels="est",
           style = "ram",
           nCharNodes = 0, nCharEdges = 0)

p_sem2 <- mark_sig(p_sem, fit_sem)
plot(p_sem2)