semptools (version 0.3.2)

mark_sig: Mark Parameter Estimates (Edge Labels) Based on p-Value

Description

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

Usage

mark_sig(
  semPaths_plot,
  object,
  alphas = c(`*` = 0.05, `**` = 0.01, `***` = 0.001),
  ests = NULL,
  std_type = FALSE,
  ests_r2 = NULL,
  r2_prefix = "R2="
)

Value

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

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).

ests

A data.frame from the parameterEstimates function, or from other function with these columns: lhs, op, rhs, and pvalue. Only used when object is not specified.

std_type

If standardized solution is used in the plot, set this either to the type of standardization (e.g., "std.all") or to TRUE. It will be passed to lavaan::standardizedSolution() to compute the p-values for the standardized solution. Used only if p-values are not supplied directly through ests.

ests_r2

A data.frame with these columns: lhs and pvalue, storing the p-values for R-squares of the variables listed on lhs. If provided, the p-values in this data.frame will override those in object or ests, if any. Used only when R-squares are present in the semPaths_plot.

r2_prefix

The prefix used to identify R-squares in semPaths_plot. Default is "R2=".

Details

Modify a qgraph::qgraph object generated by semPaths and add marks (currently asterisk, "*") to the labels based on their p-values. Require either the original object used in the semPaths call, or a data frame with the p-values for each parameter. The latter option is for p-values not computed by lavaan but by other functions.

Currently supports only plots based on lavaan output.

R-squares

Normally, lavaan does not compute p-values for R-squares. If R-squares are detected in the plot (based on r2_prefix), they will not be marked, except for the following conditions:

• Users set ests to a data frame with R-squares (op = "r2") as well as their p-values (under pvalue) computed by some methods.

• Users set ests_r2 to a data frame storing only the p-values for R-squares computed by some methods (and let the function find the p-values for other parameters from object).

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")]
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")]
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")]
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)