tests/testthat/test-mark_se_std.R

In semptools: Customizing Structural Equation Modelling Plots

library(lavaan)
library(semPlot)

mod_pa <-
  'x1 ~~ x2
   x3 ~  x1 + x2
   x4 ~  x1 + x3
  '
# Use a smaller sample to get different p-values
fit_pa <- lavaan::sem(mod_pa, pa_example[1:50, ])
m <- matrix(c("x1",   NA,  NA,   NA,
              NA, "x3",  NA, "x4",
              "x2",   NA,  NA,   NA), byrow = TRUE, 3, 4)
p_pa <- semPaths(fit_pa, whatLabels = "std",
                 sizeMan = 10,
                 edge.label.cex = 1.15,
                 layout = m,
                 DoNotPlot = TRUE)

est <- standardizedSolution(fit_pa)
id <- c(1, 2, 3, 4, 5, 6, 7, 8, 9, 1)
p_pa_se_chk <- paste0(formatC(est$est[id], digits = 2, format = "f"),
                      " (",
                      formatC(est$se[id], digits = 2, format = "f"),
                      ")")
alphas <- c("*" = .05, "**" = .01, "***" = .001)
alphas_sorted <- sort(alphas, decreasing = FALSE)
tmp <- sapply(est$pvalue[id], function(x) {
                                  ind <- which(x < alphas_sorted)[1]
                                  ifelse(is.na(ind), "", names(ind[1]))
                                })
p_pa_sig_chk <- paste0(formatC(est$est[id], digits = 2, format = "f"),
                       tmp)

test_that(
  "mark_se and mark_sig: Standardized solution", {
    p_pa_se1 <- mark_se(p_pa, fit_pa)
    p_pa_se2 <- mark_se(p_pa, est = est)
    p_pa_se3 <- mark_se(p_pa, fit_pa, std_type = TRUE)
    p_pa_se4 <- mark_se(p_pa, fit_pa, std_type = "std.all")
    expect_false(isTRUE(all.equal(p_pa_se1$graphAttributes$Edges$labels,
                                  p_pa_se_chk)))
    expect_identical(p_pa_se2$graphAttributes$Edges$labels,
                     p_pa_se_chk)
    expect_identical(p_pa_se3$graphAttributes$Edges$labels,
                     p_pa_se_chk)
    expect_identical(p_pa_se4$graphAttributes$Edges$labels,
                     p_pa_se_chk)
    p_pa_sig1 <- mark_sig(p_pa, fit_pa)
    p_pa_sig2 <- mark_sig(p_pa, ests = est)
    p_pa_sig3 <- mark_sig(p_pa, fit_pa, std_type = TRUE)
    p_pa_sig4 <- mark_sig(p_pa, fit_pa, std_type = "std.all")
    expect_false(isTRUE(all.equal(p_pa_sig1$graphAttributes$Edges$labels,
                                  p_pa_sig_chk)))
    expect_identical(p_pa_sig2$graphAttributes$Edges$labels,
                     p_pa_sig_chk)
    expect_identical(p_pa_sig3$graphAttributes$Edges$labels,
                     p_pa_sig_chk)
    expect_identical(p_pa_sig4$graphAttributes$Edges$labels,
                     p_pa_sig_chk)
  })