tests/testthat/test_cond_indirect_effects_lavaan_missing.R

In manymome: Mediation, Moderation and Moderated-Mediation After Model Fitting

# To be examined in an interactive session

library(manymome)
suppressMessages(library(lavaan))

dat <- modmed_x1m3w4y1
dat <- add_na(dat, seed = 4589)
length(complete.cases(dat))
set.seed(860314)
n <- nrow(dat)
dat$gp <- sample(c("gp1", "gp2", "gp3"), n, replace = TRUE)
dat$city <- sample(c("alpha", "beta", "gamma", "sigma"), n, replace = TRUE)
head(dat)
dat <- cbind(dat, factor2var(dat$gp, prefix = "gp", add_rownames = FALSE))
dat <- cbind(dat, factor2var(dat$city, prefix = "city", add_rownames = FALSE))


mod <-
"
m3 ~ m1 + x + gpgp2 + gpgp3 + x:gpgp2 + x:gpgp3
y ~ m2 + m3 + x + w4 + x:w4
"
fit <- sem(mod, dat, meanstructure = TRUE, fixed.x = FALSE, missing = "fiml")
set.seed(4456)
fit_boot <- sem(mod, dat, meanstructure = TRUE, fixed.x = FALSE, se = "boot", bootstrap = 5,
                warn = FALSE)

out_mm_1 <- mod_levels_list("w4", c("gpgp2", "gpgp3"), fit = fit, merge = TRUE)

# Suppress warnings due to small number of bootstrap samples.
suppressWarnings(out_1 <- cond_indirect_effects(wlevels = out_mm_1, x = "x", y = "y", m = "m3", fit = fit))
suppressWarnings(out_2 <- cond_indirect_effects(wlevels = out_mm_1, x = "x", y = "y", m = "m3", fit = fit,
                               standardized_x = TRUE))
suppressWarnings(out_3 <- cond_indirect_effects(wlevels = out_mm_1, x = "x", y = "y", m = "m3", fit = fit,
                               standardized_y = TRUE))
suppressWarnings(out_4 <- cond_indirect_effects(wlevels = out_mm_1, x = "x", y = "y", m = "m3", fit = fit,
                               standardized_x = TRUE, standardized_y = TRUE))

suppressWarnings(out_5 <- cond_indirect_effects(wlevels = out_mm_1, x = "x", y = "y", m = "m3", fit = fit_boot,
                               boot_ci = TRUE))
suppressWarnings(out_6 <- cond_indirect_effects(wlevels = out_mm_1, x = "x", y = "y", m = "m3", fit = fit_boot,
                               standardized_x = TRUE,
                               boot_ci = TRUE))
suppressWarnings(out_7 <- cond_indirect_effects(wlevels = out_mm_1, x = "x", y = "y", m = "m3", fit = fit_boot,
                               standardized_y = TRUE,
                               boot_ci = TRUE))
suppressWarnings(out_8 <- cond_indirect_effects(wlevels = out_mm_1, x = "x", y = "y", m = "m3", fit = fit_boot,
                               standardized_x = TRUE, standardized_y = TRUE,
                               boot_ci = TRUE, output_type = "list"))

# Moderation only

outmo_mm_1 <- mod_levels(c("gpgp2", "gpgp3"), fit = fit)

# Suppress warnings due to small number of bootstrap samples.
suppressWarnings(outmo_1 <- cond_indirect_effects(wlevels = outmo_mm_1, x = "x", y = "m3", fit = fit))
suppressWarnings(outmo_2 <- cond_indirect_effects(wlevels = outmo_mm_1, x = "x", y = "m3", fit = fit,
                               standardized_x = TRUE))
suppressWarnings(outmo_3 <- cond_indirect_effects(wlevels = outmo_mm_1, x = "x", y = "m3", fit = fit,
                               standardized_y = TRUE))
suppressWarnings(outmo_4 <- cond_indirect_effects(wlevels = outmo_mm_1, x = "x", y = "m3", fit = fit,
                               standardized_x = TRUE, standardized_y = TRUE))

suppressWarnings(outmo_5 <- cond_indirect_effects(wlevels = outmo_mm_1, x = "x", y = "m3", fit = fit_boot,
                               boot_ci = TRUE, seed = 87415))
fit_boot_out <- fit2boot_out(fit_boot)
suppressWarnings(outmo_6 <- cond_indirect_effects(wlevels = outmo_mm_1, x = "x", y = "m3", fit = fit,
                               standardized_x = TRUE,
                               boot_ci = TRUE, boot_out = fit_boot_out))
suppressWarnings(outmo_7 <- cond_indirect_effects(wlevels = outmo_mm_1, x = "x", y = "m3", fit = fit,
                               standardized_y = TRUE,
                               boot_ci = TRUE, boot_out = fit_boot_out))
suppressWarnings(outmo_8 <- cond_indirect_effects(wlevels = outmo_mm_1, x = "x", y = "m3", fit = fit,
                               standardized_x = TRUE, standardized_y = TRUE,
                               boot_ci = TRUE, boot_out = fit_boot_out))