tests/testthat/test_mod_levels_lm.R

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

library(testthat)
library(manymome)
suppressMessages(library(lavaan))

dat <- modmed_x1m3w4y1
n <- nrow(dat)
set.seed(860314)
dat$gp <- sample(c("gp1", "gp2", "gp3"), n, replace = TRUE)
dat$city <- sample(c("alpha", "beta", "gamma", "sigma"), n, replace = TRUE)
lm_m1 <- lm(m1 ~ x * w1, dat)
lm_m2 <- lm(m2 ~ m1 + gp + city, dat)
lm_m3 <- lm(m3 ~ m1 + x * gp, dat)
lm_y <- lm(y ~ m2 + m3 + x * w4, dat)
lm_m1_mm <- model.matrix(lm_m1)[, 4]
lm_m2_mm <- model.matrix(lm_m2)[, -c(1:2)]
lm_m3_mm <- model.matrix(lm_m3)[, 6:7]
lm_y_mm <- model.matrix(lm_y)[, 6]
dat2 <- cbind(dat, lm_m1_mm, lm_m2_mm, lm_m3_mm, lm_y_mm)
fit <- list(lm_m1, lm_m2, lm_m3, lm_y)

# mod_levels(fit, w = list(gp = c("gpgp2", "gpgp3"),
#                          w1 = "w1"))
# Output:
# gp:
# data.frame(label = c("cat1", "cat2"),
#            gpgp2 = c(1, 0),
#            gpgp3 = c(0, 1))
# w1:
# data.frame(label = c("Low", "Medium", "High"),
#            w1 = c(-2, 0, 2))

out_i_n_sd <- mod_levels_i_lm_numerical(fit, w = "w1")
out_i_n_p <- mod_levels_i_lm_numerical(fit, w = "w1", w_method = "percentile")
out_i_n_sd2 <- mod_levels_i_lm_numerical(fit, w = "w1", sd_from_mean = c(-1, 4))
out_i_n_p2 <- mod_levels_i_lm_numerical(fit, w = "w1", w_method = "percentile", percentiles = c(.25, .75))

out_i_c <- mod_levels_i_lm_categorical(fit, w = c("gpgp2", "gpgp3"))
out_i_c2 <- mod_levels_i_lm_categorical(fit, w = c("citybeta", "citygamma", "citysigma"))
out_i_c3 <- mod_levels_i_lm_categorical(fit, w = c("gpgp2", "gpgp3"), prefix = "gp")

out_i_c3b <- mod_levels_i_lm_categorical(fit, w = c("gp"))

out_n_sd <- mod_levels(fit, w = "w1")
out_n_p <- mod_levels(fit, w = "w1", w_method = "percentile")
out_n_sd2 <- mod_levels(fit, w = "w1", sd_from_mean = c(-1, 4))
out_n_p2 <- mod_levels(fit, w = "w1", w_method = "percentile", percentiles = c(.25, .75))

out_n_sd_l <- mod_levels_list("w1", fit = fit)

out_c <- mod_levels(fit, w = c("gpgp2", "gpgp3"))
out_c2 <- mod_levels(fit, w = c("citybeta", "citygamma", "citysigma"))
out_c3 <- mod_levels(fit, w = c("gpgp2", "gpgp3"), prefix = "gp")

out_c3b <- mod_levels(fit, w = c("gp"), prefix = "gp")

out_c_l <- mod_levels_list(fit = fit, c("gpgp2", "gpgp3"), merge = TRUE)
out_c3_l <- mod_levels_list(fit = fit, c("gpgp2", "gpgp3"), prefix = "gp")


out_i_n_sd_chk <- mean(dat$w1) + sd(dat$w1) * rev(c(-1, 0, 1))
out_i_n_p_chk <- quantile(dat$w1, rev(c(.16, .50, .84)))
out_i_n_sd2_chk <- mean(dat$w1) + sd(dat$w1) * rev(c(-1, 4))
out_i_n_p2_chk <- quantile(dat$w1, rev(c(.25, .75)))

out_i_c_chk <- structure(list(gpgp2 = c(0, 1, 0), gpgp3 = c(0, 0, 1)), row.names = c("Reference",
"2", "3"), class = "data.frame")
out_i_c2_chk <- structure(list(citybeta = c(0, 1, 0, 0), citygamma = c(0, 0,
1, 0), citysigma = c(0, 0, 0, 1)), row.names = c("Reference",
"beta", "gamma", "sigma"), class = "data.frame")
out_i_c3_chk <- structure(list(gpgp2 = c(0, 1, 0), gpgp3 = c(0, 0, 1)), row.names = c("Reference",
"gp2", "gp3"), class = "data.frame")

out_l_1 <- mod_levels_list("w4", "w1", fit = fit)
out_l_2 <- mod_levels_list("w4", c("gpgp2", "gpgp3"), fit = fit)
out_l_3 <- mod_levels_list(c("gpgp2", "gpgp3"), "w4", fit = fit)
out_l_4 <- mod_levels_list(c("gpgp2", "gpgp3"), c("citybeta", "citygamma", "citysigma"), "w4", fit = fit)


test_that("mod_levels: lm", {
    expect_equal(unlist(out_i_n_sd), out_i_n_sd_chk, ignore_attr = TRUE)
    expect_equal(unlist(out_i_n_p), out_i_n_p_chk, ignore_attr = TRUE)
    expect_equal(unlist(out_i_n_sd2), out_i_n_sd2_chk, ignore_attr = TRUE)
    expect_equal(unlist(out_i_n_p2), out_i_n_p2_chk, ignore_attr = TRUE)
    expect_equal(out_i_c, out_i_c_chk, ignore_attr = TRUE)
    expect_equal(out_i_c2, out_i_c2_chk, ignore_attr = TRUE)
    expect_equal(out_i_c3, out_i_c3_chk, ignore_attr = TRUE)
    expect_equal(out_i_c3, out_i_c3b, ignore_attr = TRUE)
    expect_equal(unlist(out_n_sd), out_i_n_sd_chk, ignore_attr = TRUE)
    expect_equal(unlist(out_n_p), out_i_n_p_chk, ignore_attr = TRUE)
    expect_equal(unlist(out_n_sd2), out_i_n_sd2_chk, ignore_attr = TRUE)
    expect_equal(unlist(out_n_p2), out_i_n_p2_chk, ignore_attr = TRUE)
    expect_equal(out_c, out_i_c_chk, ignore_attr = TRUE)
    expect_equal(out_c2, out_i_c2_chk, ignore_attr = TRUE)
    expect_equal(out_c3, out_i_c3_chk, ignore_attr = TRUE)
  })