tests/prep/prep_lavaan.R

In tidystats: Save Output of Statistical Tests

# Setup -------------------------------------------------------------------

library(lavaan)

statistics <- list()

# cfa() -------------------------------------------------------------------

HS_model <- "
    visual  =~ x1 + x2 + x3
    textual =~ x4 + x5 + x6
    speed   =~ x7 + x8 + x9
"
cfa <- cfa(HS_model, data = HolzingerSwineford1939)
cfa_groups <- cfa(HS_model, data = HolzingerSwineford1939, group = "school")

HS_model_intercepts <- "
    # three-factor model
    visual  =~ x1 + x2 + x3
    textual =~ x4 + x5 + x6
    speed   =~ x7 + x8 + x9
    # intercepts
    x1 ~ 1
    x2 ~ 1
    x3 ~ 1
    x4 ~ 1
    x5 ~ 1
    x6 ~ 1
    x7 ~ 1
    x8 ~ 1
    x9 ~ 1
"
cfa_intercepts <- cfa(
  HS_model_intercepts,
  data = HolzingerSwineford1939,
  meanstructure = TRUE
)

efa_model <- '
    efa("efa")*f1 +
    efa("efa")*f2 +
    efa("efa")*f3 =~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9
'
cfa_efa <- cfa(efa_model, data = HolzingerSwineford1939)

statistics <- statistics |>
  add_stats(cfa) |>
  add_stats(cfa_groups) |>
  add_stats(cfa_intercepts) |>
  add_stats(cfa_efa)

summary(cfa, standardized = TRUE, fit.measures = TRUE)
summary(cfa_groups, standardized = TRUE, fit.measures = TRUE)
summary(cfa_intercepts, standardized = TRUE, fit.measures = TRUE)
summary(cfa_efa, standardized = TRUE, fit.measures = TRUE)

# sem() -------------------------------------------------------------------

sem_model <- "
    # measurement model
    ind60 =~ x1 + x2 + x3
    dem60 =~ y1 + y2 + y3 + y4
    dem65 =~ y5 + y6 + y7 + y8
    # regressions
    dem60 ~ ind60
    dem65 ~ ind60 + dem60
    # residual correlations
    y1 ~~ y5
    y2 ~~ y4 + y6
    y3 ~~ y7
    y4 ~~ y8
    y6 ~~ y8
"

sem <- sem(sem_model, data = PoliticalDemocracy)

set.seed(1234)
data <- tibble::tibble(
  X = rnorm(100),
  M = 0.5 * X + rnorm(100),
  Y = 0.7 * M + rnorm(100)
)

sem_mediation_model <- "
    # direct effect
    Y ~ c*X
    # mediator
    M ~ a*X
    Y ~ b*M
    # indirect effect (a*b)
    ab := a*b
    # total effect
    total := c + (a*b)
"

sem_mediation <- sem(sem_mediation_model, data = data)

sem_multilevel_model <- "
    level: 1
    fw =~ y1 + y2 + y3
    fw ~ x1 + x2 + x3
    level: 2
    fb =~ y1 + y2 + y3
    fb ~ w1 + w2
"

sem_multilevel <- sem(
  sem_multilevel_model,
  data = Demo.twolevel, cluster = "cluster"
)

ex5_25 <- read.table("http://statmodel.com/usersguide/chap5/ex5.25.dat")
names(ex5_25) <- paste0("y", 1:12)

sem_esem_model <- '
    # efa block
    efa("efa1")*f1 +
    efa("efa1")*f2 =~ y1 + y2 + y3 + y4 + y5 + y6

    # cfa block
    f3 =~ y7 + y8 + y9
    f4 =~ y10 + y11 + y12

    # regressions
    f3 ~ f1 + f2
    f4 ~ f3
'
sem_esem <- sem(
  model = sem_esem_model,
  data = ex5_25,
  rotation = "geomin",
  information = "observed",
  rotation.args = list(
    rstarts = 30,
    row.weights = "none",
    algorithm = "gpa",
    std.ov = TRUE,
    geomin.epsilon = 0.0001
  )
)

statistics <- statistics |>
  add_stats(sem) |>
  add_stats(sem_mediation) |>
  add_stats(sem_multilevel) |>
  add_stats(sem_esem)

summary(sem, standardized = TRUE, fit.measures = TRUE)
summary(sem_mediation)
summary(sem_multilevel, standardized = TRUE, fit.measures = TRUE)
summary(
  sem_esem,
  standardized = TRUE,
  fit.measures = TRUE
)

# lavaan() ----------------------------------------------------------------

HS_model <- "
    visual  =~ x1 + x2 + x3
    textual =~ x4 + x5 + x6
    speed   =~ x7 + x8 + x9
"

lavaan <- lavaan(
  HS_model,
  data = HolzingerSwineford1939,
  auto.var = TRUE, auto.fix.first = TRUE, auto.cov.lv.x = TRUE
)

statistics <- add_stats(statistics, lavaan)

summary(lavaan, standardized = TRUE, fit.measures = TRUE)

# lavTestLRT() ------------------------------------------------------------

HS_model <- "
    visual  =~ x1 + x2 + x3
    textual =~ x4 + x5 + x6
    speed   =~ x7 + x8 + x9
"

fit_1 <- cfa(
  HS_model,
  data = HolzingerSwineford1939,
  group = "school"
)

fit_2 <- cfa(
  HS_model,
  data = HolzingerSwineford1939,
  group = "school",
  group.equal = "loadings"
)

fit_3 <- cfa(
  HS_model,
  data = HolzingerSwineford1939,
  group = "school",
  group.equal = c("intercepts", "loadings")
)

lrt <- lavTestLRT(fit_1, fit_2, fit_3)

statistics <- add_stats(statistics, lrt)

lrt

# growth() ----------------------------------------------------------------

model_growth <- "
  i =~ 1*t1 + 1*t2 + 1*t3 + 1*t4
  s =~ 0*t1 + 1*t2 + 2*t3 + 3*t4
"

growth <- growth(model_growth, data = Demo.growth)

statistics <- add_stats(statistics, growth)

summary(growth, fit.measures = TRUE, standardized = TRUE)

# tidy_stats_to_data_frame() ----------------------------------------------

df <- tidy_stats_to_data_frame(statistics)

# write_stats() -----------------------------------------------------------

write_test_stats(statistics, "tests/data/lavaan.json")

# Cleanup -----------------------------------------------------------------

rm(
  data, lrt, cfa, cfa_efa, cfa_groups, cfa_intercepts, efa_model, fit_1, fit_2,
  fit_3, growth, HS_model, HS_model_intercepts, lavaan, model_growth,
  sem, sem_esem, sem_esem_model, sem_mediation, sem_mediation_model,
  sem_model, sem_multilevel, sem_multilevel_model, statistics, df, ex5_25
)