Nothing
library(nlme)
skip_if_not_installed("scdhlm")
data(Thiemann2001, package = "scdhlm")
Thiemann2001 <- Thiemann2001[sample(nrow(Thiemann2001)),]
Thiemann2001_3level <- lme(fixed = outcome ~ treatment,
random = ~ 1 | case/series,
data = Thiemann2001,
control = lmeControl(tolerance = 10^-8))
Thiemann2001_CScorr <- lme(fixed = outcome ~ treatment,
random = ~ 1 | case,
correlation = corCompSymm(form = ~ 1 | case / series),
data = Thiemann2001,
control = lmeControl(tolerance = 10^-8))
# mod <- Thiemann2001_CScorr
# type <- "expected"
# invert <- TRUE
# sigma_scale <- TRUE
# R_list <- build_corr_mats(mod)
test_that("vcov matrices are equivalent for equivalent models.", {
expect_equal(fixef(Thiemann2001_3level), fixef(Thiemann2001_CScorr), tol = 10^-6)
vc_3level <- extract_varcomp(Thiemann2001_3level)
vc_CScorr <- extract_varcomp(Thiemann2001_CScorr)
expect_equal(vc_3level$Tau$case, vc_CScorr$Tau$case, tol = 10^-3)
expect_equal(as.numeric(vc_3level$Tau$series) + vc_3level$sigma_sq, vc_CScorr$sigma_sq, tol = 10^-4)
ICC_3level <- as.numeric(vc_3level$Tau$series / (vc_3level$Tau$series + vc_3level$sigma_sq))
expect_equal(ICC_3level, vc_CScorr$cor_params, tol = 10^-3)
vcov_3level_exp <- varcomp_vcov(Thiemann2001_3level)
vcov_CScorr_exp <- varcomp_vcov(Thiemann2001_CScorr)
expect_equal(vcov_3level_exp["Tau.case.var((Intercept))", "Tau.case.var((Intercept))"] /
vcov_CScorr_exp["Tau.case.var((Intercept))", "Tau.case.var((Intercept))"], 1, tol = 10^-3)
expect_equal(sum(vcov_3level_exp[c("Tau.series.var((Intercept))","sigma_sq"),c("Tau.series.var((Intercept))","sigma_sq")]) /
vcov_CScorr_exp["sigma_sq","sigma_sq"], 1, tol = 10^-3)
expect_equal(sum(vcov_3level_exp[c("Tau.series.var((Intercept))","sigma_sq"),"Tau.case.var((Intercept))"]) /
vcov_CScorr_exp["Tau.case.var((Intercept))","sigma_sq"], 1, tol = 10^-3)
})
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