.runThisTest <- Sys.getenv("RunAllinsightTests") == "yes"
if (.runThisTest && requiet("robustlmm") && utils::packageVersion("robustlmm") >= "3.0.1" &&
requiet("lme4") && getRversion() >= "4.1.0") {
data(sleepstudy)
set.seed(123)
sleepstudy$mygrp <- sample(1:5, size = 180, replace = TRUE)
sleepstudy$mysubgrp <- NA
for (i in 1:5) {
filter_group <- sleepstudy$mygrp == i
sleepstudy$mysubgrp[filter_group] <-
sample(1:30,
size = sum(filter_group),
replace = TRUE
)
}
dat <<- sleepstudy
m1 <- rlmer(
Reaction ~ Days + (Days | Subject),
data = dat,
rho.sigma.e = psi2propII(smoothPsi, k = 2.28),
rho.sigma.b = chgDefaults(smoothPsi, k = 5.11, s = 10)
)
m2 <- rlmer(
Reaction ~ Days + (1 | mygrp / mysubgrp) + (1 | Subject),
data = dat,
rho.sigma.e = psi2propII(smoothPsi, k = 2.28),
rho.sigma.b = chgDefaults(smoothPsi, k = 5.11, s = 10)
)
test_that("model_info", {
expect_true(model_info(m1)$is_linear)
expect_true(model_info(m2)$is_linear)
})
test_that("find_predictors", {
expect_identical(
find_predictors(m1, effects = "all"),
list(conditional = "Days", random = "Subject")
)
expect_identical(
find_predictors(m1, effects = "all", flatten = TRUE),
c("Days", "Subject")
)
expect_identical(
find_predictors(m1, effects = "fixed"),
list(conditional = "Days")
)
expect_identical(
find_predictors(m1, effects = "fixed", flatten = TRUE),
"Days"
)
expect_identical(
find_predictors(m1, effects = "random"),
list(random = "Subject")
)
expect_identical(
find_predictors(m1, effects = "random", flatten = TRUE),
"Subject"
)
expect_identical(
find_predictors(m2, effects = "all"),
list(
conditional = "Days",
random = c("mysubgrp", "mygrp", "Subject")
)
)
expect_identical(
find_predictors(m2, effects = "all", flatten = TRUE),
c("Days", "mysubgrp", "mygrp", "Subject")
)
expect_identical(
find_predictors(m2, effects = "fixed"),
list(conditional = "Days")
)
expect_identical(find_predictors(m2, effects = "random"), list(random = c("mysubgrp", "mygrp", "Subject")))
expect_null(find_predictors(m2, effects = "all", component = "zi"))
expect_null(find_predictors(m2, effects = "fixed", component = "zi"))
expect_null(find_predictors(m2, effects = "random", component = "zi"))
})
test_that("find_random", {
expect_identical(find_random(m1), list(random = "Subject"))
expect_identical(find_random(m1, flatten = TRUE), "Subject")
expect_identical(find_random(m2), list(random = c(
"mysubgrp:mygrp", "mygrp", "Subject"
)))
expect_identical(find_random(m2, split_nested = TRUE), list(random = c("mysubgrp", "mygrp", "Subject")))
expect_identical(
find_random(m2, flatten = TRUE),
c("mysubgrp:mygrp", "mygrp", "Subject")
)
expect_identical(
find_random(m2, split_nested = TRUE, flatten = TRUE),
c("mysubgrp", "mygrp", "Subject")
)
})
test_that("find_response", {
expect_identical(find_response(m1), "Reaction")
expect_identical(find_response(m2), "Reaction")
})
test_that("get_response", {
expect_identical(get_response(m1), sleepstudy$Reaction)
})
test_that("link_inverse", {
expect_identical(link_inverse(m1)(0.2), 0.2)
expect_identical(link_inverse(m2)(0.2), 0.2)
})
test_that("get_data", {
expect_identical(colnames(get_data(m1)), c("Reaction", "Days", "Subject"))
expect_identical(colnames(get_data(m1, effects = "all")), c("Reaction", "Days", "Subject"))
expect_identical(colnames(get_data(m1, effects = "random")), "Subject")
expect_identical(
colnames(get_data(m2)),
c("Reaction", "Days", "mysubgrp", "mygrp", "Subject")
)
expect_identical(
colnames(get_data(m2, effects = "all")),
c("Reaction", "Days", "mysubgrp", "mygrp", "Subject")
)
expect_identical(colnames(get_data(m2, effects = "random")), c("mysubgrp", "mygrp", "Subject"))
})
test_that("find_formula", {
expect_length(find_formula(m1), 2)
expect_length(find_formula(m2), 2)
expect_equal(
find_formula(m1, component = "conditional"),
list(
conditional = as.formula("Reaction ~ Days"),
random = as.formula("~Days | Subject")
),
ignore_attr = TRUE
)
expect_equal(
find_formula(m2, component = "conditional"),
list(
conditional = as.formula("Reaction ~ Days"),
random = list(
as.formula("~1 | mysubgrp:mygrp"),
as.formula("~1 | mygrp"),
as.formula("~1 | Subject")
)
),
ignore_attr = TRUE
)
})
test_that("find_terms", {
expect_identical(
find_terms(m1),
list(
response = "Reaction",
conditional = "Days",
random = c("Days", "Subject")
)
)
expect_identical(
find_terms(m1, flatten = TRUE),
c("Reaction", "Days", "Subject")
)
expect_identical(
find_terms(m2),
list(
response = "Reaction",
conditional = "Days",
random = c("mysubgrp", "mygrp", "Subject")
)
)
expect_identical(
find_terms(m2, flatten = TRUE),
c("Reaction", "Days", "mysubgrp", "mygrp", "Subject")
)
})
test_that("find_variables", {
expect_identical(
find_variables(m1),
list(
response = "Reaction",
conditional = "Days",
random = "Subject"
)
)
})
test_that("get_response", {
expect_identical(get_response(m1), sleepstudy$Reaction)
})
test_that("get_predictors", {
expect_identical(colnames(get_predictors(m1)), "Days")
expect_identical(colnames(get_predictors(m2)), "Days")
})
test_that("get_random", {
expect_identical(colnames(get_random(m1)), "Subject")
expect_identical(
colnames(get_random(m2)),
c("mysubgrp", "mygrp", "Subject")
)
})
test_that("clean_names", {
expect_identical(clean_names(m1), c("Reaction", "Days", "Subject"))
expect_identical(
clean_names(m2),
c("Reaction", "Days", "mysubgrp", "mygrp", "Subject")
)
})
test_that("linkfun", {
expect_false(is.null(link_function(m1)))
expect_false(is.null(link_function(m2)))
})
test_that("find_parameters", {
expect_identical(
find_parameters(m1),
list(
conditional = c("(Intercept)", "Days"),
random = list(Subject = c("(Intercept)", "Days"))
)
)
expect_identical(nrow(get_parameters(m1)), 2L)
expect_identical(get_parameters(m1)$Parameter, c("(Intercept)", "Days"))
expect_identical(
find_parameters(m2),
list(
conditional = c("(Intercept)", "Days"),
random = list(
`mysubgrp:mygrp` = "(Intercept)",
Subject = "(Intercept)",
mygrp = "(Intercept)"
)
)
)
expect_identical(nrow(get_parameters(m2)), 2L)
expect_identical(get_parameters(m2)$Parameter, c("(Intercept)", "Days"))
expect_named(
get_parameters(m2, effects = "random"),
c("mysubgrp:mygrp", "Subject", "mygrp")
)
})
test_that("is_multivariate", {
expect_false(is_multivariate(m1))
expect_false(is_multivariate(m2))
})
test_that("get_variance", {
skip_on_cran()
expect_equal(
get_variance(m1),
list(
var.fixed = 944.68388146469, var.random = 1911.1173962696,
var.residual = 399.07090932584, var.distribution = 399.07090932584,
var.dispersion = 0, var.intercept = c(Subject = 782.758817383975),
var.slope = c(Subject.Days = 41.8070895953001),
cor.slope_intercept = c(Subject = -0.0387835013909591)
),
tolerance = 1e-3
)
expect_equal(
get_variance(m2),
list(
var.fixed = 914.841369705921, var.random = 1406.78220075798,
var.residual = 809.318117542254, var.distribution = 809.318117542254,
var.dispersion = 0,
var.intercept = c(`mysubgrp:mygrp` = 0, Subject = 1390.66848960835, mygrp = 16.1137111496379)
),
tolerance = 1e-3
)
})
test_that("find_algorithm", {
expect_identical(
find_algorithm(m1),
list(algorithm = "REML", optimizer = "rlmer.fit.DAS.nondiag")
)
})
test_that("find_random_slopes", {
expect_identical(find_random_slopes(m1), list(random = "Days"))
expect_null(find_random_slopes(m2))
})
test_that("find_statistic", {
expect_identical(find_statistic(m1), "t-statistic")
expect_identical(find_statistic(m2), "t-statistic")
})
}
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