1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
|
skip_on_cran()
skip_if_not_installed("lme4")
data("cbpp", package = "lme4")
set.seed(123)
model <- lme4::glmer(
cbind(incidence, size - incidence) ~ period + (1 | herd),
data = cbpp,
family = binomial(),
nAGQ = 0
)
params <- model_parameters(model, effects = "fixed")
test_that("model_parameters.glmer", {
expect_equal(params$SE, c(0.22758, 0.30329, 0.32351, 0.42445), tolerance = 1e-2)
})
test_that("print model_parameters", {
skip_if_not_installed("withr")
skip_if_not_installed("merDeriv")
withr::local_options(
list(
parameters_exponentiate = TRUE,
parameters_warning_exponentiate = TRUE
)
)
expect_snapshot(params)
suppressMessages({
mp <- model_parameters(model, effects = "all", exponentiate = TRUE)
})
expect_snapshot(mp)
set.seed(123)
model <- lme4::glmer(
cbind(incidence, size - incidence) ~ period + (1 | herd),
data = cbpp,
family = binomial(),
nAGQ = 2
)
mp <- model_parameters(model, effects = "all")
expect_snapshot(mp)
})
test_that("model_parameters.glmer ml1", {
params <- model_parameters(model, ci_method = "ml1", effects = "fixed")
expect_equal(params$SE, c(0.22758, 0.30329, 0.32351, 0.42445), tolerance = 1e-2)
expect_equal(params$df, c(54, 54, 54, 54), tolerance = 1e-2)
})
test_that("model_parameters.glmer betwithin", {
params <- model_parameters(model, ci_method = "betwithin", effects = "fixed")
expect_equal(params$SE, c(0.23009, 0.30433, 0.32476, 0.42632), tolerance = 1e-2)
expect_equal(params$df, c(822, 822, 822, 822), tolerance = 1e-2)
})
set.seed(123)
cbpp$time <- runif(nrow(cbpp), 1, 4)
model <- lme4::glmer(
cbind(incidence, size - incidence) ~ period + time + (1 + time | herd),
data = cbpp,
family = binomial(),
nAGQ = 0
)
test_that("model_parameters.glmer", {
params <- model_parameters(model, effects = "fixed")
expect_equal(params$SE, c(0.66539, 0.36178, 0.36223, 0.45528, 0.2379), tolerance = 1e-2)
})
test_that("model_parameters.glmer ml1", {
params <- model_parameters(model, ci_method = "ml1", effects = "fixed")
expect_equal(params$SE, c(0.66539, 0.36178, 0.36223, 0.45528, 0.2379), tolerance = 1e-2)
expect_equal(params$df, c(53, 53, 53, 53, 53), tolerance = 1e-2)
})
test_that("model_parameters.glmer betwithin", {
params <- model_parameters(model, ci_method = "betwithin", effects = "fixed")
expect_equal(params$SE, c(0.66539, 0.36178, 0.36223, 0.45528, 0.2379), tolerance = 1e-2)
expect_equal(params$df, c(821, 821, 821, 821, 9), tolerance = 1e-2)
})
|
