tests/testthat/test-format_model_parameters2.R
In easystats/parameters: Processing of Model Parameters
test_that("format_model_parameters", {
skip_on_cran()
skip_if_not_installed("lme4")
withr::with_options(
list(parameters_interaction = "*"),
{
d <- structure(list(
Drought = structure(c(
1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L
), levels = c("no", "yes"), class = "factor"), Tree.ID = structure(c(
1L,
1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L,
9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L,
16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L,
22L, 23L, 23L, 24L, 24L, 25L, 25L, 26L, 26L, 27L, 27L, 28L, 28L,
29L, 29L, 30L, 30L, 31L, 31L, 32L, 32L, 33L, 33L, 34L, 34L, 35L,
35L, 36L, 36L, 37L, 37L, 38L, 38L, 39L, 39L, 40L, 40L, 41L, 41L,
42L, 42L, 43L, 43L, 44L, 44L, 45L, 45L, 46L, 46L, 47L, 47L, 48L,
48L, 1L, 1L, 2L, 2L, 3L, 3L, 10L, 10L, 11L, 11L, 12L, 12L, 13L,
13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L,
21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L, 26L, 26L, 27L,
27L, 28L, 28L, 29L, 29L, 30L, 30L, 31L, 31L, 32L, 32L, 33L, 33L,
37L, 37L, 38L, 38L, 39L, 39L, 43L, 43L, 44L, 44L, 45L, 45L, 46L,
46L, 47L, 47L, 48L, 48L
), levels = c(
"102_6", "102_7", "102_8",
"105_1", "105_2", "105_4", "111_7", "111_8", "111_9", "113_2",
"113_4", "113_5", "114_7", "114_8", "114_9", "116_6", "116_7",
"116_9", "122_3", "122_4", "122_5", "132_3", "132_4", "132_5",
"242_2", "242_4", "242_5", "243_1", "243_2", "243_4", "245_1",
"245_2", "245_5", "246_1", "246_2", "246_3", "251_10", "251_8",
"251_9", "253_7", "253_8", "253_9", "254_6", "254_7", "254_8",
"267_10", "267_6", "267_8"
), class = "factor"), Stratum = structure(c(
1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L
), levels = c("lower", "upper"), class = "factor"),
Year = structure(c(
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L
), levels = c("1", "2"), class = "factor"),
Treatment = c(
"Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control"
), branch_miner_No = c(
41L, 25L, 47L, 49L, 50L, 49L, 49L,
50L, 49L, 50L, 48L, 47L, 49L, 49L, 50L, 49L, 49L, 43L, 41L,
45L, 49L, 37L, 50L, 49L, 50L, 50L, 50L, 49L, 45L, 44L, 49L,
48L, 50L, 48L, 50L, 49L, 44L, 38L, 50L, 34L, 38L, 28L, 47L,
39L, 50L, 49L, 47L, 50L, 42L, 19L, 47L, 46L, 50L, 50L, 49L,
46L, 49L, 50L, 40L, 45L, 50L, 50L, 41L, 44L, 50L, 50L, 50L,
46L, 50L, 48L, 50L, 50L, 48L, 38L, 49L, 42L, 39L, 31L, 49L,
33L, 38L, 49L, 48L, 48L, 49L, 49L, 48L, 50L, 45L, 37L, 28L,
25L, 45L, 45L, 39L, 35L, 38L, 43L, 46L, 34L, 49L, 33L, 40L,
47L, 47L, 39L, 46L, 31L, 47L, 40L, 47L, 45L, 47L, 42L, 48L,
47L, 39L, 25L, 37L, 46L, 38L, 42L, 44L, 48L, 47L, 46L, 48L,
49L, 38L, 44L, 39L, 31L, 41L, 42L, 44L, 18L, 23L, 48L, 26L,
26L, 28L, 32L, 47L, 46L, 49L, 33L, 47L, 38L, 35L, 17L, 39L,
30L, 44L, 42L, 47L, 36L, 8L, 33L, 32L, 37L, 33L, 38L, 32L,
45L, 47L, 41L
), branch_miner_Yes = c(
9L, 25L, 3L, 1L, 0L,
1L, 1L, 0L, 1L, 0L, 2L, 3L, 1L, 1L, 0L, 1L, 1L, 7L, 9L, 5L,
1L, 13L, 0L, 1L, 0L, 0L, 0L, 1L, 5L, 6L, 1L, 2L, 0L, 2L,
0L, 1L, 6L, 12L, 0L, 16L, 12L, 22L, 3L, 11L, 0L, 1L, 3L,
0L, 8L, 31L, 3L, 4L, 0L, 0L, 1L, 4L, 1L, 0L, 10L, 5L, 0L,
0L, 9L, 6L, 0L, 0L, 0L, 4L, 0L, 2L, 0L, 0L, 2L, 12L, 1L,
8L, 11L, 19L, 1L, 17L, 12L, 1L, 2L, 2L, 1L, 1L, 2L, 0L, 5L,
13L, 22L, 25L, 5L, 5L, 11L, 15L, 12L, 7L, 4L, 16L, 1L, 17L,
10L, 3L, 3L, 11L, 4L, 19L, 3L, 10L, 3L, 5L, 3L, 8L, 2L, 3L,
11L, 25L, 13L, 4L, 12L, 8L, 6L, 2L, 3L, 4L, 2L, 1L, 12L,
6L, 11L, 19L, 9L, 8L, 6L, 32L, 27L, 2L, 24L, 24L, 22L, 18L,
3L, 4L, 1L, 17L, 3L, 12L, 15L, 33L, 11L, 20L, 6L, 8L, 3L,
14L, 42L, 17L, 18L, 13L, 17L, 12L, 18L, 5L, 3L, 9L
)
), row.names = c(
NA,
-166L
), class = "data.frame")
d$Year <- factor(d$Year)
d$Drought <- as.factor(d$Drought)
d$Stratum <- as.factor(d$Stratum)
levels(d$Stratum) <- list(lower = "shade", upper = "sun")
d$Tree.ID <- as.factor(d$Tree.ID)
mod <- lme4::glmer(
cbind(branch_miner_Yes, branch_miner_No) ~ Drought * Stratum + Drought * Year + Year * Stratum + (1 | Tree.ID),
data = d,
family = binomial(),
na.action = na.exclude
)
out <- model_parameters(mod, component = "conditional")
expect_identical(
attributes(out)$pretty_names,
c(
`(Intercept)` = "(Intercept)", Droughtyes = "Drought [yes]",
Stratumupper = "Stratum [upper]", Year2 = "Year [2]",
`Droughtyes:Stratumupper` = "Drought [yes] * Stratum [upper]",
`Droughtyes:Year2` = "Drought [yes] * Year [2]",
`Stratumupper:Year2` = "Stratum [upper] * Year [2]"
)
)
}
)
})
easystats/parameters documentation built on April 27, 2024, 7:28 p.m.
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test_that("format_model_parameters", {
skip_on_cran()
skip_if_not_installed("lme4")
withr::with_options(
list(parameters_interaction = "*"),
{
d <- structure(list(
Drought = structure(c(
1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L
), levels = c("no", "yes"), class = "factor"), Tree.ID = structure(c(
1L,
1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L,
9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L,
16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L,
22L, 23L, 23L, 24L, 24L, 25L, 25L, 26L, 26L, 27L, 27L, 28L, 28L,
29L, 29L, 30L, 30L, 31L, 31L, 32L, 32L, 33L, 33L, 34L, 34L, 35L,
35L, 36L, 36L, 37L, 37L, 38L, 38L, 39L, 39L, 40L, 40L, 41L, 41L,
42L, 42L, 43L, 43L, 44L, 44L, 45L, 45L, 46L, 46L, 47L, 47L, 48L,
48L, 1L, 1L, 2L, 2L, 3L, 3L, 10L, 10L, 11L, 11L, 12L, 12L, 13L,
13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L,
21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L, 26L, 26L, 27L,
27L, 28L, 28L, 29L, 29L, 30L, 30L, 31L, 31L, 32L, 32L, 33L, 33L,
37L, 37L, 38L, 38L, 39L, 39L, 43L, 43L, 44L, 44L, 45L, 45L, 46L,
46L, 47L, 47L, 48L, 48L
), levels = c(
"102_6", "102_7", "102_8",
"105_1", "105_2", "105_4", "111_7", "111_8", "111_9", "113_2",
"113_4", "113_5", "114_7", "114_8", "114_9", "116_6", "116_7",
"116_9", "122_3", "122_4", "122_5", "132_3", "132_4", "132_5",
"242_2", "242_4", "242_5", "243_1", "243_2", "243_4", "245_1",
"245_2", "245_5", "246_1", "246_2", "246_3", "251_10", "251_8",
"251_9", "253_7", "253_8", "253_9", "254_6", "254_7", "254_8",
"267_10", "267_6", "267_8"
), class = "factor"), Stratum = structure(c(
1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L
), levels = c("lower", "upper"), class = "factor"),
Year = structure(c(
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L
), levels = c("1", "2"), class = "factor"),
Treatment = c(
"Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Drought", "Drought", "Drought", "Drought", "Drought", "Drought",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control",
"Control", "Control", "Control", "Control", "Control", "Control"
), branch_miner_No = c(
41L, 25L, 47L, 49L, 50L, 49L, 49L,
50L, 49L, 50L, 48L, 47L, 49L, 49L, 50L, 49L, 49L, 43L, 41L,
45L, 49L, 37L, 50L, 49L, 50L, 50L, 50L, 49L, 45L, 44L, 49L,
48L, 50L, 48L, 50L, 49L, 44L, 38L, 50L, 34L, 38L, 28L, 47L,
39L, 50L, 49L, 47L, 50L, 42L, 19L, 47L, 46L, 50L, 50L, 49L,
46L, 49L, 50L, 40L, 45L, 50L, 50L, 41L, 44L, 50L, 50L, 50L,
46L, 50L, 48L, 50L, 50L, 48L, 38L, 49L, 42L, 39L, 31L, 49L,
33L, 38L, 49L, 48L, 48L, 49L, 49L, 48L, 50L, 45L, 37L, 28L,
25L, 45L, 45L, 39L, 35L, 38L, 43L, 46L, 34L, 49L, 33L, 40L,
47L, 47L, 39L, 46L, 31L, 47L, 40L, 47L, 45L, 47L, 42L, 48L,
47L, 39L, 25L, 37L, 46L, 38L, 42L, 44L, 48L, 47L, 46L, 48L,
49L, 38L, 44L, 39L, 31L, 41L, 42L, 44L, 18L, 23L, 48L, 26L,
26L, 28L, 32L, 47L, 46L, 49L, 33L, 47L, 38L, 35L, 17L, 39L,
30L, 44L, 42L, 47L, 36L, 8L, 33L, 32L, 37L, 33L, 38L, 32L,
45L, 47L, 41L
), branch_miner_Yes = c(
9L, 25L, 3L, 1L, 0L,
1L, 1L, 0L, 1L, 0L, 2L, 3L, 1L, 1L, 0L, 1L, 1L, 7L, 9L, 5L,
1L, 13L, 0L, 1L, 0L, 0L, 0L, 1L, 5L, 6L, 1L, 2L, 0L, 2L,
0L, 1L, 6L, 12L, 0L, 16L, 12L, 22L, 3L, 11L, 0L, 1L, 3L,
0L, 8L, 31L, 3L, 4L, 0L, 0L, 1L, 4L, 1L, 0L, 10L, 5L, 0L,
0L, 9L, 6L, 0L, 0L, 0L, 4L, 0L, 2L, 0L, 0L, 2L, 12L, 1L,
8L, 11L, 19L, 1L, 17L, 12L, 1L, 2L, 2L, 1L, 1L, 2L, 0L, 5L,
13L, 22L, 25L, 5L, 5L, 11L, 15L, 12L, 7L, 4L, 16L, 1L, 17L,
10L, 3L, 3L, 11L, 4L, 19L, 3L, 10L, 3L, 5L, 3L, 8L, 2L, 3L,
11L, 25L, 13L, 4L, 12L, 8L, 6L, 2L, 3L, 4L, 2L, 1L, 12L,
6L, 11L, 19L, 9L, 8L, 6L, 32L, 27L, 2L, 24L, 24L, 22L, 18L,
3L, 4L, 1L, 17L, 3L, 12L, 15L, 33L, 11L, 20L, 6L, 8L, 3L,
14L, 42L, 17L, 18L, 13L, 17L, 12L, 18L, 5L, 3L, 9L
)
), row.names = c(
NA,
-166L
), class = "data.frame")
d$Year <- factor(d$Year)
d$Drought <- as.factor(d$Drought)
d$Stratum <- as.factor(d$Stratum)
levels(d$Stratum) <- list(lower = "shade", upper = "sun")
d$Tree.ID <- as.factor(d$Tree.ID)
mod <- lme4::glmer(
cbind(branch_miner_Yes, branch_miner_No) ~ Drought * Stratum + Drought * Year + Year * Stratum + (1 | Tree.ID),
data = d,
family = binomial(),
na.action = na.exclude
)
out <- model_parameters(mod, component = "conditional")
expect_identical(
attributes(out)$pretty_names,
c(
`(Intercept)` = "(Intercept)", Droughtyes = "Drought [yes]",
Stratumupper = "Stratum [upper]", Year2 = "Year [2]",
`Droughtyes:Stratumupper` = "Drought [yes] * Stratum [upper]",
`Droughtyes:Year2` = "Drought [yes] * Year [2]",
`Stratumupper:Year2` = "Stratum [upper] * Year [2]"
)
)
}
)
})
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