tests/testthat/test-occumb-set_modargs.R
In fukayak/occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding
### Test data ------------------------------------------------------------------
I <- 2
J <- 3
K <- 4
cov1 <- rnorm(I)
cov2 <- factor(1:I)
cov3 <- rnorm(J)
cov4 <- factor(1:J)
cov5 <- matrix(rnorm(J * K), nrow = J)
cov6 <- matrix(rep(factor(1:K), each = J), nrow = J)
#cov2 <- as.character(1:I)
#cov4 <- as.character(factor(1:J))
#cov6 <- matrix(rep(as.character(1:K), each = J), nrow = J)
data <- occumbData(y = array(1, dim = c(I, J, K)),
spec_cov = list(cov1 = cov1, cov2 = cov2),
site_cov = list(cov3 = cov3, cov4 = cov4),
repl_cov = list(cov5 = cov5, cov6 = cov6))
### Tests for formula_phi_shared -----------------------------------------------
test_that("Procedures for phi_shared correct", {
## Output
# spec_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "i")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
}
colnames(ans_cov) <- "cov1"
expect_equal(result$cov_phi_shared, ans_cov)
# spec_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov2, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "i")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov22")
expect_equal(result$cov_phi_shared, ans_cov)
# spec_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov1 * cov2, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "i")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 3)
ans_cov <- array(dim = c(I, 3))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
ans_cov[i, 2] <- as.numeric((cov2[i] == 2))
ans_cov[i, 3] <- cov1[i] * as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov1", "cov22", "cov1:cov22")
expect_equal(result$cov_phi_shared, ans_cov)
# site_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov3, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 1)
ans_cov <- array(dim = c(I, J, 1))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
}
}
dimnames(ans_cov)[[3]] <- "cov3"
expect_equal(result$cov_phi_shared, ans_cov)
# site_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov4, ~ 1, ~ 1, data = data)
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 2)
ans_cov <- array(dim = c(I, J, 2))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov42", "cov43")
expect_equal(result$cov_phi_shared, ans_cov)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov3 * cov4, ~ 1, ~ 1, data = data)
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov3[j] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_phi_shared, ans_cov)
# spec_cov * site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov1 * cov4, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov1[i]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov1[i] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov1", "cov42", "cov43",
"cov1:cov42", "cov1:cov43")
expect_equal(result$cov_phi_shared, ans_cov)
# repl_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov5, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 1)
ans_cov <- array(dim = c(I, J, K, 1))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- "cov5"
expect_equal(result$cov_phi_shared, ans_cov)
# repl_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov6, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 3)
ans_cov <- array(dim = c(I, J, K, 3))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 2] <- as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 3] <- as.numeric(cov6[j, k] == 4)
}
}
}
dimnames(ans_cov)[[4]] <- c("cov62", "cov63", "cov64")
expect_equal(result$cov_phi_shared, ans_cov)
# repl_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov5 * cov6, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 7)
ans_cov <- array(dim = c(I, J, K, 7))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov5[j, k]
ans_cov[i, j, k, 2] <- as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 3] <- as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 4] <- as.numeric(cov6[j, k] == 4)
ans_cov[i, j, k, 5] <- cov5[j, k] * as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 6] <- cov5[j, k] * as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 7] <- cov5[j, k] * as.numeric(cov6[j, k] == 4)
}
}
}
dimnames(ans_cov)[[4]] <- c("cov5", "cov62", "cov63", "cov64",
"cov5:cov62", "cov5:cov63", "cov5:cov64")
expect_equal(result$cov_phi_shared, ans_cov)
# spec_cov * site_cov * repl_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov2 * cov3 * cov5, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 7)
ans_cov <- array(dim = c(I, J, K, 7))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- as.numeric(cov2[i] == 2)
ans_cov[i, j, k, 2] <- cov3[j]
ans_cov[i, j, k, 3] <- cov5[j, k]
ans_cov[i, j, k, 4] <- as.numeric(cov2[i] == 2) * cov3[j]
ans_cov[i, j, k, 5] <- as.numeric(cov2[i] == 2) * cov5[j, k]
ans_cov[i, j, k, 6] <- cov3[j] * cov5[j, k]
ans_cov[i, j, k, 7] <- as.numeric(cov2[i] == 2) * cov3[j] * cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- c("cov22", "cov3", "cov5",
"cov22:cov3", "cov22:cov5", "cov3:cov5",
"cov22:cov3:cov5")
expect_equal(result$cov_phi_shared, ans_cov)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov1 * cov4 * cov5, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 11)
ans_cov <- array(dim = c(I, J, K, 11))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov1[i]
ans_cov[i, j, k, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, k, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, k, 4] <- cov5[j, k]
ans_cov[i, j, k, 5] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, k, 6] <- cov1[i] * as.numeric(cov4[j] == 3)
ans_cov[i, j, k, 7] <- cov1[i] * cov5[j, k]
ans_cov[i, j, k, 8] <- as.numeric(cov4[j] == 2) * cov5[j, k]
ans_cov[i, j, k, 9] <- as.numeric(cov4[j] == 3) * cov5[j, k]
ans_cov[i, j, k, 10] <- cov1[i] * as.numeric(cov4[j] == 2) * cov5[j, k]
ans_cov[i, j, k, 11] <- cov1[i] * as.numeric(cov4[j] == 3) * cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- c("cov1", "cov42", "cov43", "cov5",
"cov1:cov42", "cov1:cov43",
"cov1:cov5",
"cov42:cov5", "cov43:cov5",
"cov1:cov42:cov5", "cov1:cov43:cov5")
expect_equal(result$cov_phi_shared, ans_cov)
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ ., ~ 1, ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_phi_shared\\)")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ xxx, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi_shared: xxx
Make sure they are included in either 'spec_cov', 'site_cov', or 'repl_cov'.")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ xxx + yyy, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi_shared: xxx, yyy
Make sure they are included in either 'spec_cov', 'site_cov', or 'repl_cov'.")
})
### Tests for formula_theta_shared ---------------------------------------------
test_that("Procedures for theta_shared correct", {
## Output
# spec_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov1, ~ 1, data = data)
expect_equal(result$theta, "i")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
}
colnames(ans_cov) <- "cov1"
expect_equal(result$cov_theta_shared, ans_cov)
# spec_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov2, ~ 1, data = data)
expect_equal(result$theta, "i")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov22")
expect_equal(result$cov_theta_shared, ans_cov)
# spec_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov2, ~ 1, data = data)
expect_equal(result$theta, "i")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 3)
ans_cov <- array(dim = c(I, 3))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
ans_cov[i, 2] <- as.numeric((cov2[i] == 2))
ans_cov[i, 3] <- cov1[i] * as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov1", "cov22", "cov1:cov22")
expect_equal(result$cov_theta_shared, ans_cov)
# site_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov3, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 1)
ans_cov <- array(dim = c(I, J, 1))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
}
}
dimnames(ans_cov)[[3]] <- "cov3"
expect_equal(result$cov_theta_shared, ans_cov)
# site_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov4, ~ 1, data = data)
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 2)
ans_cov <- array(dim = c(I, J, 2))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov42", "cov43")
expect_equal(result$cov_theta_shared, ans_cov)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov3 * cov4, ~ 1, data = data)
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov3[j] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_theta_shared, ans_cov)
# spec_cov * site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov4, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov1[i]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov1[i] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov1", "cov42", "cov43",
"cov1:cov42", "cov1:cov43")
expect_equal(result$cov_theta_shared, ans_cov)
# repl_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov5, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 1)
ans_cov <- array(dim = c(I, J, K, 1))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- "cov5"
expect_equal(result$cov_theta_shared, ans_cov)
# repl_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov6, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 3)
ans_cov <- array(dim = c(I, J, K, 3))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 2] <- as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 3] <- as.numeric(cov6[j, k] == 4)
}
}
}
dimnames(ans_cov)[[4]] <- c("cov62", "cov63", "cov64")
expect_equal(result$cov_theta_shared, ans_cov)
# repl_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov5 * cov6, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 7)
ans_cov <- array(dim = c(I, J, K, 7))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov5[j, k]
ans_cov[i, j, k, 2] <- as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 3] <- as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 4] <- as.numeric(cov6[j, k] == 4)
ans_cov[i, j, k, 5] <- cov5[j, k] * as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 6] <- cov5[j, k] * as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 7] <- cov5[j, k] * as.numeric(cov6[j, k] == 4)
}
}
}
dimnames(ans_cov)[[4]] <- c("cov5", "cov62", "cov63", "cov64",
"cov5:cov62", "cov5:cov63", "cov5:cov64")
expect_equal(result$cov_theta_shared, ans_cov)
# spec_cov * site_cov * repl_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov2 * cov3 * cov5, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 7)
ans_cov <- array(dim = c(I, J, K, 7))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- as.numeric(cov2[i] == 2)
ans_cov[i, j, k, 2] <- cov3[j]
ans_cov[i, j, k, 3] <- cov5[j, k]
ans_cov[i, j, k, 4] <- as.numeric(cov2[i] == 2) * cov3[j]
ans_cov[i, j, k, 5] <- as.numeric(cov2[i] == 2) * cov5[j, k]
ans_cov[i, j, k, 6] <- cov3[j] * cov5[j, k]
ans_cov[i, j, k, 7] <- as.numeric(cov2[i] == 2) * cov3[j] * cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- c("cov22", "cov3", "cov5",
"cov22:cov3", "cov22:cov5", "cov3:cov5",
"cov22:cov3:cov5")
expect_equal(result$cov_theta_shared, ans_cov)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov4 * cov5, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 11)
ans_cov <- array(dim = c(I, J, K, 11))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov1[i]
ans_cov[i, j, k, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, k, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, k, 4] <- cov5[j, k]
ans_cov[i, j, k, 5] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, k, 6] <- cov1[i] * as.numeric(cov4[j] == 3)
ans_cov[i, j, k, 7] <- cov1[i] * cov5[j, k]
ans_cov[i, j, k, 8] <- as.numeric(cov4[j] == 2) * cov5[j, k]
ans_cov[i, j, k, 9] <- as.numeric(cov4[j] == 3) * cov5[j, k]
ans_cov[i, j, k, 10] <- cov1[i] * as.numeric(cov4[j] == 2) * cov5[j, k]
ans_cov[i, j, k, 11] <- cov1[i] * as.numeric(cov4[j] == 3) * cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- c("cov1", "cov42", "cov43", "cov5",
"cov1:cov42", "cov1:cov43",
"cov1:cov5",
"cov42:cov5", "cov43:cov5",
"cov1:cov42:cov5", "cov1:cov43:cov5")
expect_equal(result$cov_theta_shared, ans_cov)
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ ., ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_theta_shared\\)")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ xxx, ~ 1, data = data),
"Unexpected terms in formula_theta_shared: xxx
Make sure they are included in either 'spec_cov', 'site_cov', or 'repl_cov'.")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ xxx + yyy, ~ 1, data = data),
"Unexpected terms in formula_theta_shared: xxx, yyy
Make sure they are included in either 'spec_cov', 'site_cov', or 'repl_cov'.")
})
### Tests for formula_psi_shared -----------------------------------------------
test_that("Procedures for psi_shared correct", {
## Output
# spec_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov1, data = data)
expect_equal(result$psi, "i")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
}
colnames(ans_cov) <- "cov1"
expect_equal(result$cov_psi_shared, ans_cov)
# spec_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov2, data = data)
expect_equal(result$psi, "i")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov22")
expect_equal(result$cov_psi_shared, ans_cov)
# spec_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov2, data = data)
expect_equal(result$psi, "i")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 3)
ans_cov <- array(dim = c(I, 3))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
ans_cov[i, 2] <- as.numeric((cov2[i] == 2))
ans_cov[i, 3] <- cov1[i] * as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov1", "cov22", "cov1:cov22")
expect_equal(result$cov_psi_shared, ans_cov)
# site_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov3, data = data)
expect_equal(result$psi, "ij")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 1)
ans_cov <- array(dim = c(I, J, 1))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
}
}
dimnames(ans_cov)[[3]] <- "cov3"
expect_equal(result$cov_psi_shared, ans_cov)
# site_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov4, data = data)
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 2)
ans_cov <- array(dim = c(I, J, 2))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov42", "cov43")
expect_equal(result$cov_psi_shared, ans_cov)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov3 * cov4, data = data)
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov3[j] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_psi_shared, ans_cov)
# spec_cov * site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov4, data = data)
expect_equal(result$psi, "ij")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov1[i]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov1[i] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov1", "cov42", "cov43",
"cov1:cov42", "cov1:cov43")
expect_equal(result$cov_psi_shared, ans_cov)
# repl_cov (not allowed)
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov5, data = data),
"Unexpected terms in formula_psi_shared: cov5
Make sure they are included in either 'spec_cov' or 'site_cov'.")
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ ., data = data),
"'.' cannot be used to specify covariates \\(formula_psi_shared\\)")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ xxx, data = data),
"Unexpected terms in formula_psi_shared: xxx
Make sure they are included in either 'spec_cov' or 'site_cov'.")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ xxx + yyy, data = data),
"Unexpected terms in formula_psi_shared: xxx, yyy
Make sure they are included in either 'spec_cov' or 'site_cov'.")
})
### Tests for formula_phi ------------------------------------------------------
test_that("Arguments are correct for the null model", {
## Output
# null model
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "i")
expect_equal(result$M, 3)
expect_equal(result$cov_phi, 1)
expect_equal(result$m_phi, 1)
})
test_that("Errors are correct for the spec_cov in phi", {
# spec_cov (not allowed)
expect_error(set_modargs(~ cov1, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi: cov1
Make sure they are included in either 'site_cov' or 'repl_cov'.")
})
test_that("Procedures for phi correct", {
# site_cov (continuous)
result <- set_modargs(~ cov3, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, 2))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
}
colnames(ans_cov) <- c("(Intercept)", "cov3")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:2)
# site_cov (factor)
result <- set_modargs(~ cov4, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_equal(result$M, 5)
ans_cov <- array(dim = c(J, 3))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- as.numeric((cov4[j] == 2))
ans_cov[j, 3] <- as.numeric((cov4[j] == 3))
}
colnames(ans_cov) <- c("(Intercept)", "cov42", "cov43")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:3)
# site_cov (interaction)
result <- set_modargs(~ cov3 * cov4, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_equal(result$M, 8)
ans_cov <- array(dim = c(J, 6))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
ans_cov[j, 3] <- as.numeric(cov4[j] == 2)
ans_cov[j, 4] <- as.numeric(cov4[j] == 3)
ans_cov[j, 5] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[j, 6] <- cov3[j] * as.numeric(cov4[j] == 3)
}
colnames(ans_cov) <- c("(Intercept)", "cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:6)
# repl_cov (continuous)
result <- set_modargs(~ cov5, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, K, 2))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov5[j, k]
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov5")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:2)
# repl_cov (factor)
result <- set_modargs(~ cov6, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_equal(result$M, 6)
ans_cov <- array(dim = c(J, K, 4))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- as.numeric((cov6[j, k] == 2))
ans_cov[j, k, 3] <- as.numeric((cov6[j, k] == 3))
ans_cov[j, k, 4] <- as.numeric((cov6[j, k] == 4))
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov62", "cov63", "cov64")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:4)
# repl_cov (interaction)
result <- set_modargs(~ cov5 * cov6, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_equal(result$M, 10)
ans_cov <- array(dim = c(J, K, 8))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov5[j, k]
ans_cov[j, k, 3] <- as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 4] <- as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 5] <- as.numeric(cov6[j, k] == 4)
ans_cov[j, k, 6] <- cov5[j, k] * as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 7] <- cov5[j, k] * as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 8] <- cov5[j, k] * as.numeric(cov6[j, k] == 4)
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov5", "cov62", "cov63", "cov64",
"cov5:cov62", "cov5:cov63", "cov5:cov64")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:8)
# site_cov * repl_cov (interaction)
result <- set_modargs(~ cov3 * cov6, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_equal(result$M, 10)
ans_cov <- array(dim = c(J, K, 8))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov3[j]
ans_cov[j, k, 3] <- as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 4] <- as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 5] <- as.numeric(cov6[j, k] == 4)
ans_cov[j, k, 6] <- cov3[j] * as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 7] <- cov3[j] * as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 8] <- cov3[j] * as.numeric(cov6[j, k] == 4)
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov3", "cov62", "cov63", "cov64",
"cov3:cov62", "cov3:cov63", "cov3:cov64")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:8)
## Errors and Warnings
expect_error(set_modargs(~ ., ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_phi\\)")
expect_error(set_modargs(~ xxx, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi: xxx
Make sure they are included in either 'site_cov' or 'repl_cov'.")
expect_error(set_modargs(~ xxx + yyy, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi: xxx, yyy
Make sure they are included in either 'site_cov' or 'repl_cov'.")
})
### Tests for formula_theta ----------------------------------------------------
test_that("Procedures for theta correct", {
## Output
# null model
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "i")
expect_equal(result$M, 3)
expect_equal(result$cov_theta, 1)
expect_equal(result$m_theta, 2)
# spec_cov (not allowed)
expect_error(set_modargs(~ 1, ~ cov1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_theta: cov1
Make sure they are included in either 'site_cov' or 'repl_cov'.")
# site_cov (continuous)
result <- set_modargs(~ 1, ~ cov3, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, 2))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
}
colnames(ans_cov) <- c("(Intercept)", "cov3")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:3)
# site_cov (factor)
result <- set_modargs(~ 1, ~ cov4, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_equal(result$M, 5)
ans_cov <- array(dim = c(J, 3))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- as.numeric((cov4[j] == 2))
ans_cov[j, 3] <- as.numeric((cov4[j] == 3))
}
colnames(ans_cov) <- c("(Intercept)", "cov42", "cov43")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:4)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ cov3 * cov4, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_equal(result$M, 8)
ans_cov <- array(dim = c(J, 6))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
ans_cov[j, 3] <- as.numeric(cov4[j] == 2)
ans_cov[j, 4] <- as.numeric(cov4[j] == 3)
ans_cov[j, 5] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[j, 6] <- cov3[j] * as.numeric(cov4[j] == 3)
}
colnames(ans_cov) <- c("(Intercept)", "cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:7)
# repl_cov (continuous)
result <- set_modargs(~ 1, ~ cov5, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, K, 2))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov5[j, k]
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov5")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:3)
# repl_cov (factor)
result <- set_modargs(~ 1, ~ cov6, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_equal(result$M, 6)
ans_cov <- array(dim = c(J, K, 4))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- as.numeric((cov6[j, k] == 2))
ans_cov[j, k, 3] <- as.numeric((cov6[j, k] == 3))
ans_cov[j, k, 4] <- as.numeric((cov6[j, k] == 4))
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov62", "cov63", "cov64")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:5)
# repl_cov (interaction)
result <- set_modargs(~ 1, ~ cov5 * cov6, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_equal(result$M, 10)
ans_cov <- array(dim = c(J, K, 8))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov5[j, k]
ans_cov[j, k, 3] <- as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 4] <- as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 5] <- as.numeric(cov6[j, k] == 4)
ans_cov[j, k, 6] <- cov5[j, k] * as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 7] <- cov5[j, k] * as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 8] <- cov5[j, k] * as.numeric(cov6[j, k] == 4)
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov5", "cov62", "cov63", "cov64",
"cov5:cov62", "cov5:cov63", "cov5:cov64")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:9)
# site_cov * repl_cov (interaction)
result <- set_modargs(~ 1, ~ cov3 * cov6, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_equal(result$M, 10)
ans_cov <- array(dim = c(J, K, 8))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov3[j]
ans_cov[j, k, 3] <- as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 4] <- as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 5] <- as.numeric(cov6[j, k] == 4)
ans_cov[j, k, 6] <- cov3[j] * as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 7] <- cov3[j] * as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 8] <- cov3[j] * as.numeric(cov6[j, k] == 4)
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov3", "cov62", "cov63", "cov64",
"cov3:cov62", "cov3:cov63", "cov3:cov64")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:9)
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ ., ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_theta\\)")
expect_error(set_modargs(~ 1, ~ xxx, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_theta: xxx
Make sure they are included in either 'site_cov' or 'repl_cov'.")
expect_error(set_modargs(~ 1, ~ xxx + yyy, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_theta: xxx, yyy
Make sure they are included in either 'site_cov' or 'repl_cov'.")
})
### Tests for formula_psi ------------------------------------------------------
test_that("Procedures for psi correct", {
## Output
# null model
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$psi, "i")
expect_equal(result$M, 3)
expect_equal(result$cov_psi, 1)
expect_equal(result$m_psi, 3)
# spec_cov (not allowed)
expect_error(set_modargs(~ 1, ~ 1, ~ cov1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_psi: cov1
Make sure they are included in 'site_cov'.")
# site_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ cov3, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$psi, "ij")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, 2))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
}
colnames(ans_cov) <- c("(Intercept)", "cov3")
expect_equal(result$cov_psi, ans_cov)
expect_equal(result$m_psi, 3:4)
# site_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ cov4, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$psi, "ij")
expect_equal(result$M, 5)
ans_cov <- array(dim = c(J, 3))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[j, 3] <- as.numeric(cov4[j] == 3)
}
colnames(ans_cov) <- c("(Intercept)", "cov42", "cov43")
expect_equal(result$cov_psi, ans_cov)
expect_equal(result$m_psi, 3:5)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ cov3 * cov4, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$psi, "ij")
expect_equal(result$M, 8)
ans_cov <- array(dim = c(J, 6))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
ans_cov[j, 3] <- as.numeric(cov4[j] == 2)
ans_cov[j, 4] <- as.numeric(cov4[j] == 3)
ans_cov[j, 5] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[j, 6] <- cov3[j] * as.numeric(cov4[j] == 3)
}
colnames(ans_cov) <- c("(Intercept)", "cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_psi, ans_cov)
expect_equal(result$m_psi, 3:8)
# repl_cov (not allowed)
expect_error(set_modargs(~ 1, ~ 1, ~ cov5, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_psi: cov5
Make sure they are included in 'site_cov'.")
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ 1, ~ ., ~ 1, ~ 1, ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_psi\\)")
expect_error(set_modargs(~ 1, ~ 1, ~ xxx, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_psi: xxx
Make sure they are included in 'site_cov'.")
expect_error(set_modargs(~ 1, ~ 1, ~ xxx + yyy, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_psi: xxx, yyy
Make sure they are included in 'site_cov'.")
})
fukayak/occumb documentation built on April 17, 2025, 11:50 a.m.
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### Test data ------------------------------------------------------------------
I <- 2
J <- 3
K <- 4
cov1 <- rnorm(I)
cov2 <- factor(1:I)
cov3 <- rnorm(J)
cov4 <- factor(1:J)
cov5 <- matrix(rnorm(J * K), nrow = J)
cov6 <- matrix(rep(factor(1:K), each = J), nrow = J)
#cov2 <- as.character(1:I)
#cov4 <- as.character(factor(1:J))
#cov6 <- matrix(rep(as.character(1:K), each = J), nrow = J)
data <- occumbData(y = array(1, dim = c(I, J, K)),
spec_cov = list(cov1 = cov1, cov2 = cov2),
site_cov = list(cov3 = cov3, cov4 = cov4),
repl_cov = list(cov5 = cov5, cov6 = cov6))
### Tests for formula_phi_shared -----------------------------------------------
test_that("Procedures for phi_shared correct", {
## Output
# spec_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "i")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
}
colnames(ans_cov) <- "cov1"
expect_equal(result$cov_phi_shared, ans_cov)
# spec_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov2, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "i")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov22")
expect_equal(result$cov_phi_shared, ans_cov)
# spec_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov1 * cov2, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "i")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 3)
ans_cov <- array(dim = c(I, 3))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
ans_cov[i, 2] <- as.numeric((cov2[i] == 2))
ans_cov[i, 3] <- cov1[i] * as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov1", "cov22", "cov1:cov22")
expect_equal(result$cov_phi_shared, ans_cov)
# site_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov3, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 1)
ans_cov <- array(dim = c(I, J, 1))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
}
}
dimnames(ans_cov)[[3]] <- "cov3"
expect_equal(result$cov_phi_shared, ans_cov)
# site_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov4, ~ 1, ~ 1, data = data)
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 2)
ans_cov <- array(dim = c(I, J, 2))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov42", "cov43")
expect_equal(result$cov_phi_shared, ans_cov)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov3 * cov4, ~ 1, ~ 1, data = data)
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov3[j] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_phi_shared, ans_cov)
# spec_cov * site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov1 * cov4, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov1[i]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov1[i] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov1", "cov42", "cov43",
"cov1:cov42", "cov1:cov43")
expect_equal(result$cov_phi_shared, ans_cov)
# repl_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov5, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 1)
ans_cov <- array(dim = c(I, J, K, 1))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- "cov5"
expect_equal(result$cov_phi_shared, ans_cov)
# repl_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov6, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 3)
ans_cov <- array(dim = c(I, J, K, 3))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 2] <- as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 3] <- as.numeric(cov6[j, k] == 4)
}
}
}
dimnames(ans_cov)[[4]] <- c("cov62", "cov63", "cov64")
expect_equal(result$cov_phi_shared, ans_cov)
# repl_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov5 * cov6, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 7)
ans_cov <- array(dim = c(I, J, K, 7))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov5[j, k]
ans_cov[i, j, k, 2] <- as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 3] <- as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 4] <- as.numeric(cov6[j, k] == 4)
ans_cov[i, j, k, 5] <- cov5[j, k] * as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 6] <- cov5[j, k] * as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 7] <- cov5[j, k] * as.numeric(cov6[j, k] == 4)
}
}
}
dimnames(ans_cov)[[4]] <- c("cov5", "cov62", "cov63", "cov64",
"cov5:cov62", "cov5:cov63", "cov5:cov64")
expect_equal(result$cov_phi_shared, ans_cov)
# spec_cov * site_cov * repl_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov2 * cov3 * cov5, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 7)
ans_cov <- array(dim = c(I, J, K, 7))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- as.numeric(cov2[i] == 2)
ans_cov[i, j, k, 2] <- cov3[j]
ans_cov[i, j, k, 3] <- cov5[j, k]
ans_cov[i, j, k, 4] <- as.numeric(cov2[i] == 2) * cov3[j]
ans_cov[i, j, k, 5] <- as.numeric(cov2[i] == 2) * cov5[j, k]
ans_cov[i, j, k, 6] <- cov3[j] * cov5[j, k]
ans_cov[i, j, k, 7] <- as.numeric(cov2[i] == 2) * cov3[j] * cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- c("cov22", "cov3", "cov5",
"cov22:cov3", "cov22:cov5", "cov3:cov5",
"cov22:cov3:cov5")
expect_equal(result$cov_phi_shared, ans_cov)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ cov1 * cov4 * cov5, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_true(result$phi_shared)
expect_equal(result$M_phi_shared, 11)
ans_cov <- array(dim = c(I, J, K, 11))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov1[i]
ans_cov[i, j, k, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, k, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, k, 4] <- cov5[j, k]
ans_cov[i, j, k, 5] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, k, 6] <- cov1[i] * as.numeric(cov4[j] == 3)
ans_cov[i, j, k, 7] <- cov1[i] * cov5[j, k]
ans_cov[i, j, k, 8] <- as.numeric(cov4[j] == 2) * cov5[j, k]
ans_cov[i, j, k, 9] <- as.numeric(cov4[j] == 3) * cov5[j, k]
ans_cov[i, j, k, 10] <- cov1[i] * as.numeric(cov4[j] == 2) * cov5[j, k]
ans_cov[i, j, k, 11] <- cov1[i] * as.numeric(cov4[j] == 3) * cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- c("cov1", "cov42", "cov43", "cov5",
"cov1:cov42", "cov1:cov43",
"cov1:cov5",
"cov42:cov5", "cov43:cov5",
"cov1:cov42:cov5", "cov1:cov43:cov5")
expect_equal(result$cov_phi_shared, ans_cov)
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ ., ~ 1, ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_phi_shared\\)")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ xxx, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi_shared: xxx
Make sure they are included in either 'spec_cov', 'site_cov', or 'repl_cov'.")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ xxx + yyy, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi_shared: xxx, yyy
Make sure they are included in either 'spec_cov', 'site_cov', or 'repl_cov'.")
})
### Tests for formula_theta_shared ---------------------------------------------
test_that("Procedures for theta_shared correct", {
## Output
# spec_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov1, ~ 1, data = data)
expect_equal(result$theta, "i")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
}
colnames(ans_cov) <- "cov1"
expect_equal(result$cov_theta_shared, ans_cov)
# spec_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov2, ~ 1, data = data)
expect_equal(result$theta, "i")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov22")
expect_equal(result$cov_theta_shared, ans_cov)
# spec_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov2, ~ 1, data = data)
expect_equal(result$theta, "i")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 3)
ans_cov <- array(dim = c(I, 3))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
ans_cov[i, 2] <- as.numeric((cov2[i] == 2))
ans_cov[i, 3] <- cov1[i] * as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov1", "cov22", "cov1:cov22")
expect_equal(result$cov_theta_shared, ans_cov)
# site_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov3, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 1)
ans_cov <- array(dim = c(I, J, 1))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
}
}
dimnames(ans_cov)[[3]] <- "cov3"
expect_equal(result$cov_theta_shared, ans_cov)
# site_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov4, ~ 1, data = data)
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 2)
ans_cov <- array(dim = c(I, J, 2))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov42", "cov43")
expect_equal(result$cov_theta_shared, ans_cov)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov3 * cov4, ~ 1, data = data)
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov3[j] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_theta_shared, ans_cov)
# spec_cov * site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov4, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov1[i]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov1[i] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov1", "cov42", "cov43",
"cov1:cov42", "cov1:cov43")
expect_equal(result$cov_theta_shared, ans_cov)
# repl_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov5, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 1)
ans_cov <- array(dim = c(I, J, K, 1))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- "cov5"
expect_equal(result$cov_theta_shared, ans_cov)
# repl_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov6, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 3)
ans_cov <- array(dim = c(I, J, K, 3))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 2] <- as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 3] <- as.numeric(cov6[j, k] == 4)
}
}
}
dimnames(ans_cov)[[4]] <- c("cov62", "cov63", "cov64")
expect_equal(result$cov_theta_shared, ans_cov)
# repl_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov5 * cov6, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 7)
ans_cov <- array(dim = c(I, J, K, 7))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov5[j, k]
ans_cov[i, j, k, 2] <- as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 3] <- as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 4] <- as.numeric(cov6[j, k] == 4)
ans_cov[i, j, k, 5] <- cov5[j, k] * as.numeric(cov6[j, k] == 2)
ans_cov[i, j, k, 6] <- cov5[j, k] * as.numeric(cov6[j, k] == 3)
ans_cov[i, j, k, 7] <- cov5[j, k] * as.numeric(cov6[j, k] == 4)
}
}
}
dimnames(ans_cov)[[4]] <- c("cov5", "cov62", "cov63", "cov64",
"cov5:cov62", "cov5:cov63", "cov5:cov64")
expect_equal(result$cov_theta_shared, ans_cov)
# spec_cov * site_cov * repl_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov2 * cov3 * cov5, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 7)
ans_cov <- array(dim = c(I, J, K, 7))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- as.numeric(cov2[i] == 2)
ans_cov[i, j, k, 2] <- cov3[j]
ans_cov[i, j, k, 3] <- cov5[j, k]
ans_cov[i, j, k, 4] <- as.numeric(cov2[i] == 2) * cov3[j]
ans_cov[i, j, k, 5] <- as.numeric(cov2[i] == 2) * cov5[j, k]
ans_cov[i, j, k, 6] <- cov3[j] * cov5[j, k]
ans_cov[i, j, k, 7] <- as.numeric(cov2[i] == 2) * cov3[j] * cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- c("cov22", "cov3", "cov5",
"cov22:cov3", "cov22:cov5", "cov3:cov5",
"cov22:cov3:cov5")
expect_equal(result$cov_theta_shared, ans_cov)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov4 * cov5, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_true(result$theta_shared)
expect_equal(result$M_theta_shared, 11)
ans_cov <- array(dim = c(I, J, K, 11))
for (i in 1:I) {
for (j in 1:J) {
for (k in 1:K) {
ans_cov[i, j, k, 1] <- cov1[i]
ans_cov[i, j, k, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, k, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, k, 4] <- cov5[j, k]
ans_cov[i, j, k, 5] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, k, 6] <- cov1[i] * as.numeric(cov4[j] == 3)
ans_cov[i, j, k, 7] <- cov1[i] * cov5[j, k]
ans_cov[i, j, k, 8] <- as.numeric(cov4[j] == 2) * cov5[j, k]
ans_cov[i, j, k, 9] <- as.numeric(cov4[j] == 3) * cov5[j, k]
ans_cov[i, j, k, 10] <- cov1[i] * as.numeric(cov4[j] == 2) * cov5[j, k]
ans_cov[i, j, k, 11] <- cov1[i] * as.numeric(cov4[j] == 3) * cov5[j, k]
}
}
}
dimnames(ans_cov)[[4]] <- c("cov1", "cov42", "cov43", "cov5",
"cov1:cov42", "cov1:cov43",
"cov1:cov5",
"cov42:cov5", "cov43:cov5",
"cov1:cov42:cov5", "cov1:cov43:cov5")
expect_equal(result$cov_theta_shared, ans_cov)
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ ., ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_theta_shared\\)")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ xxx, ~ 1, data = data),
"Unexpected terms in formula_theta_shared: xxx
Make sure they are included in either 'spec_cov', 'site_cov', or 'repl_cov'.")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ xxx + yyy, ~ 1, data = data),
"Unexpected terms in formula_theta_shared: xxx, yyy
Make sure they are included in either 'spec_cov', 'site_cov', or 'repl_cov'.")
})
### Tests for formula_psi_shared -----------------------------------------------
test_that("Procedures for psi_shared correct", {
## Output
# spec_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov1, data = data)
expect_equal(result$psi, "i")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
}
colnames(ans_cov) <- "cov1"
expect_equal(result$cov_psi_shared, ans_cov)
# spec_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov2, data = data)
expect_equal(result$psi, "i")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 1)
ans_cov <- array(dim = c(I, 1))
for (i in 1:I) {
ans_cov[i, 1] <- as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov22")
expect_equal(result$cov_psi_shared, ans_cov)
# spec_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov2, data = data)
expect_equal(result$psi, "i")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 3)
ans_cov <- array(dim = c(I, 3))
for (i in 1:I) {
ans_cov[i, 1] <- cov1[i]
ans_cov[i, 2] <- as.numeric((cov2[i] == 2))
ans_cov[i, 3] <- cov1[i] * as.numeric((cov2[i] == 2))
}
colnames(ans_cov) <- c("cov1", "cov22", "cov1:cov22")
expect_equal(result$cov_psi_shared, ans_cov)
# site_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov3, data = data)
expect_equal(result$psi, "ij")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 1)
ans_cov <- array(dim = c(I, J, 1))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
}
}
dimnames(ans_cov)[[3]] <- "cov3"
expect_equal(result$cov_psi_shared, ans_cov)
# site_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov4, data = data)
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 2)
ans_cov <- array(dim = c(I, J, 2))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov42", "cov43")
expect_equal(result$cov_psi_shared, ans_cov)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov3 * cov4, data = data)
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov3[j]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov3[j] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_psi_shared, ans_cov)
# spec_cov * site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov1 * cov4, data = data)
expect_equal(result$psi, "ij")
expect_true(result$psi_shared)
expect_equal(result$M_psi_shared, 5)
ans_cov <- array(dim = c(I, J, 5))
for (i in 1:I) {
for (j in 1:J) {
ans_cov[i, j, 1] <- cov1[i]
ans_cov[i, j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[i, j, 3] <- as.numeric(cov4[j] == 3)
ans_cov[i, j, 4] <- cov1[i] * as.numeric(cov4[j] == 2)
ans_cov[i, j, 5] <- cov1[i] * as.numeric(cov4[j] == 3)
}
}
dimnames(ans_cov)[[3]] <- c("cov1", "cov42", "cov43",
"cov1:cov42", "cov1:cov43")
expect_equal(result$cov_psi_shared, ans_cov)
# repl_cov (not allowed)
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ cov5, data = data),
"Unexpected terms in formula_psi_shared: cov5
Make sure they are included in either 'spec_cov' or 'site_cov'.")
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ ., data = data),
"'.' cannot be used to specify covariates \\(formula_psi_shared\\)")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ xxx, data = data),
"Unexpected terms in formula_psi_shared: xxx
Make sure they are included in either 'spec_cov' or 'site_cov'.")
expect_error(set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ xxx + yyy, data = data),
"Unexpected terms in formula_psi_shared: xxx, yyy
Make sure they are included in either 'spec_cov' or 'site_cov'.")
})
### Tests for formula_phi ------------------------------------------------------
test_that("Arguments are correct for the null model", {
## Output
# null model
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "i")
expect_equal(result$M, 3)
expect_equal(result$cov_phi, 1)
expect_equal(result$m_phi, 1)
})
test_that("Errors are correct for the spec_cov in phi", {
# spec_cov (not allowed)
expect_error(set_modargs(~ cov1, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi: cov1
Make sure they are included in either 'site_cov' or 'repl_cov'.")
})
test_that("Procedures for phi correct", {
# site_cov (continuous)
result <- set_modargs(~ cov3, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, 2))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
}
colnames(ans_cov) <- c("(Intercept)", "cov3")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:2)
# site_cov (factor)
result <- set_modargs(~ cov4, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_equal(result$M, 5)
ans_cov <- array(dim = c(J, 3))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- as.numeric((cov4[j] == 2))
ans_cov[j, 3] <- as.numeric((cov4[j] == 3))
}
colnames(ans_cov) <- c("(Intercept)", "cov42", "cov43")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:3)
# site_cov (interaction)
result <- set_modargs(~ cov3 * cov4, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ij")
expect_equal(result$M, 8)
ans_cov <- array(dim = c(J, 6))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
ans_cov[j, 3] <- as.numeric(cov4[j] == 2)
ans_cov[j, 4] <- as.numeric(cov4[j] == 3)
ans_cov[j, 5] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[j, 6] <- cov3[j] * as.numeric(cov4[j] == 3)
}
colnames(ans_cov) <- c("(Intercept)", "cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:6)
# repl_cov (continuous)
result <- set_modargs(~ cov5, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, K, 2))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov5[j, k]
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov5")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:2)
# repl_cov (factor)
result <- set_modargs(~ cov6, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_equal(result$M, 6)
ans_cov <- array(dim = c(J, K, 4))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- as.numeric((cov6[j, k] == 2))
ans_cov[j, k, 3] <- as.numeric((cov6[j, k] == 3))
ans_cov[j, k, 4] <- as.numeric((cov6[j, k] == 4))
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov62", "cov63", "cov64")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:4)
# repl_cov (interaction)
result <- set_modargs(~ cov5 * cov6, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_equal(result$M, 10)
ans_cov <- array(dim = c(J, K, 8))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov5[j, k]
ans_cov[j, k, 3] <- as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 4] <- as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 5] <- as.numeric(cov6[j, k] == 4)
ans_cov[j, k, 6] <- cov5[j, k] * as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 7] <- cov5[j, k] * as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 8] <- cov5[j, k] * as.numeric(cov6[j, k] == 4)
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov5", "cov62", "cov63", "cov64",
"cov5:cov62", "cov5:cov63", "cov5:cov64")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:8)
# site_cov * repl_cov (interaction)
result <- set_modargs(~ cov3 * cov6, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$phi, "ijk")
expect_equal(result$M, 10)
ans_cov <- array(dim = c(J, K, 8))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov3[j]
ans_cov[j, k, 3] <- as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 4] <- as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 5] <- as.numeric(cov6[j, k] == 4)
ans_cov[j, k, 6] <- cov3[j] * as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 7] <- cov3[j] * as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 8] <- cov3[j] * as.numeric(cov6[j, k] == 4)
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov3", "cov62", "cov63", "cov64",
"cov3:cov62", "cov3:cov63", "cov3:cov64")
expect_equal(result$cov_phi, ans_cov)
expect_equal(result$m_phi, 1:8)
## Errors and Warnings
expect_error(set_modargs(~ ., ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_phi\\)")
expect_error(set_modargs(~ xxx, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi: xxx
Make sure they are included in either 'site_cov' or 'repl_cov'.")
expect_error(set_modargs(~ xxx + yyy, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_phi: xxx, yyy
Make sure they are included in either 'site_cov' or 'repl_cov'.")
})
### Tests for formula_theta ----------------------------------------------------
test_that("Procedures for theta correct", {
## Output
# null model
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "i")
expect_equal(result$M, 3)
expect_equal(result$cov_theta, 1)
expect_equal(result$m_theta, 2)
# spec_cov (not allowed)
expect_error(set_modargs(~ 1, ~ cov1, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_theta: cov1
Make sure they are included in either 'site_cov' or 'repl_cov'.")
# site_cov (continuous)
result <- set_modargs(~ 1, ~ cov3, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, 2))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
}
colnames(ans_cov) <- c("(Intercept)", "cov3")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:3)
# site_cov (factor)
result <- set_modargs(~ 1, ~ cov4, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_equal(result$M, 5)
ans_cov <- array(dim = c(J, 3))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- as.numeric((cov4[j] == 2))
ans_cov[j, 3] <- as.numeric((cov4[j] == 3))
}
colnames(ans_cov) <- c("(Intercept)", "cov42", "cov43")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:4)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ cov3 * cov4, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ij")
expect_equal(result$M, 8)
ans_cov <- array(dim = c(J, 6))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
ans_cov[j, 3] <- as.numeric(cov4[j] == 2)
ans_cov[j, 4] <- as.numeric(cov4[j] == 3)
ans_cov[j, 5] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[j, 6] <- cov3[j] * as.numeric(cov4[j] == 3)
}
colnames(ans_cov) <- c("(Intercept)", "cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:7)
# repl_cov (continuous)
result <- set_modargs(~ 1, ~ cov5, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, K, 2))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov5[j, k]
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov5")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:3)
# repl_cov (factor)
result <- set_modargs(~ 1, ~ cov6, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_equal(result$M, 6)
ans_cov <- array(dim = c(J, K, 4))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- as.numeric((cov6[j, k] == 2))
ans_cov[j, k, 3] <- as.numeric((cov6[j, k] == 3))
ans_cov[j, k, 4] <- as.numeric((cov6[j, k] == 4))
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov62", "cov63", "cov64")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:5)
# repl_cov (interaction)
result <- set_modargs(~ 1, ~ cov5 * cov6, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_equal(result$M, 10)
ans_cov <- array(dim = c(J, K, 8))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov5[j, k]
ans_cov[j, k, 3] <- as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 4] <- as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 5] <- as.numeric(cov6[j, k] == 4)
ans_cov[j, k, 6] <- cov5[j, k] * as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 7] <- cov5[j, k] * as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 8] <- cov5[j, k] * as.numeric(cov6[j, k] == 4)
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov5", "cov62", "cov63", "cov64",
"cov5:cov62", "cov5:cov63", "cov5:cov64")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:9)
# site_cov * repl_cov (interaction)
result <- set_modargs(~ 1, ~ cov3 * cov6, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$theta, "ijk")
expect_equal(result$M, 10)
ans_cov <- array(dim = c(J, K, 8))
for (j in 1:J) {
for (k in 1:K) {
ans_cov[j, k, 1] <- 1
ans_cov[j, k, 2] <- cov3[j]
ans_cov[j, k, 3] <- as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 4] <- as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 5] <- as.numeric(cov6[j, k] == 4)
ans_cov[j, k, 6] <- cov3[j] * as.numeric(cov6[j, k] == 2)
ans_cov[j, k, 7] <- cov3[j] * as.numeric(cov6[j, k] == 3)
ans_cov[j, k, 8] <- cov3[j] * as.numeric(cov6[j, k] == 4)
}
}
dimnames(ans_cov)[[3]] <- c("(Intercept)", "cov3", "cov62", "cov63", "cov64",
"cov3:cov62", "cov3:cov63", "cov3:cov64")
expect_equal(result$cov_theta, ans_cov)
expect_equal(result$m_theta, 2:9)
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ ., ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_theta\\)")
expect_error(set_modargs(~ 1, ~ xxx, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_theta: xxx
Make sure they are included in either 'site_cov' or 'repl_cov'.")
expect_error(set_modargs(~ 1, ~ xxx + yyy, ~ 1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_theta: xxx, yyy
Make sure they are included in either 'site_cov' or 'repl_cov'.")
})
### Tests for formula_psi ------------------------------------------------------
test_that("Procedures for psi correct", {
## Output
# null model
result <- set_modargs(~ 1, ~ 1, ~ 1, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$psi, "i")
expect_equal(result$M, 3)
expect_equal(result$cov_psi, 1)
expect_equal(result$m_psi, 3)
# spec_cov (not allowed)
expect_error(set_modargs(~ 1, ~ 1, ~ cov1, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_psi: cov1
Make sure they are included in 'site_cov'.")
# site_cov (continuous)
result <- set_modargs(~ 1, ~ 1, ~ cov3, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$psi, "ij")
expect_equal(result$M, 4)
ans_cov <- array(dim = c(J, 2))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
}
colnames(ans_cov) <- c("(Intercept)", "cov3")
expect_equal(result$cov_psi, ans_cov)
expect_equal(result$m_psi, 3:4)
# site_cov (factor)
result <- set_modargs(~ 1, ~ 1, ~ cov4, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$psi, "ij")
expect_equal(result$M, 5)
ans_cov <- array(dim = c(J, 3))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- as.numeric(cov4[j] == 2)
ans_cov[j, 3] <- as.numeric(cov4[j] == 3)
}
colnames(ans_cov) <- c("(Intercept)", "cov42", "cov43")
expect_equal(result$cov_psi, ans_cov)
expect_equal(result$m_psi, 3:5)
# site_cov (interaction)
result <- set_modargs(~ 1, ~ 1, ~ cov3 * cov4, ~ 1, ~ 1, ~ 1, data = data)
expect_equal(result$psi, "ij")
expect_equal(result$M, 8)
ans_cov <- array(dim = c(J, 6))
for (j in 1:J) {
ans_cov[j, 1] <- 1
ans_cov[j, 2] <- cov3[j]
ans_cov[j, 3] <- as.numeric(cov4[j] == 2)
ans_cov[j, 4] <- as.numeric(cov4[j] == 3)
ans_cov[j, 5] <- cov3[j] * as.numeric(cov4[j] == 2)
ans_cov[j, 6] <- cov3[j] * as.numeric(cov4[j] == 3)
}
colnames(ans_cov) <- c("(Intercept)", "cov3", "cov42", "cov43",
"cov3:cov42", "cov3:cov43")
expect_equal(result$cov_psi, ans_cov)
expect_equal(result$m_psi, 3:8)
# repl_cov (not allowed)
expect_error(set_modargs(~ 1, ~ 1, ~ cov5, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_psi: cov5
Make sure they are included in 'site_cov'.")
## Errors and Warnings
expect_error(set_modargs(~ 1, ~ 1, ~ ., ~ 1, ~ 1, ~ 1, data = data),
"'.' cannot be used to specify covariates \\(formula_psi\\)")
expect_error(set_modargs(~ 1, ~ 1, ~ xxx, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_psi: xxx
Make sure they are included in 'site_cov'.")
expect_error(set_modargs(~ 1, ~ 1, ~ xxx + yyy, ~ 1, ~ 1, ~ 1, data = data),
"Unexpected terms in formula_psi: xxx, yyy
Make sure they are included in 'site_cov'.")
})
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