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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,120 @@ | ||
| context("random effects tools") | ||
| skip_on_cran() | ||
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| set.seed(123) | ||
| M <- 10 | ||
| J <- 3 | ||
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| sc <- data.frame(x1 = rnorm(M), | ||
| x2 = factor(sample(letters[1:2], M, replace=TRUE)), | ||
| x3 = factor(sample(letters[3:4], M, replace=TRUE)), | ||
| g = factor(sample(letters[5:7], M, replace=TRUE))) | ||
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| test_that("random factor slopes work", { | ||
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| test1 <- get_Z(~x1 + x2 + (x1 + x2 || g), sc) | ||
| expect_is(test1, "dgCMatrix") | ||
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| test1 <- as.matrix(test1) | ||
| expect_equal(colnames(test1), rep(letters[5:7], 4)) | ||
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| expect_equal(test1, structure(c(0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, | ||
| 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1.55870831414912, | ||
| 0, 0.129287735160946, 1.71506498688328, 0, 0, 0, -0.445661970099958, | ||
| 0, -0.23017748948328, 0, 0, 0, 0, 0.460916205989202, 0, 0, 0, | ||
| -0.560475646552213, 0, 0, 0.070508391424576, 0, 0, 0, -1.26506123460653, | ||
| -0.686852851893526, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, | ||
| 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, | ||
| 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, | ||
| 0, 0, 1, 0, 0), dim = c(10L, 12L), dimnames = list(c("1", "2", | ||
| "3", "4", "5", "6", "7", "8", "9", "10"), c("e", "f", "g", "e", | ||
| "f", "g", "e", "f", "g", "e", "f", "g")))) | ||
|
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| sig <- sigma_names(~x1 + x2 + (x1 + x2 || g), sc) | ||
| expect_equal(sig, | ||
| c("1|g", "x1|g", "x2a|g", "x2b|g")) | ||
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| nr <- get_nrandom(~x1 + x2 + (x1 + x2 || g), sc) | ||
| expect_equal(length(nr), length(sig)) | ||
| expect_equal(sum(nr), ncol(test1)) | ||
|
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| test2 <- as.matrix(get_Z(~0 + x2:x3 + (0 + x2:x3 | g), sc)) | ||
| sig <- sigma_names(~0 + x2:x3 + (0 + x2:x3 | g), sc) | ||
| expect_equal(sig, c("x2a:x3c|g", "x2b:x3c|g", "x2a:x3d|g", "x2b:x3d|g")) | ||
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| expect_equal(test2, structure(c(0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, | ||
| 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, | ||
| 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, | ||
| 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, | ||
| 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, | ||
| 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), dim = c(10L, | ||
| 12L), dimnames = list(c("1", "2", "3", "4", "5", "6", "7", "8", | ||
| "9", "10"), c("e", "f", "g", "e", "f", "g", "e", "f", "g", "e", | ||
| "f", "g")))) | ||
|
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| nr <- get_nrandom(~0 + x2:x3 + (0 + x2:x3 | g), sc) | ||
| expect_equal(length(nr), length(sig)) | ||
| expect_equal(sum(nr), ncol(test2)) | ||
| }) | ||
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| test_that("random factor slope estimates work", { | ||
| skip_on_ci() | ||
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| M <- 10000 | ||
| J <- 3 | ||
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| set.seed(123) | ||
| sc <- data.frame(x1 = rnorm(M), | ||
| x2 = factor(sample(letters[1:2], M, replace=TRUE)), | ||
| x3 = factor(sample(letters[3:4], M, replace=TRUE)), | ||
| g = factor(sample(letters[5:26], M, replace=TRUE))) | ||
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| X <- model.matrix(~x1 + x2, sc) | ||
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| b <- c(-0.3, 0.3, 0.5) | ||
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| b2 <- c(-0.3, 0.3, 0, 0.5) | ||
|
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| re <- lapply(1:length(b2), function(i){ | ||
| rnorm(length(levels(sc$g)), 0, 0.2) | ||
| }) | ||
|
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| Z <- as.matrix(unmarked:::get_Z(~x1 + x2 + (x1 + x2 ||g), sc)) | ||
|
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| Xall <- cbind(X, Z) | ||
|
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| ball <- c(b, unlist(re)) | ||
|
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| psi <- plogis(Xall %*% ball) | ||
| z <- rbinom(M, 1, psi) | ||
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| y <- matrix(NA, M, J) | ||
| for (i in 1:M){ | ||
| y[i,] <- rbinom(3, 1, 0.4) * z[i] | ||
| } | ||
|
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| umf <- unmarkedFrameOccu(y=y, siteCovs=sc) | ||
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| fit <- occu(~1~x1 + x2 + (x1 + x2 || g), umf) | ||
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| expect_equivalent(coef(fit), | ||
| c(b, qlogis(0.4)), tol=0.1) | ||
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| expect_equivalent(sigma(fit)$sigma, | ||
| c(0.2865,0.1859,0.3004,0.1928), tol=1e-4) | ||
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| re_est <- randomTerms(fit) | ||
| expect_equal(re_est$Level, rep(levels(sc$g), 4)) | ||
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| pr <- predict(fit, 'state', level=NULL)$Predicted | ||
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| expect_true(cor(psi, pr) > 0.95) | ||
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| # Two grouping variables | ||
| fit2 <- occu(~1~x1 + x2 + (x1 + x2 || g) + (1|x3), umf[1:100,]) | ||
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| expect_equal(nrow(sigma(fit2)), 5) | ||
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| re <- randomTerms(fit2) | ||
| expect_equal(re$Groups[89:90], c("x3", "x3")) | ||
| }) |