test_that("bru: inla copy feature", { skip_on_cran() local_bru_safe_inla() # Seed influences data as well as predict()! set.seed(123L) df1 <- data.frame(x = cos(1:100)) df2 <- data.frame(x = sin(1:100)) df1 <- within(df1, y <- 1 + exp(2 * x) + rnorm(length(x), mean = 0, sd = 0.1)) df2 <- within(df2, y <- 1 + (6 * x) + rnorm(length(x), mean = 0, sd = 0.1)) cmp <- ~ +1 + myLin1(x, model = "rw1", mapper = bru_mapper(INLA::inla.mesh.1d(seq(-1, 1, length.out = 100)), indexed = FALSE ) ) + myLin2(x, copy = "myLin1", fixed = FALSE) cmps <- component_list(cmp) fit <- bru( cmp, like(y ~ Intercept + exp(myLin1), family = "gaussian", data = df1, exclude = "myLin2"), like(y ~ Intercept + (myLin2), family = "gaussian", data = df2, exclude = "myLin1"), options = list(control.inla = list(int.strategy = "eb")) ) expect_equal( fit$summary.fixed["Intercept", "mean"], 1, tolerance = midtol ) expect_equal( fit$summary.hyperpar["Beta for myLin2", "mean"], 3, tolerance = midtol ) skip_if_not_installed("sn") pr <- predict( fit, data.frame(x = c(0.5, 1)), ~myLin2, n.samples = 500, seed = 1L ) expect_equal(pr[, "mean"], c(3, 6), tolerance = midtol) }) test_that("Component copy feature", { skip_on_cran() local_bru_safe_inla() # Seed influences data as well as predict()! set.seed(123L) mydata <- data.frame( x1 = rep(1:4, times = 2), x2 = rep(c(1, 2), each = 4) ) mydata <- within(mydata, { y <- rpois(8, exp(x1^0.5 + x2^0.5 * 2 - 1)) }) inlaform <- y ~ -1 + f(x1, model = "rw2", values = 1:4, scale.model = TRUE) + f(x2, copy = "x1", fixed = FALSE) fit <- INLA::inla( formula = inlaform, data = mydata, family = "poisson", inla.mode = bru_options_get("inla.mode"), control.compute = list(config = TRUE), control.inla = list(int.strategy = "eb") ) cmp <- y ~ -1 + x1(x1, model = "rw2", scale.model = TRUE) + x2(x2, copy = "x1", fixed = FALSE) fit_bru <- bru( cmp, family = "poisson", data = mydata, options = list(control.inla = list(int.strategy = "eb")) ) expect_equal( fit_bru$summary.hyperpar, fit$summary.hyperpar, tolerance = midtol ) }) test_that("Component copy feature with group", { skip_on_cran() local_bru_safe_inla() # Seed influences data as well as predict()! set.seed(123L) n <- c(16, 8) mydata <- data.frame( x1 = rep(seq_len(n[1]), times = n[2]), x2 = rep(seq_len(n[2]), each = n[1]) ) mydata <- rbind(mydata, mydata) mydata <- within(mydata, { Intercept <- 1 z <- rep(c(1, 2), times = length(x1) / 2) z2 <- rep(c(1, 2), each = length(x1) / 2) }) mydata <- within(mydata, { y <- rnorm(prod(n), x1^1.0 / n[1] * 4 + x2^1.0 / n[1] * 4 * 10, 1) }) inlaform <- y ~ -1 + Intercept + f(x1, model = "rw1", values = seq_len(n[1]), scale.model = TRUE, group = z) + f(x2, copy = "x1", fixed = FALSE, group = z2) fit <- INLA::inla( formula = inlaform, data = mydata, family = "normal", control.inla = list(int.strategy = "eb"), control.compute = list(config = TRUE), inla.mode = bru_options_get("inla.mode") ) cmp <- ~ -1 + Intercept + x1(x1, model = "rw1", scale.model = TRUE, group = z) + x2(x2, copy = "x1", fixed = FALSE, group = z2) fit_bru <- bru( cmp, formula = y ~ Intercept + x1 + x2, family = "normal", data = mydata, options = list( bru_max_iter = 1, control.inla = list(int.strategy = "eb") ) ) cmp2 <- ~ -1 + Intercept + x1(x1, model = "rw1", scale.model = TRUE, group = z) + x1copy(x2, copy = "x1", fixed = TRUE, group = z2) + beta(1, model = "linear") fit_bru2 <- bru( cmp2, formula = y ~ Intercept + x1 + beta * x1copy, family = "normal", data = mydata, options = list( bru_max_iter = 5, bru_initial = list(beta = 1), control.inla = list(int.strategy = "eb") ) ) expect_equal( fit_bru$summary.hyperpar$mean, fit$summary.hyperpar$mean, tolerance = hitol ) expect_equal( fit_bru$summary.hyperpar$sd, fit$summary.hyperpar$sd, tolerance = hitol ) })