test_that("Standard errors on overall predictions from delta models work", { skip_on_cran() skip_on_ci() mesh <- make_mesh(pcod, c("X", "Y"), cutoff = 12) fit <- sdmTMB( density ~ depth_scaled + I(depth_scaled^2), data = pcod, mesh = mesh, family = delta_gamma(), ) fit nd <- data.frame(depth_scaled = seq(min(pcod$depth_scaled), max(pcod$depth_scaled), length.out = 50)) # link p <- predict(fit, model = NA, re_form = NA, newdata = nd, type = "link") head(p) p <- predict(fit, model = 1, re_form = NA, newdata = nd, type = "link") head(p) p <- predict(fit, model = 2, re_form = NA, newdata = nd, type = "link") head(p) # response p <- predict(fit, model = NA, re_form = NA, newdata = nd, type = "response") head(p) p <- predict(fit, model = 1, re_form = NA, newdata = nd, type = "response") head(p) p <- predict(fit, model = 2, re_form = NA, newdata = nd, type = "response") head(p) # re_form = NULL, se_fit = FALSE nd$X <- mean(pcod$X) nd$Y <- mean(pcod$Y) p <- predict(fit, model = NA, newdata = nd, type = "response") head(p) p <- predict(fit, model = 1, newdata = nd, type = "response") head(p) p <- predict(fit, model = 2, newdata = nd, type = "response") head(p) # link with se_fit = TRUE, re_form = NA p <- predict(fit, model = NA, re_form = NA, newdata = nd, type = "link", se_fit = TRUE) head(p) expect_true("est" %in% names(p)) expect_true("est_se" %in% names(p)) plot(p$depth_scaled, p$est) lines(p$depth_scaled, p$est - 2 * p$est_se) lines(p$depth_scaled, p$est + 2 * p$est_se) expect_equal(as.numeric(p$est), as.numeric(log(plogis(p$est1) * exp(p$est2)))) p <- predict(fit, model = 1, re_form = NA, newdata = nd, type = "link", se_fit = TRUE) head(p) plot(p$depth_scaled, p$est) lines(p$depth_scaled, p$est - 2 * p$est_se) lines(p$depth_scaled, p$est + 2 * p$est_se) expect_equal(p$est, p$est1) p <- predict(fit, model = 2, re_form = NA, newdata = nd, type = "link", se_fit = TRUE) head(p) plot(p$depth_scaled, p$est) lines(p$depth_scaled, p$est - 2 * p$est_se) lines(p$depth_scaled, p$est + 2 * p$est_se) expect_equal(p$est, p$est2) visreg_delta(fit, xvar = "depth_scaled", nn = 10, model = 1) visreg_delta(fit, xvar = "depth_scaled", nn = 10, model = 2) # *response* with se_fit = TRUE, re_form = NA # should go link anyways with warning expect_warning({ p <- predict(fit, model = NA, re_form = NA, newdata = nd, type = "response", se_fit = TRUE) }, regexp = "link") })