## 'augment' --------------------------------------------------------------- test_that("'augment' works with Poisson, disp - has data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod_fitted <- fit(mod) ans <- augment(mod_fitted) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), c(".observed", ".fitted", ".expected"))) }) test_that("'augment' calculates fitted in cells with missing outcome or offset - Poisson", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2010, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) data$popn[1] <- NA data$deaths[2] <- NA formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) ans_unfit <- augment(mod, quiet = TRUE) mod_fitted <- fit(mod) ans_fit <- augment(mod_fitted) expect_false(any(rvec::draws_any(is.na(ans_fit$.fitted)))) expect_true(".deaths" %in% names(ans_fit)) expect_true(all(rvec::draws_all(ans_fit$.deaths[-2] == ans_fit$deaths[-2]))) expect_equal(rvec::draws_mean(ans_fit$.deaths[2]), rvec::draws_mean(ans_fit$.fitted[2] * ans_fit$popn[2]), tolerance = 0.02) expect_false(".deaths" %in% names(ans_unfit)) }) test_that("'augment' works with Poisson, disp - no data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) aug_notfitted <- augment(mod, quiet = TRUE) mod_fitted <- fit(mod) aug_fitted <- augment(mod_fitted) expect_identical(names(aug_fitted), names(aug_notfitted)) }) test_that("'augment' works with binomial, no disp - has data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.5) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_disp(mod, mean = 0) mod_fitted <- fit(mod) ans <- augment(mod_fitted) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), c(".observed", ".fitted"))) }) test_that("'augment' works with normal - with data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$deaths <- rpois(n = nrow(data), lambda = 100) data$deaths[1] <- NA formula <- deaths ~ age + sex + time mod <- mod_norm(formula = formula, data = data, weights = 1) mod_fitted <- fit(mod) ans <- augment(mod_fitted) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), ".deaths", ".fitted")) }) test_that("'augment' works with normal - no data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$deaths <- rpois(n = nrow(data), lambda = 100) formula <- deaths ~ age + sex + time mod <- mod_norm(formula = formula, data = data, weights = 1) ans <- augment(mod, quiet = TRUE) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), ".fitted")) }) test_that("'augment' gives same answer when run twice - with data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.5) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod_fitted <- fit(mod) ans1 <- augment(mod_fitted, quiet = TRUE) ans2 <- augment(mod_fitted, quiet = TRUE) expect_identical(ans1, ans2) }) test_that("'augment' gives same answer when run twice - no data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.5) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) ans1 <- augment(mod, quiet = TRUE) ans2 <- augment(mod, quiet = TRUE) expect_identical(ans1, ans2) }) test_that("'augment' gives message when used unfitted and quiet is FALSE", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) expect_message(augment(mod), "Model not fitted, so values drawn straight from prior distribution.") }) ## 'components' --------------------------------------------------------------- test_that("'components' works with no disp", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_disp(mod, mean = 0) mod_fitted <- fit(mod) ans <- components(mod_fitted) expect_true(is.data.frame(ans)) expect_identical(unique(ans$component), c("effect", "hyper")) }) test_that("'components' works with no data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) comp_nodata <- components(mod, quiet = TRUE) mod_data <- fit(mod) comp_data <- components(mod_data) comp_merge <- merge(comp_nodata, comp_data, by = c("term", "component", "level")) expect_identical(nrow(comp_merge), nrow(comp_data)) }) test_that("'components' gives same answer when run twice - with data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_disp(mod, mean = 0) mod_fitted <- fit(mod) ans1 <- components(mod_fitted, quiet = TRUE) ans2 <- components(mod_fitted, quiet = TRUE) expect_identical(ans1, ans2) }) test_that("'components' gives same answer when run twice - no data", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) ans1 <- components(mod, quiet = TRUE) ans2 <- components(mod, quiet = TRUE) expect_identical(ans1, ans2) }) test_that("'components' gives message when used unfitted and quiet is FALSE", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) expect_message(components(mod), "Model not fitted, so values drawn straight from prior distribution.") }) test_that("'disp' estimates not affected by weights in normal model", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$income <- rnorm(n = nrow(data), mean = 10, sd = 3) data$wt1 <- runif(n = nrow(data), max = 5) data$wt2 <- 20 * data$wt1 formula <- income ~ age + sex + time mod1 <- mod_norm(formula = formula, data = data, weights = wt1) mod1_fitted <- fit(mod1) comp1 <- components(mod1_fitted) disp1 <- comp1$.fitted[comp1$term == "disp"] mod2 <- mod_norm(formula = formula, data = data, weights = wt2) mod2_fitted <- fit(mod2) comp2 <- components(mod1_fitted) disp2 <- comp2$.fitted[comp1$term == "disp"] expect_equal(rvec::draws_mean(disp1), rvec::draws_mean(disp2)) }) ## 'computations' ------------------------------------------------------------- test_that("'computations' returns NULL (with warning) if applied to unfitted model", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) expect_message({x <- computations(mod)}, "Model not fitted..") expect_true(is.null(x)) }) test_that("'computations' returns tibble if applied to fitted model", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) |> fit() expect_true(tibble::is_tibble(computations(mod))) }) ## 'draw_vals_augment_fitted' ------------------------------------------------- test_that("'draw_vals_augment_fitted' works with Poisson, has disp", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod_fitted <- fit(mod) ans <- draw_vals_augment_fitted(mod_fitted) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), c(".observed", ".fitted", ".expected"))) }) test_that("'draw_vals_augment_fitted' calculates fitted in cells with missing outcome or offset - Poisson", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) data$popn[1] <- NA data$deaths[2] <- NA formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod_fitted <- fit(mod) ans <- draw_vals_augment_fitted(mod_fitted) expect_false(any(rvec::draws_any(is.na(ans$.fitted)))) }) test_that("'draw_vals_augment_fitted' works with binomial, no disp", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.5) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_disp(mod, mean = 0) mod_fitted <- fit(mod) ans <- draw_vals_augment_fitted(mod_fitted) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), c(".observed", ".fitted"))) }) test_that("'draw_vals_augment_fitted' works with normal", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$deaths <- rpois(n = nrow(data), lambda = 100) formula <- deaths ~ age + sex + time mod <- mod_norm(formula = formula, data = data, weights = 1) mod_fitted <- fit(mod) ans <- draw_vals_augment_fitted(mod_fitted) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), ".fitted")) }) test_that("'draw_vals_augment_fitted' works with Poisson, has rr3", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- poputils::rr3(rpois(n = nrow(data), lambda = 10)) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) |> set_datamod_outcome_rr3() |> set_n_draw(5) mod_fitted <- fit(mod) ans <- draw_vals_augment_fitted(mod_fitted) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), c(".deaths", ".observed", ".fitted", ".expected"))) aug_nodisp <- mod |> set_disp(mean = 0) |> fit() |> augment() expect_identical(names(aug_nodisp), c(names(data), c(".deaths", ".observed", ".fitted"))) }) test_that("'draw_vals_augment_fitted' works with binomial, has rr3", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- poputils::rr3(rbinom(n = nrow(data), size = data$popn, prob = 0.4)) formula <- deaths ~ age + sex + time mod <- mod_binom(formula = formula, data = data, size = popn) |> set_datamod_outcome_rr3() |> set_n_draw(5) mod_fitted <- fit(mod) ans <- draw_vals_augment_fitted(mod_fitted) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), c(".deaths", ".observed", ".fitted", ".expected"))) aug_nodisp <- mod |> set_disp(mean = 0) |> fit() |> augment() expect_identical(names(aug_nodisp), c(names(data), c(".deaths", ".observed", ".fitted"))) }) ## 'draw_vals_augment_unfitted' -------------------------------------------------------- test_that("'draw_vals_augment_unfitted' works with normal", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M"), KEEP.OUT.ATTRS = FALSE) data$deaths <- rpois(n = nrow(data), lambda = 100) formula <- deaths ~ age + sex + time mod <- mod_norm(formula = formula, data = data, weights = 1) ans <- draw_vals_augment_unfitted(mod) expect_true(is.data.frame(ans)) expect_identical(names(ans), c(names(data), ".fitted")) }) test_that("'draw_vals_augment_unfitted' works with 'bage_mod_pois' - has disp", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$deaths <- rpois(n = nrow(data), lambda = 20) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = 1) mod <- set_n_draw(mod, 10) ans_obtained <- draw_vals_augment_unfitted(mod) vals_components <- draw_vals_components_unfitted(mod, n_sim = 10) vals_disp <- vals_components$.fitted[vals_components$component == "disp"] vals_expected <- exp(make_linpred_comp(components = vals_components, data = mod$data, dimnames_terms = mod$dimnames_terms)) set.seed(mod$seed_augment) vals_fitted <- draw_vals_fitted(mod = mod, vals_expected = vals_expected, vals_disp = vals_disp) vals_outcome <- draw_vals_outcome_true(datamod = NULL, nm_distn = "pois", outcome_obs = rep(NA_real_, times = nrow(data)), fitted = vals_fitted, disp = vals_disp, offset = mod$offset) ans_expected <- tibble::as_tibble(data) ans_expected$deaths <- vals_outcome ans_expected$.observed <- vals_outcome / mod$offset ans_expected$.fitted <- vals_fitted ans_expected$.expected <- vals_expected expect_equal(ans_obtained, ans_expected) expect_identical(names(augment(fit(mod))), names(ans_obtained)) }) test_that("'draw_vals_augment_unfitted' works with 'bage_mod_pois' - no disp", { set.seed(0) n_sim <- 10 data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$deaths <- rpois(n = nrow(data), lambda = 20) data$popn <- rpois(n = nrow(data), lambda = 30) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_disp(mod, mean = 0) mod <- set_n_draw(mod, 10) ans_obtained <- draw_vals_augment_unfitted(mod) vals_components <- draw_vals_components_unfitted(mod = mod, n_sim = n_sim) vals_fitted <- exp(make_linpred_comp(components = vals_components, data = mod$data, dimnames_term = mod$dimnames_terms)) set.seed(mod$seed_augment) vals_outcome <- draw_vals_outcome_true(datamod = NULL, nm_distn = "pois", outcome_obs = rep(NA_real_, times = nrow(data)), fitted = vals_fitted, disp = vals_disp, offset = mod$offset) ans_expected <- tibble::as_tibble(data) ans_expected$deaths <- vals_outcome ans_expected$.observed <- vals_outcome / data$popn ans_expected$.fitted <- vals_fitted expect_equal(ans_obtained, ans_expected) expect_identical(names(augment(fit(mod))), names(ans_obtained)) }) test_that("'draw_vals_augment_unfitted' works with 'bage_mod_norm'", { set.seed(0) n_sim <- 10 data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$income <- rnorm(n = nrow(data), mean = 20, sd = 3) data$wt <- rpois(n = nrow(data), lambda = 100) formula <- income ~ age + sex + time mod <- mod_norm(formula = formula, data = data, weights = wt) mod <- set_n_draw(mod, 10) set.seed(1) ans_obtained <- draw_vals_augment_unfitted(mod) vals_components <- draw_vals_components_unfitted(mod = mod, n_sim = n_sim) vals_disp <- vals_components$.fitted[vals_components$component == "disp"] vals_disp <- mod$outcome_sd * vals_disp scale_outcome <- get_fun_scale_outcome(mod) vals_fitted <- scale_outcome(make_linpred_comp(components = vals_components, data = mod$data, dimnames_term = mod$dimnames_terms)) set.seed(mod$seed_augment) vals_outcome <- draw_vals_outcome_true(datamod = NULL, nm_distn = "norm", outcome_obs = rep(NA_real_, times = nrow(data)), fitted = vals_fitted, disp = vals_disp, offset = mod$offset) ans_expected <- tibble::as_tibble(mod$data) ans_expected$income <- vals_outcome ans_expected$.fitted <- vals_fitted expect_equal(ans_obtained, ans_expected) expect_identical(names(augment(fit(mod))), names(ans_obtained)) }) ## 'draw_vals_fitted' --------------------------------------------------------- test_that("'draw_vals_fitted' works with 'bage_mod_pois'", { set.seed(0) n_sim <- 10 data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) vals_disp <- draw_vals_disp(mod, n_sim = n_sim) vals_components <- draw_vals_components_unfitted(mod = mod, n_sim = n_sim) vals_expected <- exp(make_linpred_comp(components = vals_components, data = mod$data, dimnames_term = mod$dimnames_terms)) set.seed(1) ans_obtained <- draw_vals_fitted(mod, vals_expected = vals_expected, vals_disp = vals_disp) set.seed(1) ans_expected <- rvec::rgamma_rvec(n = nrow(data), shape = 1 / vals_disp, rate = 1 / (vals_disp * vals_expected)) expect_equal(ans_obtained, ans_expected) }) test_that("'draw_vals_fitted' works with 'bage_mod_binom'", { set.seed(0) n_sim <- 10 data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age + sex + time mod <- mod_binom(formula = formula, data = data, size = popn) vals_disp <- draw_vals_disp(mod, n_sim = n_sim) vals_components <- draw_vals_components_unfitted(mod = mod, n_sim = n_sim) invlogit <- function(x) exp(x) / (1 + exp(x)) vals_expected <- invlogit(make_linpred_comp(components = vals_components, data = mod$data, dimnames_term = mod$dimnames_terms)) set.seed(1) ans_obtained <- draw_vals_fitted(mod, vals_expected = vals_expected, vals_disp = vals_disp) set.seed(1) ans_expected <- rvec::rbeta_rvec(n = nrow(data), shape1 = vals_expected / vals_disp, shape2 = (1 - vals_expected) / vals_disp) expect_equal(ans_obtained, ans_expected) }) ## 'fit' ----------------------------------------------------------------- test_that("'fit' works with valid inputs - pois has exposure", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with valid inputs - pois has exposure", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$deaths <- rpois(n = nrow(data), lambda = 10000) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = 1) mod <- set_prior(mod, age ~ RW2(sd = 0)) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with valid inputs - binom", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age + sex + time mod <- mod_binom(formula = formula, data = data, size = popn) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with valid inputs - binom, disp is 0", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age + sex + time mod <- mod_binom(formula = formula, data = data, size = popn) |> set_disp(mean = 0) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with valid inputs - norm", { data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data[] <- lapply(data, factor) data$wt <- rpois(n = nrow(data), lambda = 100) data$val <- rnorm(n = nrow(data), mean = (data$sex == "F")) formula <- val ~ age + sex + time mod <- mod_norm(formula = formula, data = data, weights = wt) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with known intercept and sex effect", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, `(Intercept)` ~ Known(values = -2)) mod <- set_prior(mod, sex ~ Known(values = c(-0.1, 0.1))) ans_obtained <- fit(mod) expect_equal(ans_obtained$draws_effectfree[1,1], -2) expect_equal(ans_obtained$draws_effectfree[12:13,1], c(-0.1, 0.1)) }) test_that("'fit' works with AR1", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:sex + age:time + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, time ~ AR1()) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' gives the same imputed rate when outcome is NA and offset is NA", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2002, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:sex + age:time + time ## outcome NA set.seed(0) data_outcome <- data data_outcome$deaths[5] <- NA mod_outcome <- mod_pois(formula = formula, data = data_outcome, exposure = popn) mod_outcome <- fit(mod_outcome) ans_outcome <- augment(mod_outcome)$.fitted[5] ## offset NA set.seed(0) data_offset <- data data_offset$popn[5] <- NA mod_offset <- mod_pois(formula = formula, data = data_offset, exposure = popn) mod_offset <- fit(mod_offset) ans_offset <- augment(mod_offset)$.fitted[5] ## compare expect_equal(ans_outcome, ans_offset) }) test_that("'fit' works when all observed values for one year are NA", { data <- data.frame(deaths = c(NA, 2:10), age = rep(1:2, each = 5), time = 2001:2010) mod <- mod_pois(deaths ~ age + time, data = data, exposure = 1) mod_fitted <- fit(mod) expect_true(is_fitted(mod_fitted)) }) test_that("'fit' works when model consists of intercept only", { data <- data.frame(deaths = 1:10, age = rep(1:2, each = 5), time = 2001:2010) mod <- mod_pois(deaths ~ 1, data = data, exposure = 1) mod_fitted <- fit(mod) expect_true(is_fitted(mod_fitted)) }) test_that("'fit' works when model has no hyper-parameters", { data <- data.frame(deaths = 1:10, age = rep(1:2, each = 5), time = 2001:2010) mod <- mod_pois(deaths ~ 1, data = data, exposure = 1) |> set_disp(mean = 0) mod_fitted <- fit(mod) expect_true(is_fitted(mod_fitted)) }) test_that("'fit' works when single dimension", { data <- data.frame(deaths = 1:10, time = 2001:2010) mod <- mod_pois(deaths ~ time, data = data, exposure = 1) |> set_prior(time ~ RW(sd = 0)) mod_fitted <- fit(mod) expect_identical(nrow(mod_fitted$draws_effectfree), nrow(data)) }) test_that("'fit' works with SVD", { set.seed(0) data <- expand.grid(age = poputils::age_labels(type = "five", max = 60), time = 2000:2005, sex = c("Female", "Male")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:sex + age:time + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, age:sex ~ SVD(HMD)) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with Lin", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ sex + age + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, time ~ Lin()) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with Lin, n_by > 1", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ sex * time + age mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, sex:time ~ Lin()) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with RW - n_by > 0", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ sex * time + age mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, sex:time ~ RW()) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with RW2, n_by > 1", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2019, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ sex * time + age mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, sex:time ~ RW2()) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with no hyper", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ sex mod <- mod_pois(formula = formula, data = data, exposure = popn) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with AR", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ sex * time + age mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, time ~ AR(n = 2)) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with SVD, n_by > 1", { set.seed(0) data <- expand.grid(age = c(0:59, "60+"), time = 2000:2005, reg = c("a", "b")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:reg + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, age:reg ~ SVD(HMD)) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with SVD, n_by > 1", { set.seed(0) data <- expand.grid(age = c(0:59, "60+"), time = 2000:2001, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:sex:time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, age:sex:time ~ SVD(HMD)) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with Lin_AR", { set.seed(0) data <- expand.grid(age = c(0:59, "60+"), time = 2000:2005, reg = c("a", "b")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:reg + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, time ~ Lin_AR(s = 0.2)) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with Lin(s = 0)", { set.seed(0) data <- expand.grid(age = c(0:59, "60+"), time = 2000:2005, reg = c("a", "b")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:reg + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, time ~ Lin(s = 0)) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works with RW2_Infant()", { set.seed(0) data <- expand.grid(age = c(0:59, "60+"), time = 2000:2005, reg = c("a", "b")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:reg + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_prior(mod, age:reg ~ RW2_Infant()) ans_obtained <- fit(mod) mod <- set_prior(mod, age:reg ~ RW2_Infant(con = "by")) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' and 'forecast' work with SVD_AR", { data <- expand.grid(age = poputils::age_labels(type = "five", min = 15, max = 60), time = 2001:2010) data$population <- runif(n = nrow(data), min = 100, max = 300) data$deaths <- rpois(n = nrow(data), lambda = 0.05 * data$population) data$deaths[1] <- NA mod <- mod_pois(deaths ~ age:time, data = data, exposure = population) |> set_prior(age:time ~ SVD_AR1(LFP)) mod <- suppressWarnings(fit(mod)) expect_true(is_fitted(mod)) f <- forecast(mod, labels = 2011:2012) expect_setequal(c(names(f), ".deaths"), names(augment(mod))) }) test_that("'fit' and 'forecast' work with SVD_RW", { data <- expand.grid(age = poputils::age_labels(type = "five", min = 15, max = 60), time = 2001:2010) data$population <- runif(n = nrow(data), min = 100, max = 300) data$deaths <- rpois(n = nrow(data), lambda = 0.05 * data$population) data$deaths[1] <- NA mod <- mod_pois(deaths ~ age:time, data = data, exposure = population) |> set_prior(age:time ~ SVD_RW(LFP)) mod <- fit(mod) expect_true(is_fitted(mod)) f <- forecast(mod, labels = 2011:2012) expect_setequal(c(names(f), ".deaths"), names(augment(mod))) mod <- mod |> set_prior(age:time ~ SVD_RW(LFP, sd = 0)) mod <- fit(mod) expect_true(is_fitted(mod)) }) test_that("'fit' and 'forecast' work with SVD_RW2", { data <- expand.grid(age = poputils::age_labels(type = "five", min = 15, max = 60), time = 2001:2010) data$population <- runif(n = nrow(data), min = 100, max = 300) data$deaths <- rpois(n = nrow(data), lambda = 0.05 * data$population) data$deaths[1] <- NA mod <- mod_pois(deaths ~ age:time, data = data, exposure = population) |> set_prior(age:time ~ SVD_RW2(LFP)) mod <- fit(mod) expect_true(is_fitted(mod)) f <- forecast(mod, labels = 2011:2012) expect_setequal(c(names(f), ".deaths"), names(augment(mod))) mod <- mod |> set_prior(age:time ~ SVD_RW2(LFP, sd = 0)) mod <- fit(mod) expect_true(is_fitted(mod)) }) test_that("'fit' works inner-outer", { set.seed(0) ## structure of data data <- expand.grid(age = poputils::age_labels(type = "lt"), sex = c("Female", "Male"), time = 2011:2015, region = 1:10) data$population <- runif(n = nrow(data), min = 10, max = 1000) data$deaths <- NA ## generate single dataset mod_sim <- mod_pois(deaths ~ age * sex + region + time, data = data, exposure = population) |> set_prior(`(Intercept)` ~ NFix(s = 0.1)) |> set_prior(age ~ RW(s = 0.02)) |> set_prior(sex ~ NFix(sd = 0.1)) |> set_prior(age:sex ~ SVD(HMD)) |> set_prior(time ~ Lin_AR1(s = 0.05, sd = 0.02)) |> set_prior(region ~ NFix(sd = 0.05)) |> set_disp(mean = 0.005) data_sim <- mod_sim |> set_n_draw(n = 1) |> augment(quiet = TRUE) |> dplyr::mutate(deaths = rvec::draws_median(deaths)) |> dplyr::select(age, sex, time, region, population, deaths) ## specify estimation model mod_est <- mod_pois(deaths ~ age * sex + region + time, data = data_sim, exposure = population) |> set_prior(age:sex ~ SVD(HMD)) |> set_prior(time ~ Lin_AR()) ## fit estimation model mod_est <- mod_est |> fit(method = "inner-outer") expect_true(is_fitted(mod_est)) }) test_that("'fit' works when optimizer is 'optim'", { set.seed(0) data <- expand.grid(age = c(0:59, "60+"), time = 2000:2005, reg = c("a", "b")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:reg + time mod <- mod_pois(formula = formula, data = data, exposure = popn) ans_obtained <- fit(mod) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works when 'quiet' is FALSE and optimizer is 'nlminb'", { set.seed(0) data <- expand.grid(age = c(0:59, "60+"), time = 2000:2005, reg = c("a", "b")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:reg + time mod <- mod_pois(formula = formula, data = data, exposure = popn) suppressMessages( capture.output(ans_obtained <- fit(mod, quiet = FALSE), file = NULL) ) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works when 'quiet' is FALSE and optimizer is 'BFGS'", { set.seed(0) data <- expand.grid(age = c(0:59, "60+"), time = 2000:2005, reg = c("a", "b")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:reg + time mod <- mod_pois(formula = formula, data = data, exposure = popn) suppressMessages( capture.output(ans_obtained <- fit(mod, optimizer = "BFGS", quiet = FALSE), file = NULL) ) expect_s3_class(ans_obtained, "bage_mod") }) test_that("'fit' works when 'quiet' is FALSE and optimizer is 'CG'", { set.seed(0) data <- expand.grid(age = c(0:59, "60+"), time = 2000:2005, reg = c("a", "b")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age:reg + time mod <- mod_pois(formula = formula, data = data, exposure = popn) suppressMessages( capture.output(ans_obtained <- fit(mod, optimizer = "CG", quiet = FALSE), file = NULL) ) expect_s3_class(ans_obtained, "bage_mod") }) ## 'forecast' ----------------------------------------------------------------- test_that("'forecast' works with fitted model - output is 'augment'", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2004, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- fit(mod) ans_no_est <- forecast(mod, labels = 2005:2006) ans_est <- forecast(mod, labels = 2005:2006, include_estimates = TRUE) expect_identical(names(ans_est), names(ans_no_est)) }) test_that("'forecast' works with fitted model - uses newdata", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2004, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- fit(mod) newdata <- make_data_forecast_labels(mod, labels = 2005) newdata$deaths <- rpois(n = nrow(newdata), lambda = 10) ans_est <- forecast(mod, newdata = newdata, include_estimates = TRUE) expect_identical(names(ans_est), names(augment(mod))) }) test_that("'forecast' gives same answer when run twice - output is 'augment'", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2004, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) ans1 <- forecast(mod, labels = 2005:2006) ans2 <- forecast(mod, labels = 2005:2006) ans3 <- forecast(mod, labels = 2005:2006, output = "aug", include_estimates = TRUE) ans3 <- ans3[ans3$time >= 2005,] expect_identical(ans1, ans2) expect_identical(ans1, ans3) }) test_that("'forecast' works with fitted model - output is 'components'", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2004, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- fit(mod) ans_no_est <- forecast(mod, labels = 2005:2006, output = "comp") ans_est <- forecast(mod, labels = 2005:2006, output = "comp", include_estimates = TRUE) expect_identical(names(ans_est), names(ans_no_est)) }) test_that("'forecast' gives same answer when run twice - output is 'components'", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2004, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) ans1 <- forecast(mod, labels = 2005:2006, output = "comp") ans2 <- forecast(mod, labels = 2005:2006, output = "components") expect_identical(ans1, ans2) }) test_that("'forecast' gives same answer when run twice - output is 'components'", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2004, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) ans1 <- forecast(mod, labels = 2005:2006, output = "comp") ans2 <- forecast(mod, labels = 2005:2006, output = "components") expect_identical(ans1, ans2) }) test_that("'forecast' throws correct error when time var not identified'", { set.seed(0) data <- expand.grid(age = 0:4, epoch = 2000:2004, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age * sex mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- fit(mod) expect_error(forecast(mod, labels = 2005:2006, output = "comp"), "Can't forecast when time variable not identified.") }) test_that("'forecast' throws correct error when labels and newdata both supplied'", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2004, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age * sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- fit(mod) labels <- 2007:2008 newdata <- make_data_forecast_labels(mod = mod, labels = labels) expect_error(forecast(mod, labels = labels, newdata = newdata), "Values supplied for `newdata` and for `labels`.") }) test_that("'forecast' throws error when neither labels nor newdata supplied", { set.seed(0) data <- expand.grid(age = 0:4, time = 2000:2004, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- fit(mod) newdata <- make_data_forecast_labels(mod, 2005:2006) newdata$deaths <- rpois(n = nrow(newdata), lambda = 10) expect_error(forecast(mod, include_estimates = TRUE), "No value supplied for `newdata` or for `labels`.") }) ## 'forecast_augment' -------------------------------------------------------- test_that("'forecast_augment' works - Poisson, has disp, no forecasted offset", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$deaths <- rpois(n = nrow(data), lambda = 100) data$exposure <- rpois(n = nrow(data), lambda = 1000) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = exposure) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) components_est <- components(mod) labels_forecast <- 2006:2008 data_forecast <- make_data_forecast_labels(mod = mod, labels_forecast = labels_forecast) set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) }) test_that("'forecast_augment' works - Poisson, no offset", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$deaths <- rpois(n = nrow(data), lambda = 100) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = 1) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) components_est <- components(mod) data_forecast <- make_data_forecast_labels(mod = mod, labels_forecast = 2006:2008) labels_forecast <- 2006:2008 set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) expect_true(rvec::is_rvec(ans$deaths)) expect_true(all(is.na(ans$.observed))) }) test_that("'forecast_augment' works - Poisson, has disp, has forecasted offset", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$deaths <- rpois(n = nrow(data), lambda = 100) data$exposure <- rpois(n = nrow(data), lambda = 1000) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = exposure) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) components_est <- components(mod) data_forecast <- make_data_forecast_labels(mod = mod, labels_forecast = 2006:2008) labels_forecast <- 2006:2008 data_forecast$exposure <- rpois(n = nrow(data_forecast), lambda = 1000) set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) expect_true(rvec::is_rvec(ans$deaths)) expect_true(all(is.na(ans$.observed))) }) test_that("'forecast_augment' works - Poisson, has disp, has forecasted offset, imputed historical est", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$deaths <- rpois(n = nrow(data), lambda = 100) data$deaths[1] <- NA data$exposure <- rpois(n = nrow(data), lambda = 1000) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = exposure) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) components_est <- components(mod) data_forecast <- make_data_forecast_labels(mod = mod, labels_forecast = 2006:2008) labels_forecast <- 2006:2008 data_forecast$exposure <- rpois(n = nrow(data_forecast), lambda = 1000) set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) expect_true(all(is.na(ans$deaths))) expect_true(all(is.na(ans$.observed))) expect_true(rvec::is_rvec(ans$.deaths)) }) test_that("'forecast_augment' works - Poisson, has disp, has forecasted offset, datamod", { set.seed(0) data <- expand.grid(age = 0:5, time = 2000:2005, sex = c("F", "M")) data$deaths <- rpois(n = nrow(data), lambda = 30) * 3 data$deaths[1] <- NA data$exposure <- rpois(n = nrow(data), lambda = 1000) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = exposure) mod <- set_n_draw(mod, n = 10) mod <- set_datamod_outcome_rr3(mod) mod <- fit(mod) components_est <- components(mod) data_forecast <- make_data_forecast_labels(mod = mod, labels_forecast = 2006:2008) labels_forecast <- 2006:2008 data_forecast$exposure <- rpois(n = nrow(data_forecast), lambda = 1000) set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) expect_true(rvec::is_rvec(ans$deaths)) expect_true(all(is.na(ans$.observed))) expect_true(rvec::is_rvec(ans$.deaths)) expect_true(all(rvec::extract_draw(ans$deaths) %% 3 == 0)) }) test_that("'forecast_augment' works - binomial, no disp", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age + sex + time mod <- mod_binom(formula = formula, data = data, size = popn) mod <- set_n_draw(mod, n = 10) mod <- set_disp(mod, mean = 0) mod <- fit(mod) components_est <- components(mod) labels_forecast <- 2006:2008 data_forecast <- make_data_forecast_labels(mod= mod, labels_forecast = labels_forecast) set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) }) test_that("'forecast_augment' works - normal", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data)) formula <- income ~ age + sex * time mod <- mod_norm(formula = formula, data = data, weights = popn) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) components_est <- components(mod) labels_forecast <- 2006:2008 data_forecast <- make_data_forecast_labels(mod= mod, labels_forecast = labels_forecast) set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) }) test_that("'forecast_augment' works - normal, has forecasted offset", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data)) formula <- income ~ age + sex * time mod <- mod_norm(formula = formula, data = data, weights = popn) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) components_est <- components(mod) labels_forecast <- 2006:2008 data_forecast <- make_data_forecast_labels(mod= mod, labels_forecast = labels_forecast) data_forecast$popn <- rpois(n = nrow(data_forecast), lambda = 1000) set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) expect_true(rvec::is_rvec(ans$income)) }) test_that("'forecast_augment' works - normal, no offset", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$income <- rnorm(n = nrow(data)) formula <- income ~ age + sex * time mod <- mod_norm(formula = formula, data = data, weights = 1) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) components_est <- components(mod) labels_forecast <- 2006:2008 data_forecast <- make_data_forecast_labels(mod= mod, labels_forecast = labels_forecast) set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) expect_true(rvec::is_rvec(ans$income)) }) test_that("'forecast_augment' works - normal, estimated has imputed", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data)) data$income[1] <- NA formula <- income ~ age + sex * time mod <- mod_norm(formula = formula, data = data, weights = popn) mod <- set_n_draw(mod, n = 10) mod <- fit(mod) components_est <- components(mod) labels_forecast <- 2006:2008 data_forecast <- make_data_forecast_labels(mod= mod, labels_forecast = labels_forecast) data_forecast$popn <- rpois(n = nrow(data_forecast), lambda = 1000) set.seed(1) components_forecast <- forecast_components(mod = mod, components_est = components_est, labels_forecast = labels_forecast) components <- vctrs::vec_rbind(components_est, components_forecast) dimnames_forecast <- make_dimnames_terms_forecast(dimnames_terms = mod$dimnames_terms, var_time = mod$var_time, labels_forecast = labels_forecast, time_only = FALSE) linpred_forecast <- make_linpred_comp(components = components, data = data_forecast, dimnames_terms = dimnames_forecast) ans <- forecast_augment(mod = mod, data_forecast = data_forecast, linpred_forecast = linpred_forecast) aug_est <- augment(mod) expect_setequal(ans$age, aug_est$age) expect_setequal(ans$sex, aug_est$sex) expect_setequal(ans$time, 2006:2008) expect_identical(names(ans), names(aug_est)) expect_true(rvec::is_rvec(ans$.income)) expect_true(all(is.na(ans$income))) }) ## 'get_fun_ag_offset' -------------------------------------------------------- test_that("'get_fun_ag_offset' works with binom", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age + sex + time mod <- mod_binom(formula = formula, data = data, size = popn) f <- get_fun_ag_offset(mod) ans_obtained <- f(mod$offset) ans_expected <- sum(mod$offset) expect_identical(ans_obtained, ans_expected) }) test_that("'get_fun_ag_offset' works with norm", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$wt <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data)) formula <- income ~ age + sex + time mod <- mod_norm(formula = formula, data = data, weights = wt) f <- get_fun_ag_offset(mod) ans_obtained <- f(mod$offset) n <- length(mod$offset) ans_expected <- (n^2) / sum(1 / mod$offset) expect_identical(ans_obtained, ans_expected) }) ## 'get_fun_ag_outcome' -------------------------------------------------------- test_that("'get_fun_ag_outcome' works with binom", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age + sex + time mod <- mod_binom(formula = formula, data = data, size = popn) f <- get_fun_ag_outcome(mod) ans_obtained <- f(mod$outcome) ans_expected <- sum(mod$outcome) expect_identical(ans_obtained, ans_expected) }) test_that("'get_fun_ag_outcome' works with norm", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$wt <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data)) formula <- income ~ age + sex + time mod <- mod_norm(formula = formula, data = data, weights = wt) f <- get_fun_ag_outcome(mod) ans_obtained <- f(mod$outcome) ans_expected <- mean(mod$outcome) expect_identical(ans_obtained, ans_expected) }) ## 'get_fun_inv_transform' ---------------------------------------------------- test_that("'get_fun_inv_transform' works with valid inputs", { set.seed(0) x <- runif(100) logit <- function(x) log(x) - log(1 - x) expect_equal(get_fun_inv_transform(structure(1, class = "bage_mod_pois"))(log(x)), x) expect_equal(get_fun_inv_transform(structure(1, class = "bage_mod_binom"))(logit(x)), x) expect_equal(get_fun_inv_transform(structure(1, class = "bage_mod_norm"))(x), x) }) ## 'get_fun_scale_outcome' -------------------------------------------------------- test_that("'get_fun_scale_outcome' works with valid inputs", { expect_equal(get_fun_scale_outcome(structure(1, class = c("bage_mod_pois", "bage_mod")))(1), 1) expect_equal(get_fun_scale_outcome(structure(1, class = c("bage_mod_binom", "bage_mod")))(1), 1) expect_equal(get_fun_scale_outcome(structure(list(outcome_mean = 3, outcome_sd = 2), class = c("bage_mod_norm", "bage_mod")))(1), 5) }) ## 'get_nm_outcome' ----------------------------------------------------------- test_that("'get_nm_outcome' works with 'bage_mod_pois'", { set.seed(0) n_sim <- 10 data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$deaths <- rpois(n = nrow(data), lambda = 20) data$popn <- rpois(n = nrow(data), lambda = 30) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) expect_identical(get_nm_outcome(mod), "deaths") }) ## 'get_nm_outcome_obs' ------------------------------------------------------- test_that("'get_nm_outcome_obs' works with 'bage_mod_pois'", { set.seed(0) n_sim <- 10 data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$deaths <- 3 * rpois(n = nrow(data), lambda = 10) data$popn <- rpois(n = nrow(data), lambda = 30) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) expect_identical(get_nm_outcome_obs(mod), "deaths") mod <- set_datamod_outcome_rr3(mod) expect_identical(get_nm_outcome_obs(mod), ".deaths") }) ## 'has_disp' ----------------------------------------------------------------- test_that("'has_disp' works with valid inputs", { data <- data.frame(deaths = 1:10, time = 2001:2010) mod <- mod_pois(deaths ~ time, data = data, exposure = 1) expect_true(has_disp(mod)) mod <- set_disp(mod, mean = 0) expect_false(has_disp(mod)) }) ## 'is_fitted' ---------------------------------------------------------------- test_that("'is_fitted' works with valid inputs", { data <- data.frame(deaths = 1:10, time = 2001:2010) mod <- mod_pois(deaths ~ time, data = data, exposure = 1) expect_false(is_fitted(mod)) mod <- fit(mod) expect_true(is_fitted(mod)) }) ## 'make_i_lik_mod' ----------------------------------------------------------- test_that("'make_i_lik_mod' works with bage_mod_pois", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- 3 * rpois(n = nrow(data), lambda = 5) formula <- deaths ~ age + time + sex mod <- mod_pois(formula = formula, data = data, exposure = popn) expect_identical(make_i_lik_mod(mod), 303L) mod0 <- set_disp(mod, mean = 0) expect_identical(make_i_lik_mod(mod0), 301L) expect_identical(make_i_lik_mod(set_datamod_outcome_rr3(mod)), 304L) expect_identical(make_i_lik_mod(set_datamod_outcome_rr3(mod0)), 302L) }) test_that("'make_i_lik_mod' works with bage_mod_binom", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- 3 * rbinom(n = nrow(data), size = data$popn, prob = 0.02) formula <- deaths ~ age + time + sex mod <- mod_binom(formula = formula, data = data, size = popn) expect_identical(make_i_lik_mod(mod), 103L) mod0 <- set_disp(mod, mean = 0) expect_identical(make_i_lik_mod(mod0), 101L) expect_identical(make_i_lik_mod(set_datamod_outcome_rr3(mod)), 104L) expect_identical(make_i_lik_mod(set_datamod_outcome_rr3(mod0)), 102L) }) test_that("'make_i_lik_mod' works with bage_mod_norm", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$wt <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data), sd = 10) formula <- income ~ age + time + sex mod <- mod_norm(formula = formula, data = data, weights = wt) expect_identical(make_i_lik_mod(mod), 201L) mod$datamod_outcome <- "wrong" expect_error(make_i_lik_mod(mod), "Internal error: Invalid inputs.") }) ## 'make_mod_disp' ----------------------------------------------------------- test_that("'make_mod_disp' works with pois", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rpois(n = nrow(data), lambda = 0.3 * data$popn) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- fit(mod) mod_disp <- make_mod_disp(mod) expect_setequal(names(mod_disp$priors), "(Intercept)") mu <- exp(make_linpred_raw(mod, point = TRUE)) expect_equal(mod_disp$offset, mod$offset * mu) expect_true(mod_disp$mean_disp > 0) expect_identical(length(mod_disp$dimnames_terms), 1L) }) test_that("'make_mod_disp' works with pois - large dataset", { set.seed(0) data <- expand.grid(time = 1:6000, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rpois(n = nrow(data), lambda = 0.3 * data$popn) formula <- deaths ~ sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) |> set_prior(time ~ RW(sd = 0)) mod$point_effectfree <- rnorm(1 + 5999 + 2) mod_disp <- make_mod_disp(mod) expect_true(identical(nrow(mod_disp$data), 10000L)) }) test_that("'make_mod_disp' works with binom", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age * sex + sex * time mod <- mod_binom(formula = formula, data = data, size = popn) mod <- fit(mod) mod_disp <- make_mod_disp(mod) expect_setequal(names(mod_disp$priors), names(mod$priors)) expect_true(mod_disp$mean_disp > 0) expect_s3_class(mod_disp$priors[["age"]], "bage_prior_known") expect_equal(mod_disp$offset, mod$offset) }) test_that("'make_mod_disp' works with binom", { set.seed(0) data <- expand.grid(time = 1:6, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rbinom(n = nrow(data), prob = 0.2, size = data$popn) formula <- deaths ~ sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- fit(mod) mod_disp <- make_mod_disp(mod) expect_setequal(names(mod_disp$priors), "(Intercept)") mu <- exp(make_linpred_raw(mod, point = TRUE)) expect_true(mod_disp$mean_disp > 0) }) test_that("'make_mod_disp' works with binom - large dataset", { set.seed(0) data <- expand.grid(time = 1:6000, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rbinom(n = nrow(data), prob = 0.3, size = data$popn) formula <- deaths ~ sex + time mod <- mod_binom(formula = formula, data = data, size = popn) |> set_prior(time ~ RW2(sd = 0)) mod$point_effectfree <- rnorm(1 + 5999 + 2) mod$draws_effectfree <- 1 ## to fool 'is_fitted' mod_disp <- make_mod_disp(mod) expect_true(identical(nrow(mod_disp$data), 10000L)) }) test_that("'make_mod_disp' works with norm", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$wt <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data)) formula <- income ~ age * sex + sex * time mod <- mod_norm(formula = formula, data = data, weights = wt) mod <- fit(mod) mod_disp <- make_mod_disp(mod) expect_setequal(names(mod_disp$priors), "(Intercept)") mu <- make_linpred_raw(mod, point = TRUE) expect_equal(mod_disp$outcome, mod$outcome - mu) expect_true(mod_disp$mean_disp > 0) expect_identical(length(mod_disp$dimnames_terms), 1L) }) test_that("'make_mod_disp' works with norm - large dataset", { set.seed(0) data <- expand.grid(time = 2000:8000, sex = c("F", "M")) data$wt <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data)) formula <- income ~ time + sex mod <- mod_norm(formula = formula, data = data, weights = wt) mod$point_effectfree <- rnorm(1 + 6001 + 2) mod_disp <- make_mod_disp(mod) expect_true(identical(nrow(mod_disp$data), 10000L)) }) ## 'make_mod_inner' ----------------------------------------------------------- test_that("'make_mod_inner' works with pois", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rpois(n = nrow(data), lambda = 0.3 * data$popn) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) use_term <- make_use_term(mod, vars_inner = c("age", "sex")) ans_obtained <- make_mod_inner(mod, use_term) ans_expected <- reduce_model_terms(mod, use_term = use_term) ans_expected$mean_disp <- 0 expect_identical(ans_obtained, ans_expected) }) test_that("'make_mod_inner' works with norm", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$wt <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data)) formula <- income ~ age * sex + sex * time mod <- mod_norm(formula = formula, data = data, weights = wt) use_term <- make_use_term(mod, vars_inner = c("age", "sex")) ans_obtained <- make_mod_inner(mod, use_term = use_term) ans_expected <- reduce_model_terms(mod, use_term = use_term) expect_identical(ans_obtained, ans_expected) }) ## 'make_mod_outer' ----------------------------------------------------------- test_that("'make_mod_outer' works with pois", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rpois(n = nrow(data), lambda = 0.3 * data$popn) formula <- deaths ~ age * sex + sex * time mod <- mod_pois(formula = formula, data = data, exposure = popn) use_term <- make_use_term(mod, vars_inner = c("age", "sex")) mod_inner <- reduce_model_terms(mod, use_term = use_term) mod_inner <- fit(mod_inner) mod_outer <- make_mod_outer(mod, mod_inner = mod_inner, use_term = use_term) expect_setequal(names(mod_outer$priors), c("time", "sex:time")) mu <- exp(make_linpred_raw(mod_inner, point = TRUE)) expect_equal(mod_outer$offset, mod$offset * mu) expect_equal(mod_outer$mean_disp, 0) }) test_that("'make_mod_outer' works with binom", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 1000) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age * sex + sex * time mod <- mod_binom(formula = formula, data = data, size = popn) use_term <- make_use_term(mod, vars_inner = c("age", "sex")) mod_inner <- reduce_model_terms(mod, use_term = use_term) mod_inner <- fit(mod_inner) mod_outer <- make_mod_outer(mod, mod_inner = mod_inner, use_term = use_term) expect_setequal(names(mod_outer$priors), names(mod$priors)) expect_s3_class(mod_outer$priors[["age"]], "bage_prior_known") expect_equal(mod_outer$offset, mod$offset) expect_equal(mod_outer$mean_disp, 0) }) test_that("'make_mod_outer' works with norm", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$wt <- rpois(n = nrow(data), lambda = 1000) data$income <- rnorm(n = nrow(data)) formula <- income ~ age * sex + sex * time mod <- mod_norm(formula = formula, data = data, weights = wt) use_term <- make_use_term(mod, vars_inner = c("age", "sex")) mod_inner <- reduce_model_terms(mod, use_term = use_term) mod_inner <- fit(mod_inner) mod_outer <- make_mod_outer(mod, mod_inner = mod_inner, use_term = use_term) expect_setequal(names(mod_outer$priors), c("time", "sex:time")) mu <- make_linpred_raw(mod_inner, point = TRUE) expect_equal(mod_outer$outcome, mod$outcome - mu) expect_true(mod_outer$mean_disp > 0) }) ## 'make_par_disp' --------------------------------------------------- test_that("'make_par_disp' works with bage_mod_pois - no NAs", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + time + sex mod <- mod_pois(formula = formula, data = data, exposure = popn) outcome <- data$deaths meanpar <- rvec::rpois_rvec(n = 120, lambda = outcome, n_draw = 5) disp <- rvec::runif_rvec(n = 1, min = 0.1, max = 0.5, n_draw = 5) set.seed(0) ans_obtained <- make_par_disp(mod, meanpar = meanpar, disp = disp) set.seed(0) ans_expected <- rvec::rgamma_rvec(n = length(meanpar), data$deaths + 1/disp, data$popn + 1/(disp*meanpar)) expect_equal(ans_obtained, ans_expected) }) test_that("'make_par_disp' works with bage_mod_pois - has NAs", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) data$popn[1] <- NA data$deaths[2] <- NA formula <- deaths ~ age + time + sex mod <- mod_pois(formula = formula, data = data, exposure = popn) meanpar <- rvec::rpois_rvec(n = 120, lambda = 100, n_draw = 5) disp <- rvec::runif_rvec(n = 1, min = 0.1, max = 0.5, n_draw = 5) set.seed(0) ans_obtained <- make_par_disp(mod, meanpar = meanpar, disp = disp) set.seed(0) data$popn[1:2] <- 0 data$deaths[1:2] <- 0 ans_expected <- rvec::rgamma_rvec(n = length(meanpar), data$deaths + 1/disp, data$popn + 1/(disp*meanpar)) expect_equal(ans_obtained, ans_expected) }) test_that("'make_par_disp' works with bage_mod_binom", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age + time + sex mod <- mod_binom(formula = formula, data = data, size = popn) meanpar <- rvec::runif_rvec(n = 120, n_draw = 5) disp <- rvec::runif_rvec(n = 1, min = 0.1, max = 0.8, n_draw = 5) set.seed(0) ans_obtained <- make_par_disp(mod, meanpar = meanpar, disp = disp) set.seed(0) ans_expected <- rvec::rbeta_rvec(n = length(meanpar), data$deaths + meanpar/disp, data$popn - data$deaths + (1 - meanpar)/disp) expect_equal(ans_obtained, ans_expected) }) test_that("'make_par_disp' works with bage_mod_binom - has NAs", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) data$popn[1] <- NA data$deaths[2] <- NA formula <- deaths ~ age + time + sex mod <- mod_binom(formula = formula, data = data, size = popn) outcome <- data$deaths offset <- data$popn meanpar <- rvec::runif_rvec(n = 120, n_draw = 5) disp <- rvec::runif_rvec(n = 1, min = 0.1, max = 0.8, n_draw = 5) set.seed(0) ans_obtained <- make_par_disp(mod, meanpar = meanpar, disp = disp) set.seed(0) data$popn[1:2] <- 0 data$deaths[1:2] <- 0 ans_expected <- rvec::rbeta_rvec(n = length(meanpar), data$deaths + meanpar/disp, data$popn - data$deaths + (1 - meanpar)/disp) expect_equal(ans_obtained, ans_expected) }) ## 'make_observed' ------------------------------------------------------------ test_that("'make_observed' works with bage_mod_pois", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex mod <- mod_pois(formula = formula, data = data, exposure = popn) ans_obtained <- make_observed(mod) ans_expected <- as.double(mod$outcome / mod$offset) expect_equal(ans_obtained, ans_expected) }) test_that("'make_observed' works with bage_mod_binom", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age + sex mod <- mod_binom(formula = formula, data = data, size = popn) ans_obtained <- make_observed(mod) ans_expected <- as.double(mod$outcome / mod$offset) expect_equal(ans_obtained, ans_expected) }) test_that("'make_observed' throws expected with bage_mod_norm", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 10) formula <- deaths ~ age + sex mod <- mod_norm(formula = formula, data = data, weights = 1) expect_error(make_observed(mod), "Internal error: `make_observed\\(\\)` called on object of class") }) ## 'model_descr' -------------------------------------------------------------- test_that("'model_descr' works with valid inputs", { expect_identical(model_descr(structure(1, class = "bage_mod_pois")), "Poisson") expect_identical(model_descr(structure(1, class = "bage_mod_binom")), "binomial") expect_identical(model_descr(structure(1, class = "bage_mod_norm")), "normal") }) ## 'nm_distn' ----------------------------------------------------------------- test_that("'nm_distn' works with valid inputs", { expect_identical(nm_distn(structure(1, class = "bage_mod_pois")), "pois") expect_identical(nm_distn(structure(1, class = "bage_mod_binom")), "binom") expect_identical(nm_distn(structure(1, class = "bage_mod_norm")), "norm") }) ## 'nm_offset' ---------------------------------------------------------------- test_that("'nm_offset' works with valid inputs", { expect_identical(nm_offset(structure(1, class = "bage_mod_pois")), "exposure") expect_identical(nm_offset(structure(1, class = "bage_mod_binom")), "size") expect_identical(nm_offset(structure(1, class = "bage_mod_norm")), "weights") }) ## 'print' -------------------------------------------------------------------- test_that("'print' works with mod_pois", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- 3 * rpois(n = nrow(data), lambda = 0.4 * data$popn) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) |> set_datamod_outcome_rr3() expect_snapshot(print(mod)) ## don't use snapshot, since printed option includes timings, which can change capture.output(print(fit(mod)), file = NULL) }) test_that("'print' works with mod_pois - inner-outer fitting method", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- 3 * rpois(n = nrow(data), lambda = 0.4 * data$popn) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) expect_snapshot(print(mod)) ## don't use snapshot, since printed option includes timings, which can change capture.output(print(fit(mod, method = "inner-outer", vars_inner = "age")), file = NULL) }) ## 'replicate_data' ----------------------------------------------------------- test_that("'replicate_data' works with mod_pois", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rpois(n = nrow(data), lambda = 0.4 * data$popn) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- fit(mod) ans <- replicate_data(mod) expect_identical(names(ans), c(".replicate", names(data))) expect_identical(nrow(ans), nrow(data) * 20L) tab <- tapply(ans$deaths, ans$.replicate, sd) expect_true(var(tab) > 0) ans_fit <- replicate_data(mod, condition_on = "fitted") expect_equal(mean(ans_fit$deaths), mean(ans$deaths), tolerance = 0.01) }) test_that("'replicate_data' works with mod_pois, rr3 data model", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- 3 * rpois(n = nrow(data), lambda = 0.1 * data$popn) formula <- deaths ~ age + sex + time mod <- mod_pois(formula = formula, data = data, exposure = popn) mod <- set_datamod_outcome_rr3(mod) mod <- fit(mod) ans <- replicate_data(mod) expect_identical(names(ans), c(".replicate", names(data))) expect_identical(nrow(ans), nrow(data) * 20L) tab <- tapply(ans$deaths, ans$.replicate, sd) expect_true(var(tab) > 0) ans_fit <- replicate_data(mod, condition_on = "fitted") expect_equal(mean(ans_fit$deaths), mean(ans$deaths), tolerance = 0.02) expect_true(all(ans_fit$deaths %% 3 == 0)) }) test_that("'replicate_data' works with mod_binom", { set.seed(0) data <- expand.grid(age = 0:29, time = 2000:2002, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age + sex + time mod <- mod_binom(formula = formula, data = data, size = popn) mod <- fit(mod) ans <- replicate_data(mod) expect_identical(names(ans), c(".replicate", names(data))) expect_identical(nrow(ans), nrow(data) * 20L) tab <- tapply(ans$deaths, ans$.replicate, mean) expect_true(var(tab) > 0) ans_fit <- replicate_data(mod, condition_on = "fitted") expect_equal(mean(ans_fit$deaths), mean(ans$deaths), tolerance = 0.01) }) test_that("'replicate_data' works with mod_binom, rr3 data model", { set.seed(0) data <- expand.grid(age = 0:29, time = 2000:2002, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- 3 * rbinom(n = nrow(data), size = data$popn, prob = 0.1) formula <- deaths ~ age + sex + time mod <- mod_binom(formula = formula, data = data, size = popn) mod <- set_datamod_outcome_rr3(mod) mod <- fit(mod) ans <- replicate_data(mod) expect_identical(names(ans), c(".replicate", names(data))) expect_identical(nrow(ans), nrow(data) * 20L) tab <- tapply(ans$deaths, ans$.replicate, mean) expect_true(var(tab) > 0) ans_fit <- replicate_data(mod, condition_on = "fitted") expect_equal(mean(ans_fit$deaths), mean(ans$deaths), tolerance = 0.03) expect_true(all(ans_fit$deaths %% 3 == 0)) }) test_that("'replicate_data' works with mod_norm", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$income <- rnorm(n = nrow(data)) formula <- income ~ age + sex + time mod <- mod_norm(formula = formula, data = data, weights = 1) mod <- set_prior(mod, age ~ N()) mod <- set_prior(mod, time ~ N()) mod <- fit(mod) ans <- replicate_data(mod) expect_identical(names(ans), c(".replicate", names(data))) expect_identical(nrow(ans), nrow(data) * 20L) tab <- tapply(ans$income, ans$.replicate, mean) expect_false(any(duplicated(tab))) expect_warning(replicate_data(mod, condition_on = "expected"), "Ignoring value for `condition_on`.") }) ## 'tidy' --------------------------------------------------------------------- test_that("'tidy' works with valid inputs", { set.seed(0) data <- expand.grid(age = 0:9, time = 2000:2005, sex = c("F", "M")) data$popn <- rpois(n = nrow(data), lambda = 100) data$deaths <- rbinom(n = nrow(data), size = data$popn, prob = 0.3) formula <- deaths ~ age * sex mod <- mod_binom(formula = formula, data = data, size = popn) ans_unfit <- tidy(mod) expect_true(is.data.frame(ans_unfit)) expect_identical(names(ans_unfit), c("term", "prior", "along", "n_par", "n_par_free")) mod_fitted <- fit(mod) ans_fitted <- tidy(mod_fitted) expect_true(is.data.frame(ans_fitted)) expect_identical(names(ans_fitted), c("term", "prior", "along", "n_par", "n_par_free", "std_dev")) })