test_that("deterministic calculate works with correct lists", { skip_if_not(check_tf_version()) # unknown variable x <- as_data(c(1, 2)) a <- normal(0, 1) y <- a * x vals <- calculate(y, values = list(a = 3)) expect_equal(vals$y, matrix(c(3, 6))) # unknown variable and new data x <- as_data(c(1, 2)) a <- normal(0, 1) y <- a * x vals <- calculate(y, values = list(a = 6, x = c(2, 1))) expect_equal(vals$y, matrix(c(12, 6))) # fixed value depending on multiple variables x <- as_data(c(1, 2)) a1 <- normal(0, 1) a2 <- normal(0, 1, truncation = c(0, Inf)) a <- a1 * a2 y <- a * x vals <- calculate(y, values = list(a = 6, x = c(2, 1))) expect_equal(vals$y, matrix(c(12, 6))) }) test_that("stochastic calculate works with correct lists", { skip_if_not(check_tf_version()) # nolint start # with y ~ N(100, 1 ^ 2), it should be very unlikely that y <= 90 # ( pnorm(90, 100, 1) = 7e-24 ) # nolint end nsim <- 97 # fix variable a <- normal(0, 1) y <- normal(a, 1) sims <- calculate(y, nsim = nsim, values = list(a = 100)) expect_true(all(sims$y > 90)) expect_equal(dim(sims$y), c(nsim, dim(y))) # fix variable with more dims on y a <- normal(0, 1) y <- normal(a, 1, dim = c(3, 3, 3)) sims <- calculate(y, nsim = nsim, values = list(a = 100)) expect_true(all(sims$y > 90)) expect_equal(dim(sims$y), c(nsim, dim(y))) # fix variable and new data x <- as_data(1) a <- normal(0, 1) y <- normal(a * x, 1) sims <- calculate(y, nsim = nsim, values = list(a = 50, x = 2)) expect_true(all(sims$y > 90)) expect_equal(dim(sims$y), c(nsim, dim(y))) # data with distribution x <- as_data(1) y <- as_data(randn(10)) a <- normal(0, 1) distribution(y) <- normal(a * x, 1) sims <- calculate(y, nsim = nsim, values = list(a = 50, x = 2)) expect_true(all(sims$y > 90)) expect_equal(dim(sims$y), c(nsim, dim(y))) # multivariate data with distribution n <- 10 k <- 3 x <- ones(1, k) y <- as_data(randn(n, k)) a <- normal(0, 1) distribution(y) <- multivariate_normal(a * x, diag(k), n_realisations = n) sims <- calculate(y, nsim = nsim, values = list(a = 50, x = rep(2, k))) expect_true(all(sims$y > 90)) expect_equal(dim(sims$y), c(nsim, dim(y))) # weird multivariate data with distribution n <- 10 k <- 3 x <- ones(1, k) y <- matrix(0, n, k) idx <- sample.int(k, n, replace = TRUE) y[cbind(seq_len(n), idx)] <- 1 y <- as_data(y) a <- normal(0, 1, dim = c(1, k)) distribution(y) <- categorical(ilogit(a * x), n_realisations = n) sims <- calculate(y, nsim = nsim, values = list( a = c(50, 5, 0.5), x = rep(2, k) ) ) expect_true(all(apply(sims$y, 1:2, sum) == 1)) expect_equal(dim(sims$y), c(nsim, dim(y))) }) test_that("deterministic calculate works with greta_mcmc_list objects", { skip_if_not(check_tf_version()) samples <- 10 x <- as_data(c(1, 2)) a <- normal(0, 1) y <- a * x m <- model(y) draws <- mcmc(m, warmup = 0, n_samples = samples, verbose = FALSE) # with an existing greta array y_values <- calculate(y, values = draws) # correct class expect_s3_class(y_values, "greta_mcmc_list") # correct dimensions expect_equal(dim(y_values[[1]]), c(10, 2)) # all valid values expect_true(all(is.finite(as.vector(y_values[[1]])))) # with a new greta array, based on a different element in the model new_values <- calculate(a^2, values = draws) # correct class expect_s3_class(new_values, "greta_mcmc_list") # correct dimensions expect_equal(dim(new_values[[1]]), c(10, 1)) # all valid values expect_true(all(is.finite(as.vector(new_values[[1]])))) }) test_that("calculate with greta_mcmc_list doesn't mix up variables", { skip_if_not(check_tf_version()) a <- normal(-100, 0.001) b <- normal(100, 0.001) c <- normal(0, 0.001) result <- b * c + a model <- model(a, b) draws <- mcmc(model, warmup = 100, n_samples = 100, verbose = FALSE) result_draws <- calculate(result, values = draws) vals <- as.vector(as.matrix(result_draws)) # the values should be around -100 if the variables aren't mixed up, or a long # way off if they are expect_gt(min(vals), -105) expect_lt(max(vals), -95) }) test_that("calculate with greta_mcmc_list doesn't lose track of new nodes", { skip_if_not(check_tf_version()) z <- normal(0, 1) m <- model(z) draws <- mcmc(m, warmup = 100, n_samples = 100, verbose = FALSE) x <- z^2 expect_ok(x_draws <- calculate(x, values = draws)) expect_equal(as.matrix(x_draws)[, 1], as.matrix(draws)[, 1]^2) y <- z * 2 expect_ok(y_draws <- calculate(y, values = draws)) expect_equal(as.matrix(y_draws)[, 1], as.matrix(draws)[, 1] * 2) }) test_that("stochastic calculate works with greta_mcmc_list objects", { skip_if_not(check_tf_version()) samples <- 10 chains <- 2 n <- 100 y <- as_data(rnorm(n)) x <- as_data(1) a <- normal(0, 1) distribution(y) <- normal(a, x) m <- model(a) draws <- mcmc( m, warmup = 0, n_samples = samples, chains = chains, verbose = FALSE ) # this should error without nsim being specified (y is stochastic) expect_snapshot(error = TRUE, calc_a <- calculate(a, y, values = draws) ) # this should be OK sims <- calculate(y, values = draws, nsim = 10) expect_equal(dim(sims$y), c(10, dim(y))) # for a list of targets, the result should be a list nsim <- 10 sims <- calculate(a, y, values = draws, nsim = nsim) # correct class, dimensions, and valid values expect_true(is.list(sims)) expect_equal(names(sims), c("a", "y")) expect_equal(dim(sims$a), c(nsim, 1, 1)) expect_equal(dim(sims$y), c(nsim, n, 1)) expect_true(all(is.finite(sims$a)) & all(is.finite(sims$y))) # a single array with these nsim observations sims <- calculate(y, values = draws, nsim = nsim) expect_true(is.numeric(sims$y)) expect_equal(dim(sims$y), c(nsim, n, 1)) expect_true(all(is.finite(sims$y))) # warn about resampling if nsim is greater than elements in draws expect_snapshot_warning( new_y <- calculate(y, values = draws, nsim = samples * chains + 1) ) }) test_that("calculate errors if the mcmc samples unrelated to target", { skip_if_not(check_tf_version()) samples <- 10 chains <- 2 n <- 100 y <- as_data(rnorm(n)) x <- as_data(1) a <- normal(0, 1) distribution(y) <- normal(a, x) m <- model(a) draws <- mcmc( m, warmup = 0, n_samples = samples, chains = chains, verbose = FALSE ) c <- normal(0, 1) expect_snapshot(error = TRUE, calc_c <- calculate(c, values = draws) ) }) test_that("stochastic calculate works with mcmc samples & new stochastics", { skip_if_not(check_tf_version()) samples <- 10 chains <- 2 n <- 100 y <- as_data(rnorm(n)) x <- as_data(1) a <- normal(0, 1) distribution(y) <- normal(a, x) m <- model(a) draws <- mcmc( m, warmup = 0, n_samples = samples, chains = chains, verbose = FALSE ) # new stochastic greta array b <- lognormal(a, 1) # this should error without nsim being specified (b is stochastic and not # given by draws) expect_snapshot(error = TRUE, calc_b <- calculate(b, values = draws) ) sims <- calculate(b, values = draws, nsim = 10) expect_equal(dim(sims$b), c(10, dim(b))) expect_true(all(sims$b > 0)) }) test_that("calculate errors nicely if non-greta arrays are passed", { skip_if_not(check_tf_version()) x <- c(1, 2) a <- normal(0, 1) y <- a * x # it should error nicely expect_snapshot(error = TRUE, calc_y <- calculate(y, x, values = list(x = c(2, 1))) ) # and a hint for this common error expect_snapshot(error = TRUE, calc_y <- calculate(y, list(x = c(2, 1))) ) }) test_that("calculate errors nicely if values for stochastics not passed", { skip_if_not(check_tf_version()) x <- as_data(c(1, 2)) a <- normal(0, 1) y <- a * x # it should error nicely expect_snapshot(error = TRUE, calc_y <- calculate(y, values = list(x = c(2, 1))) ) # but is should work fine if nsim is set expect_ok(calculate(y, values = list(x = c(2, 1)), nsim = 1)) }) test_that("calculate errors nicely if values have incorrect dimensions", { skip_if_not(check_tf_version()) x <- as_data(c(1, 2)) a <- normal(0, 1) y <- a * x # it should error nicely expect_snapshot(error = TRUE, calc_y <- calculate(y, values = list(a = c(1, 1))) ) }) test_that("calculate works with variable batch sizes", { skip_if_not(check_tf_version()) samples <- 100 x <- as_data(c(1, 2)) a <- normal(0, 1) y <- a * x m <- model(y) draws <- mcmc(m, warmup = 0, n_samples = samples, verbose = FALSE) # variable valid batch sizes val_1 <- calculate(y, values = draws, trace_batch_size = 1) val_10 <- calculate(y, values = draws, trace_batch_size = 10) val_100 <- calculate(y, values = draws, trace_batch_size = 100) val_inf <- calculate(y, values = draws, trace_batch_size = Inf) # check the first one expect_s3_class(val_1, "greta_mcmc_list") expect_equal(dim(val_1[[1]]), c(100, 2)) expect_true(all(is.finite(as.vector(val_1[[1]])))) # check the others are the same expect_identical(val_10, val_1) expect_identical(val_100, val_1) expect_identical(val_inf, val_1) }) test_that("calculate errors nicely with invalid batch sizes", { skip_if_not(check_tf_version()) samples <- 100 x <- as_data(c(1, 2)) a <- normal(0, 1) y <- a * x m <- model(y) draws <- mcmc(m, warmup = 0, n_samples = samples, verbose = FALSE) # variable valid batch sizes expect_snapshot(error = TRUE, calc_y <- calculate(y, values = draws, trace_batch_size = 0) ) expect_snapshot(error = TRUE, calc_y <- calculate(y, values = draws, trace_batch_size = NULL) ) expect_snapshot(error = TRUE, calc_y <- calculate(y, values = draws, trace_batch_size = NA) ) }) test_that("calculate returns a named list", { skip_if_not(check_tf_version()) a <- as_data(randn(3)) b <- a^2 c <- sqrt(b) # if target is a single greta array, the output should be a single numeric result <- calculate(b, nsim = 10) expect_true(is.list(result)) expect_true(is.numeric(result$b)) # if target is a list, the output should be a list of numerics result <- calculate(b, c, nsim = 10) expect_true(is.list(result)) # check contents are_numeric <- vapply(result, is.numeric, FUN.VALUE = logical(1)) expect_true(all(are_numeric)) # check names expect_equal(names(result), c("b", "c")) }) test_that("calculate produces the right number of samples", { skip_if_not(check_tf_version()) # fix variable a <- normal(0, 1) y <- normal(a, 1, dim = c(1, 3)) # should be vectors sims <- calculate(a, nsim = 1) expect_equal(dim(sims$a), c(1, dim(a))) sims <- calculate(a, nsim = 17) expect_equal(dim(sims$a), c(17, dim(a))) sims <- calculate(y, nsim = 1) expect_equal(dim(sims$y), c(1, dim(y))) sims <- calculate(y, nsim = 19) expect_equal(dim(sims$y), c(19, dim(y))) }) test_that("calculate works if distribution-free variables are fixed", { skip_if_not(check_tf_version()) # fix variable a <- variable() y <- normal(a, 1) sims <- calculate(a, y, nsim = 1, values = list(a = 100)) expect_true(all(sims$y > 90)) }) test_that("calculate errors if distribution-free variables are not fixed", { skip_if_not(check_tf_version()) # fix variable a <- variable() y <- normal(a, 1) expect_snapshot(error = TRUE, calc_a <- calculate(a, y, nsim = 1) ) }) test_that("calculate errors if a distribution cannot be sampled from", { skip_if_not(check_tf_version()) # fix variable y <- hypergeometric(5, 3, 2) expect_snapshot(error = TRUE, sims <- calculate(y, nsim = 1) ) }) test_that("calculate errors nicely if nsim is invalid", { skip_if_not(check_tf_version()) x <- normal(0, 1) expect_snapshot(error = TRUE, calc_x <- calculate(x, nsim = 0) ) expect_snapshot(error = TRUE, calc_x <- calculate(x, nsim = -1) ) expect_snapshot(error = TRUE, calc_x <- calculate(x, nsim = "five") ) })