add note about direct usage failing but tidybayes working

epinowcast · Nov 20, 2024 · b246737 · b246737
1 parent 6302ac9
commit b246737
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Showing 3 changed files with 6 additions and 14 deletions.
diff --git a/tests/testthat/test-gen.R b/tests/testthat/test-gen.R
@@ -104,13 +104,10 @@ test_that("epidist_gen_posterior_predict returns a function that predicts delays
 test_that("epidist_gen_posterior_epred returns a function that creates arrays with correct dimensions", { # nolint: line_length_linter.
   skip_on_cran()
   # Test lognormal
-  prep <- brms::prepare_predictions(fit)
-  epred_fn <- epidist_gen_posterior_epred(lognormal())
-  epred <- epred_fn(prep)
-  expect_setequal(class(epred), c("matrix", "array"))
-  expect_identical(nrow(epred), prep$ndraws)
-  expect_identical(ncol(epred), length(prep$data$Y))
-  expect_gte(min(epred), 0)
+  epred <- prep_obs |>
+    tidybayes::add_epred_draws(fit)
+  expect_equal(mean(epred$.epred), 5.97, tolerance = 0.1)
+  expect_gte(min(epred$.epred), 0)
 
   # Test gamma
   prep_gamma <- brms::prepare_predictions(fit_gamma)

diff --git a/tests/testthat/test-latent_model.R b/tests/testthat/test-latent_model.R
@@ -62,17 +62,15 @@ test_that("epidist_gen_log_lik_latent returns a function that produces valid log
   # Test lognormal
   prep <- brms::prepare_predictions(fit)
   i <- 1
-  family <- epidist_family(data = prep_obs, family = lognormal())
-  log_lik_fn <- epidist_gen_log_lik_latent(family)
+  log_lik_fn <- epidist_gen_log_lik_latent(lognormal())
   log_lik <- log_lik_fn(i = i, prep)
   expect_length(log_lik, prep$ndraws)
   expect_false(anyNA(log_lik))
   expect_true(all(is.finite(log_lik)))
 
   # Test gamma
   prep_gamma <- brms::prepare_predictions(fit_gamma)
-  family_gamma <- epidist_family(data = prep_obs, family = Gamma())
-  log_lik_fn_gamma <- epidist_gen_log_lik_latent(family_gamma)
+  log_lik_fn_gamma <- epidist_gen_log_lik_latent(Gamma())
   log_lik_gamma <- log_lik_fn_gamma(i = i, prep_gamma)
   expect_length(log_lik_gamma, prep_gamma$ndraws)
   expect_false(anyNA(log_lik_gamma))

diff --git a/vignettes/ebola.Rmd b/vignettes/ebola.Rmd
@@ -320,7 +320,6 @@ Figure \@ref(fig:epred)B illustrates the higher mean of men as compared with wom
 
 ```{r}
 epred_draws <- obs_prep |>
-  as.data.frame() |>
   data_grid(NA) |>
   mutate(relative_obs_time = NA, pwindow = NA, swindow = NA) |>
   add_epred_draws(fit, dpar = TRUE)
@@ -332,7 +331,6 @@ epred_base_figure <- epred_draws |>
   theme_minimal()
 
 epred_draws_sex <- obs_prep |>
-  as.data.frame() |>
   data_grid(sex) |>
   mutate(relative_obs_time = NA, pwindow = NA, swindow = NA) |>
   add_epred_draws(fit_sex, dpar = TRUE)
@@ -344,7 +342,6 @@ epred_sex_figure <- epred_draws_sex |>
   theme_minimal()
 
 epred_draws_sex_district <- obs_prep |>
-  as.data.frame() |>
   data_grid(sex, district) |>
   mutate(relative_obs_time = NA, pwindow = NA, swindow = NA) |>
   add_epred_draws(fit_sex_district, dpar = TRUE)