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Issue 228: Use silent = 2 to suppress brms output in tests #230

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merged 1 commit into from
Aug 6, 2024
Merged

Issue 228: Use silent = 2 to suppress brms output in tests #230

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18 changes: 11 additions & 7 deletions tests/testthat/test-int-latent_individual.R
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ test_that("epidist.epidist_latent_individual samples from the prior according to
skip_on_cran()
set.seed(1)
prior_samples <- epidist(
data = prep_obs, fn = brms::brm, sample_prior = "only", seed = 1
data = prep_obs, fn = brms::brm, sample_prior = "only", seed = 1, silent = 2
)
pred <- predict_delay_parameters(prior_samples)
family <- epidist_family(data = prep_obs, family = brms::lognormal())
Expand All @@ -53,7 +53,7 @@ test_that("epidist.epidist_latent_individual fits and the MCMC converges in the
# Note: this test is stochastic. See note at the top of this script
skip_on_cran()
set.seed(1)
fit <- epidist(data = prep_obs, seed = 1)
fit <- epidist(data = prep_obs, seed = 1, silent = 2)
expect_s3_class(fit, "brmsfit")
expect_s3_class(fit, "epidist_fit")
expect_convergence(fit)
Expand All @@ -63,7 +63,7 @@ test_that("epidist.epidist_latent_individual recovers the simulation settings fo
# Note: this test is stochastic. See note at the top of this script
skip_on_cran()
set.seed(1)
fit <- epidist(data = prep_obs, seed = 1)
fit <- epidist(data = prep_obs, seed = 1, silent = 2)
pred <- predict_delay_parameters(fit)
# Unclear the extent to which we should expect parameter recovery here
expect_equal(mean(pred$mu), meanlog, tolerance = 0.1)
Expand Down Expand Up @@ -93,7 +93,8 @@ test_that("epidist.epidist_latent_individual fits and the MCMC converges in the
data = prep_obs_gamma,
family = stats::Gamma(link = "log"),
formula = brms::bf(mu ~ 1, shape ~ 1),
seed = 1
seed = 1,
silent = 2
)
expect_s3_class(fit_gamma, "brmsfit")
expect_s3_class(fit_gamma, "epidist_fit")
Expand All @@ -108,7 +109,8 @@ test_that("epidist.epidist_latent_individual recovers the simulation settings fo
data = prep_obs_gamma,
family = stats::Gamma(link = "log"),
formula = brms::bf(mu ~ 1, shape ~ 1),
seed = 1
seed = 1,
silent = 2
)
# Using the Stan parameterisation of the gamma distribution
draws_gamma <- posterior::as_draws_df(fit_gamma$fit)
Expand Down Expand Up @@ -147,7 +149,8 @@ test_that("epidist.epidist_latent_individual recovers no sex effect when none is
fit_sex <- epidist(
data = prep_obs,
formula = brms::bf(mu ~ 1 + sex, sigma ~ 1 + sex),
seed = 1
seed = 1,
silent = 2
)
draws <- posterior::as_draws_df(fit_sex$fit)
expect_equal(mean(draws$b_sex), 0, tolerance = 0.2)
Expand All @@ -162,7 +165,8 @@ test_that("epidist.epidist_latent_individual fits and the MCMC converges for an
fit_sex <- epidist(
data = prep_obs,
formula = brms::bf(mu ~ 1 + sex, sigma ~ 1 + sex),
seed = 1
seed = 1,
silent = 2
)
expect_s3_class(fit_sex, "brmsfit")
expect_s3_class(fit_sex, "epidist_fit")
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-unit-postprocess.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ test_that("predict_delay_parameters works with NULL newdata and the latent logno
skip_on_cran()
set.seed(1)
prep_obs <- as_latent_individual(sim_obs)
fit <- epidist(data = prep_obs, seed = 1)
fit <- epidist(data = prep_obs, seed = 1, silent = 2)
pred <- predict_delay_parameters(fit)
expect_s3_class(pred, "data.table")
expect_named(pred, c("index", "draw", "mu", "sigma", "mean", "sd"))
Expand All @@ -16,7 +16,7 @@ test_that("predict_delay_parameters accepts newdata arguments", { # nolint: line
skip_on_cran()
set.seed(1)
prep_obs <- as_latent_individual(sim_obs)
fit <- epidist(data = prep_obs, seed = 1)
fit <- epidist(data = prep_obs, seed = 1, silent = 2)
n <- 5
pred <- predict_delay_parameters(fit, newdata = prep_obs[1:n, ])
expect_s3_class(pred, "data.table")
Expand Down