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Update Snapshot tests #360

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merged 2 commits into from
Jun 19, 2024
Merged

Update Snapshot tests #360

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91ff419
added not_cran
gowerc Jun 19, 2024
ccee7b1
Updated snapshots
gowerc Jun 19, 2024
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1 change: 1 addition & 0 deletions .github/workflows/check.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ jobs:
CMDSTAN=/root/.cmdstan
CMDSTAN_PATH=/root/.cmdstan
CMDSTANR_NO_VER_CHECK=true
NOT_CRAN=TRUE
### Temporarily removed due to cache bug (#345)
# JMPOST_CACHE_DIR=${{ github.workspace }}/.cache
# additional-caches: |
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8 changes: 4 additions & 4 deletions tests/testthat/_snaps/JointModel.md
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Expand Up @@ -12,7 +12,7 @@
Weibull-PH Survival Model with parameters:
sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5)
sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5)
beta_os_cov ~ normal(mu = 0, sigma = 5)
beta_os_cov ~ normal(mu = 0, sigma = 2)

Longitudinal:
Random Slope Longitudinal Model with parameters:
Expand Down Expand Up @@ -40,7 +40,7 @@
Weibull-PH Survival Model with parameters:
sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5)
sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5)
beta_os_cov ~ normal(mu = 0, sigma = 5)
beta_os_cov ~ normal(mu = 0, sigma = 2)

Longitudinal:
Random Slope Longitudinal Model with parameters:
Expand Down Expand Up @@ -68,7 +68,7 @@
Weibull-PH Survival Model with parameters:
sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5)
sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5)
beta_os_cov ~ normal(mu = 0, sigma = 5)
beta_os_cov ~ normal(mu = 0, sigma = 2)

Longitudinal:
Not Specified
Expand Down Expand Up @@ -121,7 +121,7 @@
Weibull-PH Survival Model with parameters:
sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5)
sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5)
beta_os_cov ~ normal(mu = 0, sigma = 5)
beta_os_cov ~ normal(mu = 0, sigma = 2)

Longitudinal:
Random Slope Longitudinal Model with parameters:
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2 changes: 1 addition & 1 deletion tests/testthat/_snaps/SurvivalExponential.md
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Expand Up @@ -7,7 +7,7 @@

Exponential Survival Model with parameters:
sm_exp_lambda ~ gamma(alpha = 2, beta = 5)
beta_os_cov ~ normal(mu = 0, sigma = 5)
beta_os_cov ~ normal(mu = 0, sigma = 2)


---
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2 changes: 1 addition & 1 deletion tests/testthat/_snaps/SurvivalLoglogistic.md
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Expand Up @@ -8,7 +8,7 @@
Log-Logistic Survival Model with parameters:
sm_loglogis_a ~ lognormal(mu = -2.30259, sigma = 5)
sm_loglogis_b ~ gamma(alpha = 2, beta = 5)
beta_os_cov ~ normal(mu = 0, sigma = 5)
beta_os_cov ~ normal(mu = 0, sigma = 2)


---
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2 changes: 1 addition & 1 deletion tests/testthat/_snaps/SurvivalWeibullPH.md
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Expand Up @@ -8,7 +8,7 @@
Weibull-PH Survival Model with parameters:
sm_weibull_ph_lambda ~ gamma(alpha = 2, beta = 0.5)
sm_weibull_ph_gamma ~ gamma(alpha = 2, beta = 0.5)
beta_os_cov ~ normal(mu = 0, sigma = 5)
beta_os_cov ~ normal(mu = 0, sigma = 2)


---
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2 changes: 1 addition & 1 deletion tests/testthat/test-LongitudinalRandomSlope.R
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Expand Up @@ -249,7 +249,7 @@ test_that("Random Slope Model left-censoring works as expected", {
sampleStanModel(
jm,
data = jdat,
iter_sampling = 200,
iter_sampling = 300,
iter_warmup = 400,
chains = 1,
refresh = 0,
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14 changes: 8 additions & 6 deletions tests/testthat/test-SurvivalQuantities.R
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Expand Up @@ -41,27 +41,29 @@ test_that("SurvivalQuantities and autoplot.SurvivalQuantities works as expected"

# Check that the relationship between the quantitites is preservered e.g.
# that `surv = exp(-cumhaz)`
time_vec <- c(0, 1, 10, 30, 40, 200, 300, 400)
preds1 <- SurvivalQuantities(
test_data_1$jsamples,
grid = GridFixed(subjects = "subject_0001", times = c(200, 300))
grid = GridFixed(subjects = "subject_0001", times = time_vec)
) |> summary()
preds2 <- SurvivalQuantities(
test_data_1$jsamples,
grid = GridFixed(subjects = "subject_0001", times = c(200, 300)),
grid = GridFixed(subjects = "subject_0001", times = time_vec),
type = "cumhaz"
) |> summary()
preds3 <- SurvivalQuantities(
test_data_1$jsamples,
grid = GridFixed(subjects = "subject_0001", times = c(200, 300)),
grid = GridFixed(subjects = "subject_0001", times = time_vec),
type = "haz"
) |> summary()
preds4 <- SurvivalQuantities(
test_data_1$jsamples,
grid = GridFixed(subjects = "subject_0001", times = c(200, 300)),
grid = GridFixed(subjects = "subject_0001", times = time_vec),
type = "loghaz"
) |> summary()
expect_equal(round(preds1$median, 5), round(exp(-preds2$median), 5))
expect_equal(round(preds3$median, 5), round(exp(preds4$median), 5))

expect_equal(preds1$median, exp(-preds2$median), tolerance = 0.00001)
expect_equal(preds3$median, exp(preds4$median), tolerance = 0.00001)
expect_true(all(preds1$median != preds3$median))
})

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