fix tutorials

CDCgov · Jun 14, 2024 · 6cd0583 · 6cd0583
1 parent d0ca000
commit 6cd0583
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/model/docs/example_with_datasets.qmd b/model/docs/example_with_datasets.qmd
@@ -214,7 +214,7 @@ axs[0].plot(sim_data.Rt)
 axs[0].set_ylabel("Rt")
 
 # Infections plot
-axs[1].plot(sim_data.sampled_observed_hosp_admissions)
+axs[1].plot(sim_data.observed_hosp_admissions)
 axs[1].set_ylabel("Infections")
 axs[1].set_yscale("log")
 
@@ -236,7 +236,7 @@ import jax
 hosp_model.run(
     num_samples=2000,
     num_warmup=2000,
-    observed_hosp_admissions=dat["daily_hosp_admits"].to_numpy(),
+    data_observed_hosp_admissions=dat["daily_hosp_admits"].to_numpy(),
     rng_key=jax.random.PRNGKey(54),
     mcmc_args=dict(progress_bar=False),
 )
@@ -281,7 +281,7 @@ dat_w_padding = np.pad(
 hosp_model.run(
     num_samples=2000,
     num_warmup=2000,
-    observed_hosp_admissions=dat_w_padding,
+    data_observed_hosp_admissions=dat_w_padding,
     rng_key=jax.random.PRNGKey(54),
     mcmc_args=dict(progress_bar=False),
     padding=days_to_impute,  # Padding the model
@@ -382,7 +382,7 @@ Running the model (with the same padding as before):
 hosp_model_weekday.run(
     num_samples=2000,
     num_warmup=2000,
-    observed_hosp_admissions=dat_w_padding,
+    data_observed_hosp_admissions=dat_w_padding,
     rng_key=jax.random.PRNGKey(54),
     mcmc_args=dict(progress_bar=False),
     padding=days_to_impute,

diff --git a/model/docs/getting_started.qmd b/model/docs/getting_started.qmd
@@ -172,7 +172,7 @@ axs[0].plot(sim_data.Rt)
 axs[0].set_ylabel("Rt")
 
 # Infections plot
-axs[1].plot(sim_data.sampled_observed_infections)
+axs[1].plot(sim_data.observed_infections)
 axs[1].set_ylabel("Infections")
 
 fig.suptitle("Basic renewal model")
@@ -190,7 +190,7 @@ import jax
 model1.run(
     num_warmup=2000,
     num_samples=1000,
-    observed_infections=sim_data.sampled_observed_infections,
+    data_observed_infections=sim_data.observed_infections,
     rng_key=jax.random.PRNGKey(54),
     mcmc_args=dict(progress_bar=False),
 )

diff --git a/model/docs/pyrenew_demo.qmd b/model/docs/pyrenew_demo.qmd
@@ -162,7 +162,7 @@ fig, ax = plt.subplots(nrows=3, sharex=True)
 ax[0].plot(x.latent_infections)
 ax[0].set_ylim([1 / 5, 5])
 ax[1].plot(x.latent_hosp_admissions)
-ax[2].plot(x.sampled_observed_hosp_admissions, "o")
+ax[2].plot(x.observed_hosp_admissions, "o")
 for axis in ax[:-1]:
     axis.set_yscale("log")
 ```
@@ -174,7 +174,7 @@ To fit the `hospmodel` to the simulated data, we call `hospmodel.run()`, an MCMC
 hospmodel.run(
     num_warmup=1000,
     num_samples=1000,
-    observed_hosp_admissions=x.sampled_observed_hosp_admissions,
+    data_observed_hosp_admissions=x.observed_hosp_admissions,
     rng_key=jax.random.PRNGKey(54),
     mcmc_args=dict(progress_bar=False),
 )