From 68c2b8d1a78a1b0c7cdd7fd06d8b3e30f543fa0e Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Mon, 9 Sep 2024 15:13:50 -0500
Subject: [PATCH 1/3] Fix text in readme (#436)

Update README.md
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index f8216081..0f26eede 100755
--- a/README.md
+++ b/README.md
@@ -48,7 +48,7 @@ pip install git+https://github.com/CDCgov/PyRenew@main
 
 ## Models Implemented With PyRenew
 
-- [CDCgov/pyrenew-covid-wastewaterpyrenew-covid-wastewater](https://github.com/CDCgov/pyrenew-covid-wastewater): _Models and infrastructure for forecasting COVID-19 hospitalizations using wastewater data with PyRenew._
+- [CDCgov/pyrenew-covid-wastewater](https://github.com/CDCgov/pyrenew-covid-wastewater): _Models and infrastructure for forecasting COVID-19 hospitalizations using wastewater data with PyRenew._
 - [CDCgov/pyrenew-flu-light](https://github.com/CDCgov/pyrenew-flu-light/): _An instantiation in PyRenew of an influenza forecasting model used in the 2023-24 respiratory season._
 
 ## Resources

From 5e149b120dd2f6b3379ca9eaaa85fd68843f6741 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 10 Sep 2024 11:28:16 -0500
Subject: [PATCH 2/3] Add default observation rate to
 `compute_delay_ascertained_incidence` (#437)

* reorder arguments and add new test

* add test description
---
 pyrenew/convolve.py                        |  3 ++-
 pyrenew/latent/hospitaladmissions.py       |  2 +-
 test/test_incidence_observed_with_delay.py | 19 ++++++++++++++++++-
 3 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/pyrenew/convolve.py b/pyrenew/convolve.py
index 44d98e4c..55b2227f 100755
--- a/pyrenew/convolve.py
+++ b/pyrenew/convolve.py
@@ -11,6 +11,7 @@
 :py:func:`jax.lax.scan` with an
 appropriate array to scan along.
 """
+
 from __future__ import annotations
 
 from typing import Callable
@@ -166,9 +167,9 @@ def _new_scanner(
 
 
 def compute_delay_ascertained_incidence(
-    p_observed_given_incident: ArrayLike,
     latent_incidence: ArrayLike,
     delay_incidence_to_observation_pmf: ArrayLike,
+    p_observed_given_incident: ArrayLike = 1,
 ) -> ArrayLike:
     """
     Computes incidences observed according
diff --git a/pyrenew/latent/hospitaladmissions.py b/pyrenew/latent/hospitaladmissions.py
index 57090528..1fcfc581 100644
--- a/pyrenew/latent/hospitaladmissions.py
+++ b/pyrenew/latent/hospitaladmissions.py
@@ -211,9 +211,9 @@ def sample(
         ) = self.infection_to_admission_interval_rv(**kwargs)
 
         latent_hospital_admissions = compute_delay_ascertained_incidence(
-            infection_hosp_rate.value,
             latent_infections.value,
             infection_to_admission_interval.value,
+            infection_hosp_rate.value,
         )
 
         # Applying the day of the week effect. For this we need to:
diff --git a/test/test_incidence_observed_with_delay.py b/test/test_incidence_observed_with_delay.py
index 9bff64ad..bcb1ff66 100644
--- a/test/test_incidence_observed_with_delay.py
+++ b/test/test_incidence_observed_with_delay.py
@@ -34,6 +34,12 @@
             jnp.array([0.25, 0.5, 0.25]),
             jnp.array([2]),
         ],
+        [
+            jnp.array([1.0]),
+            jnp.array([0, 2.0, 4.0]),
+            jnp.array([0.25, 0.5, 0.25]),
+            jnp.array([2]),
+        ],
     ],
 )
 def test(obs_rate, latent_incidence, delay_interval, expected_output):
@@ -42,8 +48,19 @@ def test(obs_rate, latent_incidence, delay_interval, expected_output):
     incidence observed with a delay
     """
     result = compute_delay_ascertained_incidence(
-        obs_rate,
         latent_incidence,
         delay_interval,
+        obs_rate,
     )
     assert_array_equal(result, expected_output)
+
+
+def test_default_obs_rate():
+    """
+    Compute incidence observed with a delay and default observation rate
+    """
+    result = compute_delay_ascertained_incidence(
+        jnp.array([1.0, 2.0, 3.0]),
+        jnp.array([1.0]),
+    )
+    assert_array_equal(result, jnp.array([1.0, 2.0, 3.0]))

From 145ced61326f693bfe2624b5e7043142181264b8 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 10 Sep 2024 12:06:01 -0500
Subject: [PATCH 3/3] Remove duplicate test introduced in #437 (#438)

remove duplicate test
---
 test/test_incidence_observed_with_delay.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/test/test_incidence_observed_with_delay.py b/test/test_incidence_observed_with_delay.py
index bcb1ff66..f510e51a 100644
--- a/test/test_incidence_observed_with_delay.py
+++ b/test/test_incidence_observed_with_delay.py
@@ -34,12 +34,6 @@
             jnp.array([0.25, 0.5, 0.25]),
             jnp.array([2]),
         ],
-        [
-            jnp.array([1.0]),
-            jnp.array([0, 2.0, 4.0]),
-            jnp.array([0.25, 0.5, 0.25]),
-            jnp.array([2]),
-        ],
     ],
 )
 def test(obs_rate, latent_incidence, delay_interval, expected_output):