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Renaming sample_infections to compute_future_infections #137

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merged 3 commits into from
May 28, 2024
Merged

Renaming sample_infections to compute_future_infections #137

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736929c
Renaming sample_infections to compute_future_infections
gvegayon May 28, 2024
4be3058
Renaming functions
gvegayon May 28, 2024
72fec94
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gvegayon May 28, 2024
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8 changes: 4 additions & 4 deletions model/src/pyrenew/latent/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@
)
from pyrenew.latent.i0 import Infections0
from pyrenew.latent.infection_functions import (
compute_infections_from_rt,
compute_infections_from_rt_with_feedback,
logistic_susceptibility_adjustment,
sample_infections_rt,
sample_infections_with_feedback,
)
from pyrenew.latent.infections import Infections

Expand All @@ -19,7 +19,7 @@
"InfectHospRate",
"Infections",
"logistic_susceptibility_adjustment",
"sample_infections_rt",
"sample_infections_with_feedback",
"compute_infections_from_rt",
"compute_infections_from_rt_with_feedback",
"Infections0",
]
12 changes: 7 additions & 5 deletions model/src/pyrenew/latent/infection_functions.py
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Expand Up @@ -9,11 +9,13 @@
from pyrenew.convolve import new_convolve_scanner, new_double_scanner


def sample_infections_rt(
I0: ArrayLike, Rt: ArrayLike, reversed_generation_interval_pmf: ArrayLike
def compute_infections_from_rt(
I0: ArrayLike,
Rt: ArrayLike,
reversed_generation_interval_pmf: ArrayLike,
) -> ArrayLike:
"""
Sample infections according to a
Generate infections according to a
renewal process with a time-varying
reproduction number R(t)

Expand Down Expand Up @@ -84,15 +86,15 @@ def logistic_susceptibility_adjustment(
return n_population * frac_susceptible * approx_frac_infected


def sample_infections_with_feedback(
def compute_infections_from_rt_with_feedback(
I0: ArrayLike,
Rt_raw: ArrayLike,
infection_feedback_strength: ArrayLike,
generation_interval_pmf: ArrayLike,
infection_feedback_pmf: ArrayLike,
) -> tuple:
"""
Sample infections according to
Generate infections according to
a renewal process with infection
feedback (generalizing Asher 2018:
https://doi.org/10.1016/j.epidem.2017.02.009)
Expand Down
2 changes: 1 addition & 1 deletion model/src/pyrenew/latent/infections.py
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Expand Up @@ -107,7 +107,7 @@ def sample(
n_lead = gen_int_rev.size - 1
I0_vec = jnp.hstack([jnp.zeros(n_lead), I0])

all_infections = inf.sample_infections_rt(
all_infections = inf.compute_future_infections_rt(
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I0=I0_vec,
Rt=Rt,
reversed_generation_interval_pmf=gen_int_rev,
Expand Down
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