From 675fb550032541f023068d94e29fe87763d7c459 Mon Sep 17 00:00:00 2001 From: Andrew Myers Date: Tue, 28 Jan 2025 11:45:45 -0800 Subject: [PATCH] Fix default immune length alpha and beta --- docs/source/usage/how_to_run.rst | 4 ++-- examples/inputs.defaults | 4 ++-- src/DiseaseParm.H | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/source/usage/how_to_run.rst b/docs/source/usage/how_to_run.rst index 793e491..8860fa0 100644 --- a/docs/source/usage/how_to_run.rst +++ b/docs/source/usage/how_to_run.rst @@ -130,10 +130,10 @@ The following inputs specify the disease parameters: * ``disease.vac_eff`` (`float`, default ``0``) The vaccine efficacy - the probability of transmission will be multiplied by one minus this factor. `Vaccination is not yet implemented, so this factor must be left at 0`. -* ``disease.immune_length_alpha`` (`float`, default ``9.0``) +* ``disease.immune_length_alpha`` (`float`, default ``540.0``) Alpha parameter for the immunity length Gamma distribution. The immunity length is the length of time in days that agents are immune to the disease after recovering from it. For a Gamma distribution, the mean is alpha*beta and the variance is alpha*beta^2. -* ``disease.immune_length_beta`` (`float`, default ``20.0``) +* ``disease.immune_length_beta`` (`float`, default ``0.33``) Beta parameter for the immunity length Gamma distribution. The immunity length is the length of time in days that agents are immune to the disease after recovering from it. For a Gamma distribution, the mean is alpha*beta and the variance is alpha*beta^2. * ``disease.latent_length_alpha`` (`float`, default ``9.0``) diff --git a/examples/inputs.defaults b/examples/inputs.defaults index f32f975..3611e06 100644 --- a/examples/inputs.defaults +++ b/examples/inputs.defaults @@ -92,9 +92,9 @@ disease.asymp_relative_inf = 0.75 # Vaccine efficacy. Not yet implemented; leave at 0. disease.vac_eff = 0 # Alpha parameter for the immume length Gamma distribution. The immune length is the length in days that agents are immune after recovery from an infection. -disease.immune_length_alpha = 9.0 +disease.immune_length_alpha =540.0 # Beta parameter for the immume length Gamma distribution. The immune length is the length in days that agents are immune after recovery from an infection. -disease.immune_length_beta = 20.0 +disease.immune_length_beta = 0.33 # Alpha parameter for the latent length Gamma distribution. The latent length is the length in days from infection until an agent becomes infectious. disease.latent_length_alpha = 9.0 # Beta parameter for the latent length Gamma distribution. The latent length is the length in days from infection until an agent becomes infectious. diff --git a/src/DiseaseParm.H b/src/DiseaseParm.H index 5479fff..6b2f957 100644 --- a/src/DiseaseParm.H +++ b/src/DiseaseParm.H @@ -82,8 +82,8 @@ struct DiseaseParm Real child_compliance; /*!< Child compliance with masking ?? */ Real child_HH_closure; /*!< Multiplier for household contacts during school closure */ - Real immune_length_alpha = Real(9.0); /*! alpha parameter for gamma distribution*/ - Real immune_length_beta = Real(20.0); /*! beta parameter for gamma distribution*/ + Real immune_length_alpha = Real(540.0); /*! alpha parameter for gamma distribution*/ + Real immune_length_beta = Real(0.33); /*! beta parameter for gamma distribution*/ Real latent_length_alpha = Real(9.0); /*! alpha parameter for gamma distribution*/ Real latent_length_beta = Real(0.33); /*! beta parameter for gamma distribution*/