From ea70d35af2471dfbedf908dc1c980a55f9220fd3 Mon Sep 17 00:00:00 2001
From: Guido Espana <ukd0@cdc.gov>
Date: Thu, 19 Dec 2024 23:04:19 +0000
Subject: [PATCH] use sample_person in contacts

---
 README.md                   | 2 +-
 src/contact.rs              | 8 +++-----
 src/main.rs                 | 3 +--
 src/transmission_manager.rs | 8 +++++---
 4 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 12eadb9..5c3fbc9 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 This project presents a general transmission model developed in [ixa](https://github.com/CDCgov/ixa), the Center for Forecasting and Outbreak Analytics' agent-based modeling framework. The transmission model goal is to possess time-varying infectioussness, immunity, interventions, and multiple co-circulating pathogens.
 
 ## How to run the model
-As of 11/29/24, `cargo run -- -i ./input/input.json -o ./output`. There is an optional `-f` or `--force-overwrite` flag that can be
+As of 11/29/24, `cargo run -- -c ./input/input.json -o ./output`. There is an optional `-f` or `--force-overwrite` flag that can be
 passed to force overwriting of reports while in development/testing modes.
 
 ## Project Admin
diff --git a/src/contact.rs b/src/contact.rs
index 9bec65f..6ba3498 100644
--- a/src/contact.rs
+++ b/src/contact.rs
@@ -1,4 +1,4 @@
-use ixa::{define_rng, Context, ContextPeopleExt, ContextRandomExt, IxaError, PersonId};
+use ixa::{define_rng, Context, ContextPeopleExt, IxaError, PersonId};
 
 use crate::population_loader::Alive;
 
@@ -26,15 +26,13 @@ impl ContextContactExt for Context {
         // Get list of eligible people (for now, all alive people). May be expanded in the future
         // to instead be list of alive people in the transmitter's contact setting or household.
         // We sample a random person from this list.
-        let eligible_contacts = self.query_people((Alive, true));
-        if eligible_contacts.len() > 1 {
+        if self.query_people((Alive, true)).len() > 1 {
             let mut contact_id = transmitter_id;
             while contact_id == transmitter_id {
                 // In the future, we might like to sample people from the list by weights according
                 // to some contact matrix. We would use sample_weighted instead. We would calculate
                 // the weights _before_ the loop and then sample from the list of people like here.
-                contact_id =
-                    eligible_contacts[self.sample_range(ContactRng, 0..eligible_contacts.len())];
+                contact_id = self.sample_person(ContactRng, (Alive, true))?;
             }
             Ok(Some(contact_id))
         } else {
diff --git a/src/main.rs b/src/main.rs
index 2d72629..55bf1c0 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -17,14 +17,13 @@ use crate::population_loader::{Age, CensusTract};
 
 #[derive(Args, Debug)]
 struct CustomArgs {
-    /// whether force overwrite of output files if they already exist
+    ///Whether force overwrite of output files if they already exist
     #[arg(short = 'f', long)]
     force_overwrite: bool,
 }
 
 fn initialize() -> Result<Context, IxaError> {
     let mut context = run_with_custom_args(|context, args, custom_args: Option<CustomArgs>| {
-        println!("Setting Overwrite parameter");
         // Read the global properties.
         let custom_args = custom_args.unwrap();
         // Set the output directory and whether to overwrite the existing file.
diff --git a/src/transmission_manager.rs b/src/transmission_manager.rs
index d0d0629..f5074f2 100644
--- a/src/transmission_manager.rs
+++ b/src/transmission_manager.rs
@@ -5,9 +5,11 @@ use ixa::{
 };
 use statrs::distribution::{ContinuousCDF, Exp, Poisson};
 
-use crate::contact::ContextContactExt;
-use crate::parameters::Parameters;
-use crate::population_loader::Alive;
+use crate::{
+    contact::ContextContactExt,
+    parameters::Parameters,
+    population_loader::Alive
+};
 
 // Define the possible infectious statuses for a person.
 // These states refer to the person's infectiousness at a given time