Read FOI specific values for age groups to attempt infection

examples/births-deaths/demographics_report.rs

@@ -4,7 +4,7 @@ use ixa::{
 use std::path::PathBuf;
 use std::path::Path;
 use serde::{Deserialize, Serialize};
-use crate::population_loader::{Age, AgeGroupType};
+use crate::population_manager::{Age, AgeGroupType};
 use crate::Parameters;
 
 #[derive(Serialize, Deserialize, Clone)]

examples/births-deaths/input.json

@@ -3,10 +3,10 @@
  "max_time": 200.0,
  "seed": 123,
  "birth_rate": 0.1,
- "age_groups": [
- {"min_age": 0, "max_age": 1, "group_name": "newborn", "foi": 0.2},
- {"min_age": 1, "max_age": 65, "group_name": "general", "foi": 0.1},
- {"min_age": 65, "max_age": 200, "group_name": "oldadult", "foi": 0.15}
+ "foi_groups": [
+ {"group_name": "NewBorn", "foi": 0.2},
+ {"group_name": "General", "foi": 0.1},
+ {"group_name": "OldAdult", "foi": 0.15}
  ],
  "infection_duration": 5.0,
  "output_file": "incidence",

examples/births-deaths/main.rs

@@ -1,27 +1,17 @@
-use ixa::people::ContextPeopleExt;
 use ixa::random::ContextRandomExt;
 use ixa::{
- context::Context, define_person_property, define_person_property_with_default,
+ context::Context,
  global_properties::ContextGlobalPropertiesExt,
 };
 use std::path::Path;
 
 mod parameters_loader;
-mod population_loader;
+mod population_manager;
 mod demographics_report;
+mod transmission_manager;
 
 use crate::parameters_loader::Parameters;
 
-use serde::{Deserialize, Serialize};
-
-#[derive(Debug, Hash, Eq, PartialEq, Clone, Copy, Serialize, Deserialize)]
-pub enum InfectionStatus {
- S,
- I,
- R,
-}
-define_person_property_with_default!(InfectionStatusType, InfectionStatus, InfectionStatus::S);
-
 fn main() {
  let mut context = Context::new();
  let current_dir = Path::new(file!()).parent().unwrap();
@@ -34,8 +24,9 @@ fn main() {
  context.init_random(parameters.seed);
 
  demographics_report::init(&mut context);
- population_loader::init(&mut context);
-
+ population_manager::init(&mut context);
+ transmission_manager::init(&mut context);
+
  context.add_plan(parameters.max_time, |context| {
  context.shutdown();
  });
@@ -47,3 +38,4 @@ fn main() {
  }
  }
 }
+

examples/births-deaths/parameters_loader.rs

@@ -7,11 +7,11 @@ use ixa::define_global_property;
 use ixa::error::IxaError;
 use serde::{Deserialize, Serialize};
 
+use crate::population_manager::AgeGroupRisk;
+
 #[derive(Serialize, Deserialize, Debug, Clone)]
-pub struct AgeGroups {
- pub min_age: f64,
- pub max_age: f64,
- pub group_name: String,
+pub struct FoiAgeGroups {
+ pub group_name: AgeGroupRisk,
  pub foi: f64,
 }
 
@@ -21,15 +21,16 @@ pub struct ParametersValues {
  pub max_time: f64,
  pub seed: u64,
  pub birth_rate: f64,
- pub age_groups: Vec<AgeGroups>,
+ pub foi_groups: Vec<FoiAgeGroups>,
  pub infection_duration: f64,
  pub output_file: String,
  pub demographic_output_file: String,
 }
 define_global_property!(Parameters, ParametersValues);
-
+//define_global_property!(Foi, HashMap);
 pub fn init_parameters(context: &mut Context, file_path: &Path) -> Result<(), IxaError> {
  let parameters_json = context.load_parameters_from_json::<ParametersValues>(file_path)?;
- context.set_global_property_value(Parameters, parameters_json);
+ context.set_global_property_value(Parameters, parameters_json.clone()); 
  Ok(())
 }
+

examples/births-deaths/population_loader.rs → examples/births-deaths/population_manager.rs

@@ -2,15 +2,25 @@ use ixa::context::Context;
 use ixa::global_properties::ContextGlobalPropertiesExt;
 use ixa::people::{ContextPeopleExt, PersonId};
 use ixa::random::ContextRandomExt;
-use ixa::{define_derived_person_property, define_person_property};
+use ixa::{define_derived_person_property, define_global_property, define_person_property, define_person_property_with_default};
+use std::collections::HashMap;
 use serde::Deserialize;
 use crate::parameters_loader::Parameters;
 use ixa::random::define_rng;
 define_rng!(PeopleRng);
 static MAX_AGE: u8 = 100;
 use std::fmt;
 use rand_distr::Exp;
-#[derive(Deserialize, Copy, Clone, PartialEq, Eq, Debug)]
+use serde::Serialize;
+
+#[derive(Debug, Hash, Eq, PartialEq, Clone, Copy, Serialize, Deserialize)]
+pub enum InfectionStatus {
+ S,
+ I,
+ R,
+}
+
+#[derive(Deserialize, Serialize, Copy, Clone, PartialEq, Eq, Debug, Hash)]
 pub enum AgeGroupRisk {
  NewBorn,
  General,
@@ -23,6 +33,12 @@ impl fmt::Display for AgeGroupRisk {
  }
 }
 
+define_global_property!(Foi, HashMap<AgeGroupRisk, f64>);
+define_person_property_with_default!(
+ InfectionStatusType,
+ InfectionStatus,
+ InfectionStatus::S
+);
 
 define_person_property!(Age, u8);
 define_person_property!(Alive, bool);
@@ -41,7 +57,6 @@ define_derived_person_property!(
  }
 );
 
-
 fn schedule_birth(context: &mut Context) {
  let parameters = context.get_global_property_value(Parameters).clone();
 
@@ -51,7 +66,6 @@ fn schedule_birth(context: &mut Context) {
 
  let next_birth_event = context.get_current_time() +
  context.sample_distr(PeopleRng, Exp::new(parameters.birth_rate).unwrap());
- println!("Next birth event: {:?}", next_birth_event);
  context.add_plan(next_birth_event,
  move |context| {
  schedule_birth(context);
@@ -80,6 +94,17 @@ fn schedule_birth(context: &mut Context) {
 
 pub fn init(context: &mut Context) {
  let parameters = context.get_global_property_value(Parameters).clone();
+
+ let foi_map = parameters
+ .foi_groups
+ .clone()
+ .into_iter()
+ .map(|x| (x.group_name,x.foi))
+ .collect::<HashMap<AgeGroupRisk, f64>>();
+
+
+ context.set_global_property_value(Foi, foi_map.clone());
+
  for _ in 0..parameters.population {
  let person = context.add_person();
  let age = context.sample_range(PeopleRng, 0..(MAX_AGE));
@@ -89,5 +114,4 @@ pub fn init(context: &mut Context) {
 
  // Plan for births and deaths
  context.add_plan(0.0, |context| {schedule_birth(context)});
-
 }

examples/births-deaths/transmission_manager.rs

@@ -0,0 +1,62 @@
+use ixa::context::Context;
+use ixa::define_rng;
+use ixa::global_properties::ContextGlobalPropertiesExt;
+use ixa::people::ContextPeopleExt;
+use ixa::random::ContextRandomExt;
+
+use crate::population_manager::InfectionStatus;
+use crate::population_manager::InfectionStatusType;
+use crate::population_manager::AgeGroupRisk;
+use crate::population_manager::Foi;
+use crate::Parameters;
+use rand_distr::Exp;
+
+define_rng!(TransmissionRng);
+
+//Attempt infection for specific age group risk (meaning diferent forces of infection)
+fn attempt_infection(context: &mut Context, age_group: AgeGroupRisk) {
+ let population_size: usize = context.get_current_population();
+
+ let person_to_infect =
+ context.get_person_id(context.sample_range(TransmissionRng, 0..population_size));
+
+ let person_status: InfectionStatus =
+ context.get_person_property(person_to_infect, InfectionStatusType);
+ let parameters = context.get_global_property_value(Parameters).clone();
+ let foi = *context
+ .get_global_property_value(Foi)
+ .get(&age_group)
+ .unwrap();
+
+ println!("Attempting infection for age group: {:?} with foi: {:?}", age_group, foi);
+
+ if matches!(person_status, InfectionStatus::S) {
+ context.set_person_property(person_to_infect, InfectionStatusType, InfectionStatus::I);
+ }
+
+ #[allow(clippy::cast_precision_loss)]
+ let next_attempt_time = context.get_current_time()
+ + context.sample_distr(TransmissionRng, Exp::new(foi).unwrap())
+ / population_size as f64;
+
+ if next_attempt_time <= parameters.max_time {
+ context.add_plan(next_attempt_time, move |context| {
+ attempt_infection(context, age_group);
+ });
+ }
+}
+
+pub fn init(context: &mut Context) {
+ // Need to convert to a more efficient way
+ context.add_plan(0.0, |context| {
+ attempt_infection(context, AgeGroupRisk::NewBorn);
+ });
+
+ context.add_plan(0.0, |context| {
+ attempt_infection(context, AgeGroupRisk::General);
+ });
+
+ context.add_plan(0.0, |context| {
+ attempt_infection(context, AgeGroupRisk::OldAdult);
+ });
+}