initial age-specific params

Author: eqmooring

input/input.json

@@ -13,10 +13,11 @@
                 "duration": 5.0
             }
         },
+        "symptom_age_groups": {"Young": 0, "Old": 50},
         "probability_mild_given_infect": 0.7,
         "infect_to_mild_mu": 0.1,
         "infect_to_mild_sigma": 0.0,
-        "probability_severe_given_mild": 0.2,
+        "probability_severe_given_mild": {"Young": 0.05, "Old": 0.3},
         "mild_to_severe_mu": 0.1,
         "mild_to_severe_sigma": 0.1,
         "mild_to_resolved_mu": 0.1,

src/parameters.rs

@@ -5,6 +5,7 @@ use std::{fmt::Debug, path::PathBuf};
 use crate::infection_importation::ImportCasesFromFile;
 use crate::reports::ReportParams;
 use crate::settings::SettingProperties;
+use crate::symptom_status_manager::{SymptomAgeGroupNames};
 
 #[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
 pub enum RateFnType {
@@ -36,14 +37,16 @@ pub struct Params {
     pub imported_cases_timeseries: ImportCasesFromFile,
     /// A library of infection rates to assign to infected people.
     pub infectiousness_rate_fn: RateFnType,
+    /// age thresholds
+    pub symptom_age_groups: HashMap<SymptomAgeGroupNames, u8>,
     /// Probability an infected person develops mild illness
     pub probability_mild_given_infect: f64,
     /// Mu parameter for log normal delay distribution from infection to mild illness
     pub infect_to_mild_mu: f64,
     /// Sigma parameter for log normal delay distribution from infection to mild illness
     pub infect_to_mild_sigma: f64,
     /// Probability a person with mild illness develops severe illness
-    pub probability_severe_given_mild: f64,
+    pub probability_severe_given_mild: HashMap<SymptomAgeGroupNames, f64>,
     /// Mu parameter for log normal delay distribution from mild to severe illness
     pub mild_to_severe_mu: f64,
     /// Sigma parameter for log normal delay distribution from mild to severe illness
@@ -120,10 +123,13 @@ fn validate_inputs(parameters: &Params) -> Result<(), IxaError> {
         ));
     }
 
-    if !(0.0..=1.0).contains(&parameters.probability_severe_given_mild) {
-        return Err(IxaError::IxaError(
-            "The probability of severe illness given mild illness must be between 0 and 1, inclusive.".to_string(),
-        ));
+    for (age_group, probability) in &parameters.probability_severe_given_mild {
+        // we also want to check whether all of the values for age_group from the enum SymptomAgeGroupNames is specified
+        if !(0.0..=1.0).contains(probability) {
+            return Err(IxaError::IxaError(
+                format!("The probability of severe illness given mild illness among {:?} must be between 0 and 1, inclusive.", age_group).to_string()
+            ));
+        }
     }
 
     if !(0.0..=1.0).contains(&parameters.probability_critical_given_severe) {
@@ -222,6 +228,7 @@ impl Default for Params {
                 rate: 1.0,
                 duration: 5.0,
             },
+            symptom_age_groups: HashMap::new(),
             probability_mild_given_infect: 0.0,
             infect_to_mild_mu: 0.0,
             infect_to_mild_sigma: 0.0,

src/symptom_status_manager.rs

@@ -1,4 +1,4 @@
-use ixa::{Context, ContextEntitiesExt, ContextRandomExt, IxaError, define_rng, impl_property, prelude::PropertyChangeEvent};
+use ixa::{Context, ContextEntitiesExt, ContextRandomExt, IxaError, define_property, define_rng, impl_property, prelude::PropertyChangeEvent};
 use rand_distr::{LogNormal};
 use serde::{Deserialize, Serialize};
 
@@ -24,6 +24,17 @@ impl_property!(
     default_const = SymptomStatus::NoSymptoms
 );
 
+#[derive(Serialize, Deserialize, Debug, Clone, Copy, Hash, PartialEq, Eq)]
+pub enum SymptomAgeGroupNames {
+    Young,
+    Old
+}
+
+define_property!(
+    SymptomAgeGroupNames,
+    Person,
+);
+
 pub fn init(context: &mut Context) -> Result<(), IxaError> {
     let &Params{
         probability_mild_given_infect,
@@ -47,6 +58,12 @@ pub fn init(context: &mut Context) -> Result<(), IxaError> {
         .. 
         } = context.get_params();
 
+    let Params{
+        symptom_age_groups, ..
+    } = context.get_params();
+
+    println!("{:?}", symptom_age_groups.clone());
+
     context.subscribe_to_event(
         move|context, event: PropertyChangeEvent<Person, InfectionStatus>|{
             if event.current == InfectionStatus::Infectious {
@@ -121,4 +138,7 @@ pub fn init(context: &mut Context) -> Result<(), IxaError> {
 // -set up parameters (essential to make it run) [DONE]
 // -add SymptomStatusData or some other mechanism to track what most symptom statuses a person had, even after resolved (and maybe track timing, too)
 // -make probabilities age (category) specific
-// -finish validation for parameters
+// -finish validation for parameters
+// -Take one of the parameters and make it a hashmap; how to validate this? (do you need to specify all groups)
+// how to implement a derived property to know what their age group is?
+// get the probability in the transitions