review clarifications

docs/transmission.md

@@ -7,16 +7,20 @@ infectious agent and other susceptible agents. Agents become infectious immediat
 upon successful infection attempt, though they may have a transmission probability of
 0 for some time (mimicking an exposed compartment). Once infectious, agents have a pre-assigned
 number of infection attempts. Infection attempt times are drawn from the generation interval.
-Once there are no more infection attempts remaining for the agent, we argue that they do not
-transition to a recovered compartment but rather back to a susceptible compartment but
-with high immunity.
+Once there are no more infection attempts remaining for the agent, we model the agent as having
+their level of immunity against the disease set to, say, 1 but have them transition back
+to the susceptible compartment. This is to simplify the disease model and make it such that
+immunity levels can be re-calculated when contacts are drawn rather than needing to update
+them on a schedule.
 
 ## Workflow
 
 The transmission model is centered around a key workflow:
 1. Watch for an agent becoming infectious (S --> I transition).
-2. For the infectious agent, draw a number of infection attempts. This can be from the
-$R_i$ distribution or the contact distribution.
+2. For the infectious agent, draw a number of infection attempts. This could be from an $R_i$ distribution
+or the distribution of the number of contacts an individual has based on their network connectivity.
+There is also an option for each infection attempt to have a probability of transmission. This serves to
+scale the contact distribution to a potential $R_i$ distribution.
 3. Draw an infection time for the agent. This consists of taking an ordered draw from the generation
 interval. The math for this is abstracted away under a generic `get_next_infection_time` method.
 4. Draw a susceptible contact from the agent's contact group. Contacts could be drawn uniformly
@@ -28,37 +32,26 @@ the infection attempt is successful. Success is based on:
     - whether any interventions are present that may reduce transmission,
     - the contact's immunity level which is updated when the contact is drawn.
 
-    If the infection attempt is successful, the infectious contact is labeled as infectious.
+    If the infection attempt is successful, the susceptible contact is labeled as infectious.
 5. Repeat steps #3 and #4, decreasing the number of infection attempts left by one each time
 regardless of whether the attempt is successful and ending when the agent has no zero
 infection attempts remaining.
-6. Re-label the agent as susceptible. The immunity manager will set their latent immunity level
-to the value of immunity based on natural infection to mimic a recovered compartment.
+6. Re-label the agent as susceptible. Doing so will trigger the immunity manager to set the
+agent's natural level of immunity to a value of immunity to mimic the agent being in
+a recovered compartment. However, since we want the model to be general to consider waning
+of immunity, labeling individuals as being in a recovered compartment where they have complete
+immunity restricts the model's flexibility.
 
 ## Relationship to other managers/out of scope for the transmission manager
 
 - The transmission manager does not implement interventions. It does not keep track
-of interventions present or how they impact transmission. Instead, those quantities are
-stored in an intervention plugin. The transmission manager can query an individual's transmissibility
-at a given time based on their person characteristics to get their realized transmissibility
-for use in the workflow described above, but it does not explicitly track which interventions
-are present at what time or how they impact transmissibility.
+of interventions present or how they impact transmission.
 
-- The transmission manager also does not track an individual's contacts. Instead, the transmission
+- The transmission manager does not track an individual's contacts. Instead, the transmission
 manager calls a generic method called `get_contact` which is in the `mod contact_manager` to obtain
 the individual's contacts.
 
-- The transmission manager does not track an individual's health status. In fact, it is
-completely independent from health status. Instead, health status is tracked in
-`mod disease_progression_manager`. However, if transmission probability is changed based on
-health status (i.e., hospitalized people are less likely to transmit), through the intervention
-plugin, the transmission manager can query all the individual's transmission modifications and
-adjust their transmission probability accordingly.
-
-- An agent's contacts may also change through time (hospitalized patients interact with people
-in the hospital). The transmission manager does not need to know about these changes as it just
-queries an individual's contacts through the `get_contact` method. However, the intervention plugin
-can store information about how an individual's contacts are changed based on their health status.
+- The transmission manager does not track an individual's health status.
 
 - The transmission manager does not track an individual's waning immunity over time. It can
 interface with other methods that do calculate an individual's immunity -- for evaluating