S_E_I_R_new_E_vacc_by_time.xml

<?xml version="1.0" encoding="UTF-8"?>

<!-- User Request: Show me S, E, I, R, incidence and vaccination counts over time. 

    What the user really wants:
    For each time step, show me the total number of people that are susceptible at the end of the time step,
    the total number of people that are exposed at the end of the time step, the total number of people that 
    are infectious at the end of the time step, the total number of people that are recovered at the end of 
    the time step, the number of people that became newly exposed during the time step, and the number of 
    people that were vaccinated during the time step.
-->

<!-- Note: This requires 2 messages as we are counting two different "things." -->
<apollo:SimulatorCountOutputSpecificationListElement
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://types.apollo.pitt.edu/v4_0/ apollo_types_4.0.xsd"
    xmlns:apollo="http://types.apollo.pitt.edu/v4_0/">
    <!-- Message 1, getting human counts -->
    <apollo:SimulatorCountOutputSpecification>
        <apollo:speciesToCount>9606</apollo:speciesToCount>
        <apollo:temporalGranularity>eachSimulationTimestep</apollo:temporalGranularity>
        <apollo:spatialGranularity>none</apollo:spatialGranularity>
        <apollo:infectionStates>susceptible</apollo:infectionStates>
        <apollo:infectionStates>latent</apollo:infectionStates>
        <apollo:infectionStates>infectious</apollo:infectionStates>
        <apollo:infectionStates>recovered</apollo:infectionStates>
        <apollo:infectionStates>newly_sick</apollo:infectionStates>
    </apollo:SimulatorCountOutputSpecification>
    <!-- Message 2, getting vaccine counts -->
    <apollo:SimulatorCountOutputSpecification>
        <apollo:thingsToCount>vaccinations</apollo:thingsToCount>
        <apollo:temporalGranularity>eachSimulationTimestep</apollo:temporalGranularity>
        <apollo:spatialGranularity>none</apollo:spatialGranularity>
    </apollo:SimulatorCountOutputSpecification>
</apollo:SimulatorCountOutputSpecificationListElement>