update glossary

Author: cliffckerr

GLOSSARY.rst

@@ -6,12 +6,13 @@ This document contains a list of commonly used terms, both in Covasim and for CO
 
 - **agent**: The basic unit of the model. Typically, one agent in the simulation corresponds to one person in the population, but the population may also be subsampled, such that a larger population is represented by a smaller number of agents. This depends on the assumption that the full population behaves the same way that a subset of the population behaves. See also *dynamic rescaling*.
 - **agent-based model**: The modeling approach that tracks individual *agents* in the population. Compared to *compartmental model*, agent-based models are typically slower, but allow much greater detail in simulations. Covasim is an agent-based model.
+- **back-tracking**: The process of finding the person who infected a person who has just been diagnosed.
 - **basic reproduction number**: See *reproduction number*.
 - **beta**: The probability of transmission from an *infectious* person to a *susceptible* person, also known as infectiousness or transmissibility. The overall transmission probability depends on the network *layer* two people are connected by, as well as the infected person's *viral load*, the susceptible person's age, and other factors.
 - **case**: A person who has tested positive (i.e., been diagnosed) with COVID-19.
 - **case detection ratio** (CDR): The proportion of all infections that have been diagnosed. For example, if 10,000 people have been infected and 1,500 have been diagnosed, the CDR will be 15%.
 - **case fatality ratio** (CFR): The proportion of people who have been diagnosed who eventually die. This is typically much higher than the *infection fatality ratio* since more severe cases are more likely to be diagnosed. Typical CFRs are 5-10%.
-- **compartmental model**: The modeling approach that does not track individual agents, but instead considers compartments with rates of transfer between them. Compared to *agent-based models*, compartmental models are typically faster but rely more heavily on assumptions and approximations.
+- **compartmental model**: The modeling approach that does not track individual agents, but instead considers compartments with rates of transfer between them (e.g., the total number of susceptible people in the compartment S, and their rate of transfer into the exposed compartment E). Compared to *agent-based models*, compartmental models are typically faster but rely more heavily on assumptions and approximations.
 - **contact tracing**: The program for getting in touch with people who have been exposed to contacts of a known positive *case*. 
 - **COVID-19**: Technically defined as the disease caused by infection with the virus *SARS-CoV-2*, but informally used to refer to both the infection and the disease.
 - **dynamic rescaling**: A method by which a smaller number of *agents* is used to represent a larger number of people. For example, 10,000 agents may be used to represent 100,000 people, with an initial 1:1 ratio at the beginning of the simulation, and as the number of infections increases during the simulation, scaling up to a 1:10 ratio.
@@ -28,7 +29,7 @@ This document contains a list of commonly used terms, both in Covasim and for CO
 - **long-term care facilities** (LTCFs): Facilities to care for people over long periods of time, also known as assisted living facilities, aged-care facilities, or nursing homes.
 - **non-pharmaceutical intervention**: Any *intervention* to reduce the spread or severity of COVID-19 other than therapeutics or vaccination. Examples including distancing, hand washing, mask wearing, etc.
 - **parameter**: One or more values (usually numbers) that define how the simulation runs. For example, "probability of developing severe disease" could be considered a parameter (i.e., list of values by age), as could "probability of developing severe disease for people aged 60-70" (i.e., a single number). Parameters can also be qualitative values (e.g., population type) or true/false values (e.g., whether or not to dynamically rescale the population).
-- **primary case**: The first (known) person in a cluster of infections; usually, but not always, the first person diagnosed. See also *secondary infections*.
+- **primary case**: The earliest-infected person diagnosed in a cluster of infections, i.e. the person who is the source of other infections in that cluster. Usually, but not always, this person is also the earliest person in the cluster to be diagnosed. (If *back-tracing* is used, the primary case may be diagnosed after one or more of the secondary cases.) See also *secondary infections*.
 - **primary infection**: Same as *primary case*, but not necessarily diagnosed.
 - **program**: See *intervention*.
 - **quarantine**: The behavior change that occurs when a person has been notified that they have been in contact with a person who has tested positive. See also *isolation*.