Glossary
Key terms used across the site. The first mention of any of these on a page links back here, and each entry lists the pages that discuss it.
Basic reproduction number
The average number of secondary infections caused by one infectious individual in a fully susceptible population.
See: The Effective Reproduction Number and Forecasting
Discussed on: BIO301 Mathematical Biology, BIO340 Infectious Disease Ecology, Force of Infection and Serocatalytic Models, Social and Structural Drivers of Transmission, Within-Host Viral Dynamics and Infectiousness, Evolutionary Epidemiology and the Evolution of Virulence, Approximate Bayesian Computation, Branching Processes, Networks in Ecology and Epidemiology, Eigenvalues and Eigenvectors, Adaptive Dynamics and the Evolution of Virulence, Expected Value, Metapopulation Networks and the Invasion Threshold, Fitting Dynamic Models to Data, The Molecular Clock and Phylodynamics, The Next-Generation Matrix and R₀, Phylodynamics, The Effective Reproduction Number and Forecasting, SEIR and Compartmental Extensions, Compartmental Models in Biology, Outbreak Analytics and Modeling, Statistical Modeling of Infectious Disease Dynamics
Compartmental model
A model that divides a population into states — such as susceptible, infectious, and recovered — and tracks the flows between them.
See: Compartmental Models in Biology
Discussed on: BIO301 Mathematical Biology, Behavior–Disease Coupled Models, Climate Forcing in Transmission Models, Exponential and Logistic Growth, Compartmental Models in Biology, Within-Host Dynamics and the Immune Response, Outbreak Analytics and Modeling, Outbreak Analytics Bootcamp
Effective reproduction number
The average number of secondary infections per case at a given time, as susceptibility and interventions change.
See: The Effective Reproduction Number and Forecasting
Discussed on: LAMP: Isothermal Amplification, qPCR and RT-qPCR, Detection Probability: Viral Kinetics and Assay Thresholds, The Speed and Strength of Epidemic Control, Antimicrobial Resistance Across Scales, Final Size, the Herd Immunity Threshold, and Overshoot, Asynchrony and the Inflationary Effect in Metapopulations, The Renewal Equation, The Effective Reproduction Number and Forecasting, Population Dynamics of Resistance, Outbreak Analytics and Modeling, Writing for Policy
Generation interval
The time between the infection of an infector and the infections they in turn cause.
See: Epidemiological Intervals and Delays
Discussed on: Epidemiology, Fitting Delay Distributions: Truncation and Censoring, The Speed and Strength of Epidemic Control, Epidemic Forecasting, Epidemiological Intervals and Delays, The Euler–Lotka Equation: From Growth Rate to R₀, Quantitative Methods, The Renewal Equation, The Effective Reproduction Number and Forecasting, SEIR and Compartmental Extensions, Outbreak Analytics and Modeling, Statistical Modeling of Infectious Disease Dynamics, Cover Letters and Reviewer Responses
Incubation period
The time between infection and the onset of symptoms in an individual.
See: Epidemiological Intervals and Delays
Discussed on: Climate and Disease Transmission, Fitting Delay Distributions: Truncation and Censoring, Epidemiological Intervals and Delays, Outbreak Investigation, Measures of Center, Moment Matching, Compartmental Models in Biology, Writing Results and Discussion
Latent period
The time between infection and the onset of infectiousness (which may differ from the incubation period).
See: Epidemiological Intervals and Delays
Discussed on: Epidemiological Intervals and Delays, Within-Host Viral Dynamics and Infectiousness, The Exponential Distribution, SEIR and Compartmental Extensions
Next-generation matrix
A matrix whose dominant eigenvalue gives the basic reproduction number in a structured or multi-type transmission model.
See: The Next-Generation Matrix and R₀
Discussed on: Social and Structural Drivers of Transmission, Social Contact Matrices and Age-Structured Mixing, The Next-Generation Matrix and R₀, Reservoir Ecology, Structured Population Models, Outbreak Analytics and Modeling
Serial interval
The time between symptom onset in an infector and symptom onset in the people they infect.
See: Epidemiological Intervals and Delays
Discussed on: Fitting Delay Distributions: Truncation and Censoring, Epidemiological Intervals and Delays, The Euler–Lotka Equation: From Growth Rate to R₀, Outbreak Investigation, Transmission Tree Reconstruction (Who Infected Whom), Moment Matching, The Renewal Equation, The Effective Reproduction Number and Forecasting, Scientific Writing, Writing Methods, Writing Results and Discussion