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Glossary
The average number of infections generated by an infected individual in an otherwise susceptible population. For birth-death models without a limited population size, this is usually equal to the effective reproduction number.
BEAUti is a graphical user-interface (GUI) application for generating BEAST XML files. This is used to install packages from CBAN and provides a simple way to install TimTam.
A scheduled sequenced sample. This manifests as multiple sequences with the same sample time.
Collection of BEAST2 packages: https://compevol.github.io/CBAN/
The rate at which an individual ceases to be infectious if they are not sampled. This is not to be confused with the “total becoming uninfectious rate” which accounts for sampling and unobserved recovery.
A scheduled unsequenced sample. Typically, this will be a time-series of cases that do not have a sequence associated with them. This type of data is considered in Tutorial 1 and 2.
A time varying function which describes the expected number of infections generated by an individual who was infected at a given time. Be careful, there is also a basic reproduction number and variations on the effective reproduction number if you are using a renewal model.
This is a lineage that exists in the full transmission tree but does not appear in the reconstructed tree. The estimates of the prevalence generated by TimTam are really estimates of the number of hidden lineages.
In the code, reference is made to intervals of time, this is used to indicate an interval of time can end in either an observation or a change in a rate. Since rates can only change between intervals this means that we can treat the calculation within each interval as a constant parameter problem.
\(λ\) is the birth rate of new infectious individuals.
Moments And Stochastic Trees from Event Reactions. This is another BEAST 2 package that is used to simulate from a birth-death process.
\(μ\) denotes the rate at which individuals cease to be infectious without being sampled.
The points in time that are represented in the data: births, unscheduled samples (both sequenced and unsequenced) and scheduled samples (both sequenced and unsequenced).
This is unscheduled data, i.e. data that is not generated during a scheduled sample. See unsequenced sample for additional information.
\(ω\) denotes the rate at which infectious individuals are sampled (without sequencing).
The time that the first individual started to be infectious. This should not be confused with the tMRCA of the reconstructed tree.
The prevalence of the infection is the number of people actively infected at a given time. In the Tutorials 0, 1, and 2 this refers to the total population size.
\(ψ\) denotes the rate at which infectious individuals are sampled (and sequenced).
The basic reproduction number.
This is the tree of all the sequenced samples, this is not to be confused with the transmission tree which every lineage, regardless of if it was observed.
A sample in which multiple lineages may be sampled at the sample time.
Data that appears in the phylogeny, as a way to distinguish from unsequenced samples.
\(σ\) denotes the net removal rate.
This is the tree of all infections in the epidemic, this is not to be confused with the reconstructed tree.
Data that is not included in the phylogeny, a.k.a. occurrence data.
A rate parameter that varies through time. For TimTam, this usually means a piece-wise constant function of time. Tutorial 2 demonstrates how to estimate a varying birth rate.