| M |
Number of infections sampled |
| N |
Total number of (relevant) infected individuals in an outbreak |
| ρ |
Proportion of outbreak infections sampled (M/N) |
| η |
Sensitivity of the linkage criteria |
| χ |
Specificity of the linkage criteria |
| ϕ |
Probability that an identified link represents a true transmission event (1-False Discovery Rate) |
| R |
Reproductive number of a pathogen |
|
Rpop
|
Average reproductive number of a pathogen in a finite population (always <1) |
| μ |
Substitution rate of the pathogen (in substitutions observed per genome per transmission event) |
