Naming Conventions

Arguments

Genealogies

• genealogy: AbstractGenealogy
• tree: coalescent tree (usually of type Tree)
• arg: ancestral recombination graph (usually of type Arg)
  • Keep in mind that by definition, a coalescent tree is an ancestral recombination graph.

Graphs

• v: vertex (usually of type VertexType)
• vs: vertices
• e: edge (usually of type Edge{VertexType}, see Graphs.Edge)
• es: edges

Sequences

• h: haplotype (usually of type Sequence, sometimes a BitVector or Vector{UInt}
• idx: index or indices of markers, i.e. element or subset or the range 1:n where n is the number of markers
• pos: position or positions of markers, i.e. element or subset of $\mathbb R$

Intervals

• ω: right semi-open interval (usually of type Ω)
• ωs: ω or collection of ωs (usually of type AIs)

Keyword Arguments

• buffer: SlabBuffer or AllocBuffer from Bumper.jl

Constructors

For a type T:

• T() is the empty constructor
• T(rng, ...) is a random constructor