Tree & ARG

Tree
Arg
- MMN
Common

Tree

Moonshine.Tree — Type

struct Tree <: AbstractGenealogy

Coalescent tree.

Arg

Moonshine.Arg — Type

struct Arg <: AbstractGenealogy

Ancestral recombination graph.

See also Tree.

Fields

graph::Moonshine.ThreeTree{Int32}: Graph's topology
latitudes::Vector{Float64}: Vertices' latitudes
recombination_mask::Vector{AncestralIntervals{Vector{IntervalSets.Interval{:closed, :open, Float64}}}}: ∩-mask for ancestral intervals
mrca::Base.RefValue{Int32}: Arg's grand MRCA
sequences::Vector{Sequence}: Vertices' haplotypes
ancestral_intervals::Dict{Graphs.SimpleGraphs.SimpleEdge{Int32}, AncestralIntervals{Vector{IntervalSets.Interval{:closed, :open, Float64}}}}: Edges' ancestral intervals
sample::Sample: Associated Sample
logdensity::Base.RefValue{DoubleFloats.Double64}: Log-value of the associated pdf

Constructors

Info

Random constructor calls Sample's random constructor.

Warning

These do not actually build the arg. For that, see build!(rng, arg).

Arg(
    graph,
    latitudes,
    recombination_mask,
    mrca,
    sequences,
    ancestral_intervals,
    sample,
    logdensity
)
Arg(
    graph,
    latitudes,
    recombination_mask,
    mrca,
    sequences,
    ancestral_intervals,
    sample,
    logdensity
)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Arg/Arg.jl:41.

Arg(tree)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Arg/Arg.jl:59.

Arg(rng, n, μ, ρ, Ne, sequence_length)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Arg/Arg.jl:75.

Arguments

tree: coalescent Tree
other arguments are identical to Sample

source

Moonshine.breakpoints — Function

breakpoints(arg)

Recombination events' positions

source

Moonshine.plot_breakpoints — Function

plot_breakpoints(arg; nbins, height, kwargs...)

Heatmap of recombination events' positions.

See also breakpoints

Keywords

nbins (clamp(nrecombinations(arg) ÷ 100, 1, 69)): number of bins. Its default maximum value of 69 produces a nice 80 columns wide plot.
height (7): height of the plot.
kwargs...: additional keywords arguments are passed directly to UnicodePlots.histogram.

source

Moonshine.otherdad — Function

otherdad(arg, s, d)
otherdad(arg, e)

Return the parent of d that is not s for a recombination vertex d. If d is not a recombination vertex, returns s. Can also take an edge as argument.

Methods

otherdad(arg, s, d)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Arg/Arg.jl:348.

otherdad(arg, e)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Arg/Arg.jl:359.

–Internal–

source

Moonshine.rlat_min — Function

rlat_min(arg, e, nextidx)

Compute the minimum latitude for a recombination event rooted on e.

–Internal–

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Moonshine.recombination_mask — Function

recombination_mask(arg, e)

Intervals of the partition of [0, ∞) induced by a recombination event for
which an edge is ancestral.

source

Moonshine.recombine! — Function

recombine!(arg, redge, cedge, breakpoint, rlat, clat[, stack]; buffer = default_buffer())

Add a recombination event to an ARG.

Methods

recombine!(
    arg,
    redge,
    cedge,
    breakpoint,
    rlat,
    clat,
    stack;
    buffer
)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Arg/Recombination.jl:86.

recombine!(
    arg,
    redge,
    cedge,
    breakpoint,
    rlat,
    clat;
    buffer
)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Arg/Recombination.jl:152.

source

Moonshine.ts — Function

ts(arg)

Convert an ARG to a tskit TreeSequence.

source

MMN

Moonshine.next_inconsistent_idx — Function

next_inconsistent_idx(
    arg,
    idx,
    stack;
    mutations_edges,
    buffer
)

Index of the next inconsistent marker, that is the next which mutates more than once in a given ancestral recombination graph.

stack must be of type CheapStack{Edge{VertexType}} (see CheapStack).

source

Common

Moonshine.build! — Function

build!(rng, genealogy; kwargs...)

Build a genealogy.

Methods

build!(rng, arg; winwidth, buffer, noprogress, conversion)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Arg/Recombination.jl:698.

build!(rng, tree; Dist, bias0, threshold_prop)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Tree.jl:236.

Arguments

winwidth (∞): width of the window of positions to consider
noprogress (false): hide progress bar
Dist (Hamming{Int}()): distance used to compute coalescence probabilities
bias0 (10): distance multiplier: higher values favour coalescence events between similar haplotypes
threshold_prop (1): proportion of events to consider when sampling

source