Observables

Dictionary of (SNP, freq).

Dictionary (SNP, population count)

allele_spectrum(state;[ threshold=0.0, read_depth=total_population_size(state)])

Return a DataFrame with count, frequency of every polymorphism. Additionally sample from the population.

common_snps(::Population; filterdead=true)

List polymorphisms that are common to all genotypes.

Optional arguments:

• filterdead=true: exclude unpopulated genotypes?

counts_on_shells(state, g, [o, a])

Return a dictionary i=>count mapping the ith shell to the number of cells of genotype g on it.

The "shell number" of a point is the integer closest to |p-o|/a.

Keyword arguments

• o=midpointcoord(state.lattice): center of shells
• a=spacing(state.lattice): spacing of shells

explode_into_shells(v, o, a; r0=)

Take a vector of cartesian coordinates v, center them around the midpoint o, and return a dictionary radius=>coordinates where r0<= radius <= max(||v||) in increments of a.

ipositions(state, g)

Returns lattice indices of cells of genotype g.

Earliest living ancestor.

Diversity (mean pairwise difference of mutations) of a population.

Return index of the most recent common ancestor between (i,j) in a phylogeny.

Return index of the most recent common ancestor in a phylogeny.

npolymorphisms(S::Population)

Number of polymrphisms

pairwise(S::Population, i, j)

Number of pairwise genomic differences between genotype indices i,j.

pairwise(S::Population)

Matrix of pairwise differences. filterdead: Do not include extinct genotypes.

polymorphisms(S::Population)

Vector of polymorphisms (segregating sites).

popsize_on_shells(T, outer, [o=midpoint(T.lattice)])

Creates a dictionary genotype => trajectory where trajectory is a vector of population size. trajectory[r] is the the population size on a L2-norm shell of radius r around o.

r ranges between 1..outer in increments of a (defaults to the lattice spacing).

Set deleteone/zero=false to keep the wildtype/count empty sites.

Dictionary (genotype, population size)

positions(state, g)

Returns coordinates of cells of genotype g.

sampled_allele_fractions(S::Population[, t=0, samples=length(S.meta.npops)])

Randomly sample genotypes(!) and calculate frequencies of contained SNPs. Return a dictionary (SNP, freq).

See https://en.wikipedia.org/wiki/Tajima%27s_D

Total population size. Duh.