model_properties: Mutation model properties

In pedmut: Mutation Models for Pedigree Likelihood Computations

Mutation model properties

Description

Functions for checking various properties of a mutation model, including stationarity, reversibility and lumpability.

Usage

isStationary(mutmat, afreq = NULL)

isReversible(mutmat, afreq = NULL)

isBounded(mutmat, afreq = NULL)

isLumpable(mutmat, lump)

alwaysLumpable(mutmat)

Arguments

mutmat	A mutationMatrix() or a mutationModel().
afreq	A vector with allele frequencies, of the same length as the size of mutmat.
lump	A nonempty subset of the colnames of mutmat (i.e. the allele labels).

Details

The function isBounded() checks that a mutation model is bounded by the allele frequencies, i.e., that mutmat[i,j] <= afreq[j] whenever i is not equal to j.

For each of these functions, if mutmat is a mutationModel object, i.e., with male and female components, the output is TRUE if and only if both components satisfy the property in question.

Value

Each of these functions returns TRUE of FALSE.

Examples

# "proportional" models are stationary and reversible
afr = c(0.2, 0.3, 0.5)
m_prop = mutationMatrix(model = "prop", alleles = 1:3, afreq = afr, rate = 0.1)
stopifnot(isStationary(m_prop, afr), isReversible(m_prop, afr))

# "equal" model is stationary and reversible only when freqs are equal
m_eq = mutationMatrix(model = "eq", alleles = 1:3, rate = 0.1)
stopifnot(isStationary(m_eq, rep(1/3, 3)), isReversible(m_eq, rep(1/3, 3)))
stopifnot(!isStationary(m_eq, afr), !isReversible(m_eq, afr))

# "equal" and "proportional" models allow allele lumping
stopifnot(isLumpable(m_eq, lump = 1:2))
stopifnot(isLumpable(m_prop, lump = 1:2))

# In fact lumpable for any allele subset
stopifnot(alwaysLumpable(m_eq), alwaysLumpable(m_prop))

pedmut documentation built on Nov. 5, 2023, 1:10 a.m.