pedmut (version 0.8.0)

model_properties: 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)

Value

Each of these functions returns TRUE of FALSE.

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.

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))