logReval {dcifer}

Logarithms of reval

Description

Calculates logarithms of reval and 1 - reval, as well as other associated quantities.

Usage

logReval(reval, M = NULL, neval = NULL, equalr = FALSE)

Arguments

reval

a matrix representing a grid of (r₁, ..., r_M) combinations, over which the likelihood will be calculated. Each column is a single combination.

M

the number of related pairs of strains.

neval

the number of relatedness values/combinations to evaluate over.

equalr

a logical value. If TRUE, the same level of relatedness is assumed for M pairs of strains (r₁ = ... = r_M).

Details

For equalr = TRUE relatedness estimation, reval should be a 1 x neval matrix.

Value

A list of length 5 that contains log(reval), log(1 - reval), the number of reval = 1 for each column, the number of 0 < reval < 1 for each column, and sum(log(1 - reval[reval < 1])) for each column.

Examples

reval <- generateReval(M = 2, nr = 1e2)
logr  <- logReval(reval, M = 2, equalr = FALSE)

reval <- generateReval(M = 1, nr = 1e3)
logr3  <- logReval(reval, M = 3, equalr = TRUE)
logr1  <- logReval(reval, M = 1)
all(logr3$sum1r == logr1$sum1r*3)