like_gknown_2: Likelihood under three parameter model when genotypes are...

In segtest: Tests for Segregation Distortion in Polyploids

Likelihood under three parameter model when genotypes are known

Description

This is under the two parameter model.

Usage

like_gknown_2(x, alpha, xi1, xi2, g1, g2, log_p = TRUE, pen = 0)

Arguments

x	A vector of length 5. x[i] is the count of individuals with genotype i-1.
alpha	The double reduction rate.
xi1	The preferential pairing parameter of parent 1.
xi2	The preferential pairing parameter of parent 2.
g1	Parent 1's genotype.
g2	Parent 2's genotype.
log_p	A logical. Should we return the log likelihood or not?
pen	A tiny penalty to help with numerical stability

Value

The (log) likelihood.

Author(s)

David Gerard

Examples

x <- c(1, 4, 5, 3, 1)
alpha <- 0.01
xi1 <- 0.5
xi2 <- 0.3
g1 <- 1
g2 <- 2
like_gknown_2(
  x = x,
  alpha = alpha,
  xi1 = xi1,
  xi2 = xi2,
  g1 = g1,
  g2 = g2)

segtest documentation built on July 1, 2025, 1:07 a.m.