R/makeEmissionFUN.R

In MPR.genotyping: Maximum Parsimony of Recombination to Infer Parental Genotypes

makeEmissionFUN <-
function (errorRate = 0.01) 
  {
    E <- log(errorRate)
    E2 <- log(1 - errorRate)
    E3 <- log(0.5)
    function(h, x, n) {
      if (h != 3) 
        return(ifelse(h == x, E2, E))
      else return(n * E3)
    }
  }