emHaplotypeImpute: Use EM Haplotype Phasing by Imputation Algorithm (internal...
In vsbuffalo/ProgenyArray: Some statistical genetics for progeny array experiments

Use EM Haplotype Phasing by Imputation Algorithm (internal function)

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emHaplotypeImpute(pgeno, fgeno, other_parents, freqs, ehet, ehom,
  free_pi = FALSE, na_thresh = 0.8, init = NULL, extra = FALSE,
  max_iter = 60L, eps = 1e-09)

`pgeno`	progeny genotypes
`fgeno`	father (or other parent) genotypes
`other_parents`	indices to corresponding father genotype columns in fgeno
`freqs`	allele frequencies
`ehet`	heterozygous error rate
`ehom`	homozygous error rate
`free_pi`	whether to allow pi to vary (can cause identifiability issues
`na_thresh`	how much missingness to tolerate before pruning individual
`init`	optional initial reponsibilities (advanced use)
`extra`	include optional debugging output (advanced use)
`max_iter`	maximum number of EM iterations before quiting
`eps`	epsilon in log likelihood before calling convergence