DNAtools (version 0.2-5)

pContrib_locus: Compute the posterior probabilities for \(\Pr(m|n_0)\) for a given prior \(\Pr(m)\).

Description

Compute a matrix of posterior probabilties \(\Pr(m|n_0)\) where \(m\) ranges from 1 to \(m_{\max}\), and \(n_0\) is \(0,\ldots,2m_{\max}\). This is done by evaluating \(\Pr(m|n_0)=Pr(n_0|m)Pr(m)/Pr(n)\), where \(\Pr(n_0|m)\) is evaluated by pNoA.

Usage

pContrib_locus(
  prob = NULL,
  m.prior = NULL,
  m.max = 8,
  pnoa.locus = NULL,
  theta = 0
)

Value

Returns a matrix \([\Pr(m|n_0)]\) for \(m = 1,\ldots,m.max\) and \(n_0 = 1,\ldots,2m.max\).

Arguments

prob

Vectors with allele probabilities for the specific locus

m.prior

A vector with prior probabilities (summing to 1), where the length of m.prior determines the plausible range of \(m\)

m.max

Derived from the length of m.prior, and if m.prior=NULL a uniform prior is speficied by m.max: m.prior = rep(1/m.max,m.max).

pnoa.locus

A named vector of locus specific probabilities \(P(N(m)=n), n=1,\ldots,2m\).

theta

The coancestery coefficient

Author

Torben Tvedebrink, James Curran

Details

Computes a matrix of \(\Pr(m|n_0)\) values for a specific locus.

References

T. Tvedebrink (2014). 'On the exact distribution of the number of alleles in DNA mixtures', International Journal of Legal Medicine; 128(3):427--37. <https://doi.org/10.1007/s00414-013-0951-3>

Examples

  ## Simulate some allele frequencies:
  freqs <-  simAlleleFreqs()
  
  ## Compute Pr(m|n0) for m = 1, ..., 5 and n0 = 1, ..., 10 for the first locus:
  pContrib_locus(prob = freqs[[1]], m.max = 5)