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Last data update: 2014.03.03

R: Compute the posterior probabilities for P(m|n0) for a given...

pContrib

R Documentation

Compute the posterior probabilities for P(m|n0) for a given prior P(m) and observed vector n0 of locus counts

Description

where m ranges from 1 to code{m.max} and n0 is the observed locus counts.

Usage

pContrib(n0, probs=NULL, m.prior=rep(1/m.max,m.max), m.max=8, pnoa=NULL, theta=0)

Arguments

`n0`	Vector of observed allele counts - same length as the number of loci.
`probs`	List of vectors with allele probabilities for each 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`	A named list of locus specific probabilities. Output from `pNoA` with `locuswise=TRUE`.
`theta`	The coancestery coefficient

Details

Computes a vector P(m|n0) evaluated over the plausible range 1,...,m.max.

Value

Returns a vector P(m|n0) for m=1,...,m.max

Author(s)

Torben Tvedebrink

References

T Tvedebrink (2013). 'On the exact distribution of the number of alleles in DNA mixtures', International Journal of Legal Medicine: (under review).

Examples

  ## Simulate some allele frequencies:
  freqs <-  structure(replicate(10, { g = rgamma(n=10,scale=4,shape=3); g/sum(g)},
              simplify=FALSE),.Names=paste("locus",1:10,sep="."))
  m <- 2
  n0 <- unlist(lapply(freqs, function(x){
      length(unique(sample(length(x),size=2*m,replace=TRUE,prob=x)))}
      ))
  ## Compute P(m|n0) for m=1,...,4 and the sampled n0
  pContrib(n0=n0,probs=freqs,m.max=4)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(DNAtools)
Loading required package: Rsolnp
Loading required package: multicool
Loading required package: Rcpp
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/DNAtools/pContrib.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pContrib
> ### Title: Compute the posterior probabilities for P(m|n0) for a given
> ###   prior P(m) and observed vector n0 of locus counts
> ### Aliases: pContrib
> 
> ### ** Examples
> 
>   ## Simulate some allele frequencies:
>   freqs <-  structure(replicate(10, { g = rgamma(n=10,scale=4,shape=3); g/sum(g)},
+               simplify=FALSE),.Names=paste("locus",1:10,sep="."))
>   m <- 2
>   n0 <- unlist(lapply(freqs, function(x){
+       length(unique(sample(length(x),size=2*m,replace=TRUE,prob=x)))}
+       ))
>   ## Compute P(m|n0) for m=1,...,4 and the sampled n0
>   pContrib(n0=n0,probs=freqs,m.max=4)
   P(m=1|n0)    P(m=2|n0)    P(m=3|n0)    P(m=4|n0) 
0.000000e+00 9.999948e-01 5.238303e-06 1.600036e-12 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>