landscape.mismatchdist: Calculate a mismatch distribution for a locus in a landscape

In rmetasim: An Individual-Based Population Genetic Simulation Environment

Description

Calculate mismatch distribution from a landscape based upon the number of seqregating sites.

Usage

  landscape.mismatchdist(Rland,lnum=1)

Arguments

lnum	locus number to calculate mismatch upon
Rland	the Rmetasim landscape object

Details

Calculates a mismatch distribution for DNA-sequence-based loci.

Value

A matrix with num loci columns and num populations rows. Each element reflects the estimated theta for that population x locus combination

Examples

  exampleland <- landscape.new.example()
  exampleland <- landscape.simulate(exampleland, 4)
  misdist <- landscape.mismatchdist(exampleland,3) #will produce       
  misdist                                          #ridiculous output

Example output

  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
286 230   2   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
  0   0   0   0   0   0   0   0   0 520  74   0 363 153 103 325  60 200  28 104 
 60  61  62  63  64 
 28  98   0 150 136 

rmetasim documentation built on Feb. 8, 2020, 1:06 a.m.