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lib/Bio/Community/Meta/Beta.pm  view on Meta::CPAN

      }

      if ($j > $min_permuted) {
         # Member rank in second community conflicts with minimum permutation
         # assumption. Increase minimum permutation.
         $min_permuted = $j;
      }

      # Finish if the permutation limit has been reached without conflicts
      last if $i >= $min_permuted;

   }

   if (defined $min_permuted) {
      if ($min_permuted == 1) {
         $min_permuted--;
      }
      $min_permuted = $min_permuted / $community1->get_richness * 100;
   }

   return $min_permuted;
}


method _maxiphi ($meta) {
   # Given S, the fraction shared, and P, the fraction permuted, calculate the
   # MaxiPhi beta diversity M as:
   #       M = 1 - S*(2-P)/2
   #
   # M ranges from 0 (low beta diversity, similar communities), to 1 (high beta
   # diversity, dissimilar communities). The weight of the percent permuted
   # parameter is proportional to the percent shared. At 0% shared, the fraction
   # permuted has no weight in the index, while at 100% shared, the fraction
   # permuted and fraction shared have the same weight.
   #
   # For example:
   #      for 100 % shared, 0   % permuted -> M = 0
   #      for 100 % shared, 100 % permuted -> M = 0.5
   #      for 0   % shared, 0   % permuted -> M = 1
   #      for 0   % shared, 100 % permuted -> M = 1


   # Calculate the fraction shared
   my $s = $self->_shared($meta) / 100;

   # Calculate the fraction permuted
   my $p = $self->_permuted($meta);
   if (not defined $p) {
      $p = 100; # but any value between 0 and 100 would work as well
   }
   $p /= 100;

   # Calculate the Maxiphi index
   my $m = 1 - $s * (2-$p) / 2;
   return $m;
}


method _unifrac ($meta, $tree) {
   #### TODO: unifrac
   $self->throw_not_implemented;
}


#######
# TODO:
# Many more beta diversity indices to calculate:
#    Unifrac
#    ...
#######


__PACKAGE__->meta->make_immutable;

1;