Bio::Tree Statistics
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Tree::Statistics - Calculate certain statistics for a Tree
Package variables
No package variables defined.
Inherit
Bio::Root::Root
Synopsis
  use Bio::Tree::Statistics;
Description
This should be where Tree statistics are calculated. It was
previously where statistics from a Coalescent simulation. Currently
it is empty because we have not added any Tree specific statistic
calculations to this module yet. We welcome any contributions.
Methods
assess_bootstrapDescriptionCode
Methods description
assess_bootstrapcode    nextTop
 Title   : assess_bootstrap
 Usage   : my $tree_with_bs = $stats->assess_bootstrap(\@bs_trees);
 Function: Calculates the bootstrap for internal nodes based on
 Returns : Bio::Tree::TreeI
 Args    : Arrayref of Bio::Tree::TreeIs
Methods code
assess_bootstrapdescriptionprevnextTop
sub assess_bootstrap {
   my ($self,$bs_trees,$guide_tree) = @_;
   my @consensus;

   # internal nodes are defined by their children
   
   my (%lookup,%internal);
   my $i = 0;
   for my $tree ( $guide_tree, @$bs_trees ) {
       # Do this as a top down approach, can probably be
       # improved by caching internal node states, but not going
       # to worry about it right now.
       
       my @allnodes = $tree->get_nodes;
       my @internalnodes = grep { ! $_->is_Leaf } @allnodes;
       for my $node ( @internalnodes ) {
	   my @tips = sort map { $_->id } 
	              grep { $_->is_Leaf() } $node->get_all_Descendents;
	   my $id = "(".join(",", @tips).")";
	   if( $i == 0 ) {
	       $internal{$id} = $node->internal_id;
	   } else { 
	       $lookup{$id}++;
	   }
       }
       $i++;
   }
   my @save;
   for my $l ( keys %lookup ) {
       if( defined $internal{$l} ) {#&& $lookup{$l} > $min_seen ) {
	   my $intnode = $guide_tree->find_node(-internal_id => $internal{$l});
	   $intnode->bootstrap(sprintf("%d",100 * $lookup{$l} / $i));
       }
   }
   return $guide_tree;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  http://bugzilla.open-bio.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
CONTRIBUTORSTop
none so far
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
 Usage   : my $obj = new Bio::Tree::Statistics();
 Function: Builds a new Bio::Tree::Statistics object 
 Returns : Bio::Tree::Statistics
 Args    :