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Bio::Tree::Statistics(User Contributed Perl DocumentatBio::Tree::Statistics(3)

NAME
       Bio::Tree::Statistics - Calculate certain statistics for	a Tree

SYNOPSIS
	 use Bio::Tree::Statistics;

DESCRIPTION
       This should be where Tree statistics are	calculated.  It	was previously
       where statistics	from a Coalescent simulation.

       It now contains several methods for calculating Tree-Trait statistics.

FEEDBACK
   Mailing Lists
       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

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the	problem	with code and
       data examples if	at all possible.

   Reporting Bugs
       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:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich
       Email jason AT bioperl.org

CONTRIBUTORS
       Heikki Lehvaslaiho, heikki at bioperl dot org

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::Tree::Statistics->new();
	Function: Builds a new Bio::Tree::Statistics object
	Returns	: Bio::Tree::Statistics
	Args	:

   assess_bootstrap
	Title	: assess_bootstrap
	Usage	: my $tree_with_bs = $stats->assess_bootstrap(\@bs_trees,$guide_tree);
	Function: Calculates the bootstrap for internal	nodes based on the percentage
		  of times \@bs_trees agree with each internal node
	Returns	: L<Bio::Tree::TreeI>
	Args	: Arrayref of L<Bio::Tree::TreeI>s
		  Guide	tree, L<Bio::Tree::TreeI>s

   cherries
	 Example    : cherries($tree, $node);
	 Description: Count number of paired leaf nodes
		      in a binary tree
	 Returns    : integer
	 Exceptions :
	 Args	    : 1. Bio::Tree::TreeI object
		      2. Bio::Tree::NodeI object within	the tree, optional

       Commonly	used statistics	assume a binary	tree, but this methods returns
       a value even for	trees with polytomies.

   Tree-Trait statistics
       The following methods produce descriptors of trait distribution among
       leaf nodes within the trees. They require that a	trait has been set for
       each leaf node. The tag methods of Bio::Tree::Node are used to store
       them as key/value pairs.	In this	way, one tree can store	more than one
       trait.

       Trees have method add_traits() to set trait values from a file. See the
       add_trait() method in Bio::Tree::TreeFunctionsI.

   fitch
	 Example    : fitch($tree, $key, $node);
	 Description: Calculates Parsimony Score (PS) and internal trait
		      values using the Fitch 1971 parsimony algorithm for
		      the subtree a defined by the (internal) node.
		      Node defaults to the root.
	 Returns    : true on success
	 Exceptions : leaf nodes have to have the trait	defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. trait name string
		      3. Bio::Tree::NodeI object within	the tree, optional

       Runs first fitch_up that	calculates parsimony scores and	then
       fitch_down that should resolve most of the trait/character state
       ambiguities.

       Fitch, W.M., 1971. Toward defining the course of	evolution: minimal
       change for a specific tree topology. Syst. Zool.	20, 406-416.

       You can access calculated parsimony values using:

	 $score	= $node->->get_tag_values('ps_score');

       and the trait value with:

	 $traitvalue = $node->->get_tag_values('ps_trait'); # only the first
	 @traitvalues =	$node->->get_tag_values('ps_trait');

       Note that there can be more that	one trait value, especially for	the
       root node.

   ps
	 Example    : ps($tree,	$key, $node);
	 Description: Calculates Parsimony Score (PS) from Fitch 1971
		      parsimony	algorithm for the subtree as defined
		      by the (internal)	node.
		      Node defaults to the root.
	 Returns    : integer, 1 < PS <	n, where n is number of	branches
	 Exceptions : leaf nodes have to have the trait	defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. trait name string
		      3. Bio::Tree::NodeI object within	the tree, optional

       This is the first half of the Fitch algorithm that is enough for
       calculating the resolved	parsimony values. The trait/chararacter	states
       are commonly left in ambiguous state. To	resolve	them, run fitch_down.

   fitch_up
	 Example    : fitch_up($tree, $key, $node);
	 Description: Calculates Parsimony Score (PS) from the Fitch 1971
		      parsimony	algorithm for the subtree as defined
		      by the (internal)	node.
		      Node defaults to the root.
	 Returns    : integer, 1< PS < n, where	n is number of branches
	 Exceptions : leaf nodes have to have the trait	defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. trait name string
		      3. Bio::Tree::NodeI object within	the tree, optional

       This is a more generic name for ps and indicates	that it	performs the
       first bottom-up tree traversal that calculates the parsimony score but
       usually leaves trait/character states ambiguous.	If you are interested
       in internal trait states, running fitch_down should resolve most	of the
       ambiguities.

   fitch_down
	 Example    : fitch_down($tree,	$node);
	 Description: Runs the second pass from	Fitch 1971
		      parsimony	algorithm to resolve ambiguous
		      trait states left	by first pass.
		      by the (internal)	node.
		      Node defaults to the root.
	 Returns    : true
	 Exceptions : dies unless the trait is defined in all nodes
	 Args	    : 1. Bio::Tree::TreeI object
		      2. Bio::Tree::NodeI object within	the tree, optional

       Before running this method you should have ran fitch_up (alias to ps ).
       Note that it is not guaranteed that all states are completely resolved.

   persistence
	 Example    : persistence($tree, $node);
	 Description: Calculates the persistence
		      for node in the subtree defined by the (internal)
		      node.  Node defaults to the root.
	 Returns    : int, number of generations trait value has to remain same
	 Exceptions : all the  nodes need to have the trait defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. Bio::Tree::NodeI object within	the tree, optional

       Persistence measures the	stability that the trait value has in a	tree.
       It expresses the	number of generations the trait	value remains the
       same. All the decendants	of the root in the same	generation have	to
       share the same value.

       Depends on Fitch's parsimony score (PS).

   count_subclusters
	 Example    : count_clusters($tree, $node);
	 Description: Calculates the number of sub-clusters
		      in the subtree defined by	the (internal)
		      node.  Node defaults to the root.
	 Returns    : int, count
	 Exceptions : all the  nodes need to have the trait defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. Bio::Tree::NodeI object within	the tree, optional

       Depends on Fitch's parsimony score (PS).

   count_leaves
	 Example    : count_leaves($tree, $node);
	 Description: Calculates the number of leaves with same	trait
		      value as root in the subtree defined by the (internal)
		      node.  Requires an unbroken line of identical trait values.
		      Node defaults to the root.
	 Returns    : int, number of leaves with this trait value
	 Exceptions : all the  nodes need to have the trait defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. Bio::Tree::NodeI object within	the tree, optional

       Depends on Fitch's parsimony score (PS).

   phylotype_length
	 Example    : phylotype_length($tree, $node);
	 Description: Sums up the branch lengths within	phylotype
		      exluding the subclusters where the trait values
		      are different
	 Returns    : float, length
	 Exceptions : all the  nodes need to have the trait defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. Bio::Tree::NodeI object within	the tree, optional

       Depends on Fitch's parsimony score (PS).

   sum_of_leaf_distances
	 Example    : sum_of_leaf_distances($tree, $node);
	 Description: Sums up the branch lengths from root to leaf
		      exluding the subclusters where the trait values
		      are different
	 Returns    : float, length
	 Exceptions : all the  nodes need to have the trait defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. Bio::Tree::NodeI object within	the tree, optional

       Depends on Fitch's parsimony score (PS).

   genetic_diversity
	 Example    : genetic_diversity($tree, $node);
	 Description: Diversity	is the sum of root to leaf distances
		      within the phylotype normalised by number	of leaf
		      nodes
	 Returns    : float, value of genetic diversity
	 Exceptions : all the  nodes need to have the trait defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. Bio::Tree::NodeI object within	the tree, optional

       Depends on Fitch's parsimony score (PS).

   statratio
	 Example    : statratio($tree, $node);
	 Description: Ratio of the stem	length and the genetic diversity of the
		      phylotype	L<genetic_diversity>
	 Returns    : float, separation	score
	 Exceptions : all the  nodes need to have the trait defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. Bio::Tree::NodeI object within	the tree, optional

       Statratio gives a measure of separation and variability within the
       phylotype.  Larger values identify more rapidly evolving	and recent
       phylotypes.

       Depends on Fitch's parsimony score (PS).

   ai
	 Example    : ai($tree,	$key, $node);
	 Description: Calculates the Association Index (AI) of Whang et
		      al. 2001 for the subtree defined by the (internal)
		      node.  Node defaults to the root.
	 Returns    : real
	 Exceptions : leaf nodes have to have the trait	defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. trait name string
		      3. Bio::Tree::NodeI object within	the tree, optional

	 Association index (AI)	gives a	more fine grained results than PS since
	 the result is a real number. ~0 E<lt>=	AI.

	 Wang, T.H., Donaldson,	Y.K., Brettle, R.P., Bell, J.E., Simmonds, P.,
	 2001.	Identification of shared populations of	human immunodeficiency
	 Virus Type 1 infecting	microglia and tissue macrophages outside the
	 central nervous system. J. Virol. 75 (23), 11686-11699.

   mc
	 Example    : mc($tree,	$key, $node);
	 Description: Calculates the Monophyletic Clade	(MC) size statistics
		      for the subtree a	defined	by the (internal) node.
		      Node defaults to the root;
	 Returns    : hashref with trait values	as keys
	 Exceptions : leaf nodes have to have the trait	defined
	 Args	    : 1. Bio::Tree::TreeI object
		      2. trait name string
		      3. Bio::Tree::NodeI object within	the tree, optional

	 Monophyletic Clade (MC) size statistics by Salemi at al 2005. It is
	 calculated for	each trait value. 1 E<lt>= MC E<lt>= nx, where nx is the
	 number	of tips	with value x:

	  pick the internal node with maximim value for
	     number of of tips with only trait x

	 MC was	defined	by Parker et al	2008.

	 Salemi, M., Lamers, S.L., Yu, S., de Oliveira,	T., Fitch, W.M., McGrath, M.S.,
	  2005.	Phylodynamic analysis of Human Immunodeficiency	Virus Type 1 in
	  distinct brain compartments provides a model for the neuropathogenesis of
	  AIDS.	J. Virol. 79 (17), 11343-11352.

	 Parker, J., Rambaut A., Pybus O., 2008. Correlating viral phenotypes
	  with phylogeny: Accounting for phylogenetic uncertainty Infection,
	  Genetics and Evolution 8 (2008), 239-246.

perl v5.24.1			  2017-07-08	      Bio::Tree::Statistics(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

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