Bio::Tree::Statistics(3pm)

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

  transfer_bootstrap_expectation
 Title   : transfer_bootstrap_expectation
 Usage   : my $tree_with_bs = $stats->transfer_bootstrap_expectation(\@bs_trees,$guide_tree);
 Function: Calculates the Transfer Bootstrap Expectation (TBE) for internal nodes based on
           the methods outlined in Lemoine et al, Nature, 2018.
           Currently experimental.
 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
               excluding 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
               excluding 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.