distribution: Plot the distribution of Colless-Like, Sackin and cophenetic...

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/distribution.R

Description

Given alpha, gamma and a phylogenetic tree, plot the distribution of the Colless-Like, Sackin and cophenetic normalized balance indices under the alpha-gamma model and computes the percentile of that tree of the previous normalized balance indices under the alpha-gamma model.

Usage

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distribution(tree, alpha = NA, gamma = NA, set.indices = NULL,
  new.simulation = FALSE, repetitions = 1000,
  legend.location = "topright", cex = 0.75, percentile.plot = FALSE,
  db.path = getwd())

Arguments

tree

a single phylogenetic tree. It can be entered as a string in Newick format, as a "phylo" object (ape package) or as an "igraph" object (igraph package).

alpha

parametrer of the alpha-gamma model, between 0 and 1.

gamma

parametrer of the alpha-gamma model, between 0 and alpha.

set.indices

If NULL (default) the values of the balance indices are taken from stored data or from a new simulated data (See "Details"). If not, it must be a 3-column data.frame with the three balance indices (Colles-like, Sackin, Cophenetic). See indices.simulation.

new.simulation

if FALSE(default) the values of the balance indices are taken from a data.frame entered by the user or from our database. If TRUE, the values of the balance indices are computed from a new simulation. See indices.simulation.

repetitions

if the value of the new.simulation parameter is TRUE, the number of trees to be generated.

legend.location

location of the legend. See "Details".

cex

expansion factor of the legend. See "Details".

percentile.plot

if FALSE (default), density plots of the normalized balance indices are shown. if TRUE, percentiles plots of the normalized balance indices are shown.

db.path

the current working directory. If our database is used, the db.path parameter should be the directory where the database is located.

Details

Two plots are available: one represents the percentile plots of the normalized balance indices (percentile.plot=TRUE), and the other one represents the density plots of the normalized balance indices (percentile.plot=FALSE).

The trees stored in our database have between 3 and 50 leaves and the values of the parameters alpha and gamma are in {0,0.1,...,1} such that gamma alpha. If the introduced parameters are not in the list, a new computation is done with them and a new dataset of trees is generated, and their indices are also computed. The number of trees generated can be modified by the parameter repetitions (see indices.simulation for more information). This computation may take some time, therefore you can computate them separately with indices.simulation, save their values and then call this function by setting the parameter set.indices=NULL.

Our database is available to download at https://github.com/LuciaRotger/CollessLike/tree/master/CollessLikeDataBase.

The legend is placed with the graphics function legend(), so its location can be specified by setting legend.position to a single keyword from the list "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". The expansion factor for the legend is controlled by the parameter cex, by default cex=1. See legend.

Value

A numeric vector with the three percentiles.

Author(s)

Lucia Rotger

References

B. Chen, D. Ford, M. Winkel, A new family of Markov branching trees: the alpha-gamma model. Electr. J. Probab. 14 (2009), 400-430.

A. Mir, F. Rossello, L.Rotger, A Colless-like balance index for multifurcating phylogenetic trees.

A. Mir, F. Rossello, L.Rotger, A new balance index for phylogenetic trees. Mathematical Biosciences 241 (2013), 125-136.

M. J. Sackin, "Good" and "bad" phenograms. Sys. Zool, 21 (1972), 225-226.

See Also

legend, indices.simulation, balance.indices

Examples

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#The parameter folder contains the location of the database
#If not specified folder=getwd()

## Different ways to introduce the tree
#From a newick string
distribution("(1,2,3,4,5);",0.5,0.3,db.path=folder)
distribution("(1,(2,(3,(4,5))));",0.5,0.3,db.path=folder)

#From a phylo object
require(ape)
random.tree = rtree(5,rooted=TRUE)
distribution(random.tree,0.5,0.3,db.path=folder)

#An example of a tree generated by the alpha-gamma model (igraph object)
a.g.tree = a.g.model(5,0.5,0.3)
distribution(a.g.tree,0.5,0.3,db.path=folder)

## Different indices data
# From our data base
distribution(a.g.tree,0.5,0.3,db.path=folder)

# From a data.frame generated by 'indices.simulation'
# ('Repetitions' set as 10 for a fast example)
indices.data = indices.simulation(5,0.5,0.3,10)
distribution(a.g.tree,0.5,0.3,set.indices=indices.data) 

# Allow the function to do a new generation of data and compute their indices
distribution(a.g.tree,0.5,0.3,new.simulation=TRUE,repetitions=10)
# WARNING! it might take a long time, it depends on the parameters 
# 'n' (number of leaves) and 'repetition' (number of repetitions)

LuciaRotger/CollessLike documentation built on April 18, 2018, 11:07 p.m.