Description Usage Arguments Details Value Author(s) References Examples

View source: R/colles.like.index.R

Given a phylogenetic tree, computes the Colless-like balance index of that phylogenetic tree.

1 | ```
colless.like.index(tree, f.size = "ln", diss = "MDM", norm = FALSE)
``` |

`tree` |
a single phylogenetic tree. It can be entered as a string in Newick format, as a 'phylo' object ( |

`f.size` |
function to compute the f-size of the tree. See (Mir et al. , 2017) for details. Its default value is "ln" for f(n)=ln(n+e). Other value can be "exp" (f(n)=exp(n)). It can also be a user-defined function but in this case, the index cannot be normalized |

`diss` |
by default, the dissimilarity used to compute the balance index. See (Mir et al. , 2017) for details. Its default value is MDM (mean deviation from the median). Other values can be set as "sd" (sample standard deviation) or "var" (sample variance) . It can also be a user-defined function but in this case the index cannot be normalized. |

`norm` |
a logical object indicating if the indices should be normalized or not. |

The Colless-Like balance index is the generalization of the Colless balance index (see Colless,1982) for non-binary trees.

Given a function that computes the f-size of a tree and a dissimarity function that computes the difference of the f-sizes of the subtrees rooted at the children of every internal node of the tree, the Colless-Like index is defined as the sum of these dissimilarities for all internal nodes of the tree. (Mir et al. , 2017)

By default, the f-size function is `f(n)=exp(n)`

and the dissimilarity is the mean deviation from the median (MDM).
It is possible to change them by specifying it with the parameters `f.size`

and `diss`

, with "exp" the f-size would be `f(n)=exp(n)`

, and with "var" (or "sd") the dissimilarity would be the sample variance (or the sample standard deviation).
It is also possible to set a new function for both parameters, see "References".

A numeric value.

Lucia Rotger

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

D. H. Colless, Review of "Phylogenetics: the theory and practice of phylogenetic systematics".
*Sys. Zool*, **31** (1982), 100–104.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | ```
# Computation of the Colless-Like balance index of trees
# entered in newick format:
colless.like.index("(1,2,3,4,5);")
colless.like.index("(1,(2,(3,(4,5))));")
# Computation of the Colless-Like balance index of trees
# entered as a phylo object:
require(ape)
random.tree = rtree(5,rooted=TRUE)
colless.like.index(random.tree)
# Computation of the Colless-Like balance index of a tree
# entered as a igraph object. The tree is randomly
# generated from all trees with 5 leaves following
# the alpha-gamma model with alpha=0.5 and gamma=0.3.
a.g.tree = a.g.model(5,0.5,0.3)
colless.like.index(a.g.tree)
# All of them can be normalized (values between 0 and 1)
colless.like.index("(1,2,3,4,5);",norm=TRUE)
colless.like.index("(1,(2,(3,(4,5))));",norm=TRUE)
colless.like.index(random.tree,norm=TRUE)
colless.like.index(a.g.tree,norm=TRUE)
# Computation of the Colless-Like balance index of the
# previous generated tree with f-size function f(n)=exp(n):
colless.like.index(a.g.tree,f.size="exp")
# Computation of the Colless-Like balance index of the
# previous generated tree that sets the sample variance
# and the sample standard deviation as dissimilarity.
colless.like.index(a.g.tree,diss="var")
colless.like.index(a.g.tree,diss="sd")
# Computation of the Colless-Like balance index of the
# previous generated tree with f-size function f(n)=exp(n)
# that sets the sample variance and the sample standard
# deviation as dissimilarity.
colless.like.index(a.g.tree,f.size="exp",diss="var")
colless.like.index(a.g.tree,f.size="exp",diss="sd")
``` |

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

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