Description Usage Arguments Value Author(s) References Examples

This function calculates the Colless-like index for a given rooted
tree *T* according to the chosen weight function *f* and dissimilarity *D*.
The Colless-like index *CL(T)*
relative to *D* and *f* is the sum of the *(D,f)*-balance values
over all inner vertices of the tree. More precisely,

*CL(T)=∑_{v in V_in(T)} bal_{D,f}(v)*

where *V_in(T)* is the
set of inner vertices of *T*. The *(D,f)*-balance value
of *v* with children *v1,...,vk* is computed as

*bal_{D,f}(v)=D(fs(T_v1),...,fs(T_vk)))*

with *D* denoting the dissimilarity and *fs* denoting the f.size.

The f.size *fs(T)* of a tree *T* uses the function *f*, which maps any
integer to a non-negative real number, to build a weighted sum of
the out-degrees of all vertices in *T*. More precisely,

*fs(T)=∑_{v in V(T)} f(deg+(v))*

where *V(T)* is the set of all
vertices of *T* and *deg+(v)* denotes the out-degree (i.e. the number of
children) of the vertex *v*. The *f*-functions that are already
implemented are *f(x)=e^x* and *f(x)=ln(x+e)*.

The dissimilarity *D(x_1,...,x_k)* of a vector *x_1,...,x_k* assigns
a non-negative value to the vector, is independent of the order of the vector
entries and equals zero if and only if *x_1=...=x_k*. In this
implementation the following dissimilarity functions are already built-in:
mean deviation from the median (*mdm*),
the sample variance (*var*) and the sample standard deviation (*sd*).

`collesslikeI`

also allows the use of other functions for the weight function *f*
and the dissimilarity *D*.

Special cases: For *n=1* the function returns *CL(T)=0* and a warning.

1 | ```
collesslikeI(tree, f.size, dissim)
``` |

`tree` |
A rooted binary tree in phylo format. |

`f.size` |
A character string specifying the function |

`dissim` |
A character string specifying the dissimilarity that shall be used. It can be one of the following: "mdm", "var", "sd" or the name of a function as a string. |

`collesslikeI`

returns the Colless-like index of the given tree according to the chosen
function and dissimilarity.

Luise Kuehn, Sophie Kersting

A. Mir, L. Rotger, and F. Rosselló. Sound Colless-like balance indices for multifurcating trees. PLOSONE, 13(9):e0203401, 2018. doi: 10.1371/journal.pone.0203401

1 2 3 4 5 6 7 | ```
tree <- ape::read.tree(text="((((,),),(,)),(((,),),(,)));")
collesslikeI(tree, f.size="exp", dissim="mdm")
collesslikeI(tree, f.size="exp", dissim="var")
collesslikeI(tree, f.size="ln", dissim="sd")
myfsize <- function(x) return(x+1)
mydissim <- function(x) return (var(x))
collesslikeI(tree, f.size="myfsize",dissim = "mydissim")
``` |

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