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

View source: R/indices.simulation.R

Generates a list of trees according to the introduced parameters for the alpha-gamma model. Then, this 3 balance index are calulated: Colless-like, Sackin and Cophenetic.

1 2 |

`n` |
the number of leaves of the tree. |

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

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

`repetitions` |
the number of trees to generate. |

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

Given a number of leaves, the function generates a tree with that number of leaves and computates the three indeces of balance (Colles-like, Sackin and Cophenetic with function `balance.indices`

). This is done as many times as it is set by 'repetitions' parameter, and it generates a 3-column data.frame of indices.

The trees are generated according to the alpha-gamma model. These parameters can be specified by `alpha`

and `gamma`

parameters of the function. The following cases are distinguished:

`alpha = NA`

and`gamma = NA`

: All the 66 combinations of`alpha`

in { 0, 0.1, 0.2, ... ,0.9, 1 } and`gamma`

in { 0, 0.1, ... ,`alpha`

} are done.`alpha`

in [0,1] and`gamma = NA`

: Since`alpha`

is fixed, all the combinations with that`alpha`

and`gamma`

in { 0, 0.1, ... ,`alpha`

} are done.`alpha`

in [0,1] and`gamma`

in [0,`alpha`

] : Both parameters are fixed. Then, only that combination is done.

A 3-column data.frame with the Colless-like, Sackin and Cophenetic balance indices for every generated tree. If more than one data.frame has to be generated, then the returned value is a data.frame list (its names specify which alpha and gamma parameters have generated that data.frame, for instance "a0.5g0.3" indicates alpha=0.5 and gamma=0.3).

Lucia Rotger

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
#('Repetitions' set as 100 for a fast example)
indices.table = indices.simulation(5,0.5,0.3,repetitions=10)
head(indices.table)
#Normalized indices (between 0 and 1)
indices.table = indices.simulation(5,0.5,0.3,repetitions=10,norm=TRUE)
head(indices.table)
#Without specifying alpha and gamma
indices.list = indices.simulation(5,repetitions=100)
#by default alpha=seq(0,1,0.1) and gamma=seq(0,alpha,0.1), thus
length(indices.list) #=66
#all the elements of the list have a name that identifies its parameters
indices.list$a0.5g0.3
indices.list$a0.7g0.2
``` |

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

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