PD_deficit: Title Calculate the amount of phylogenetic deficit in...

In GabrielNakamura/FishPhyloMaker: Phylogenies for a List of Finned-Ray Fishes

Title Calculate the amount of phylogenetic deficit in assemblages

Description

Title Calculate the amount of phylogenetic deficit in assemblages

Usage

PD_deficit(phylo, data, level = "Congeneric_insertion")

Arguments

phylo	Phylogenetic tree in newick format, can be an object from FishPhyloMaker function
data	A data frame containing the classification informing the level of insertions. This can be obtained from FishPhyloMaker function
level	Character indicating which level must be considered in the calculation of PD deficit. Can be a vector with the levels ("Congeneric_insertion", "Congeneric_Family_level", "Family_insertion", "Order_insertion") which will be considered in the calculation of phylogenetic deficit. default is "Congeneric_insertion".

Value

A vector containing four values:

- Amount phylogenetic information present in the tree before insertions (PDintree)

- Amount of phylogenetic information inserted in the tree (PDdeficit)

- Total Phylogenetic information of the tree (PDtotal)

- A ratio calculated as PDdeficit/PDtotal (Darwinian_deficit)

See Also

FishPhyloMaker for phylogeny and data frame containing the classification of insertions

GabrielNakamura/FishPhyloMaker documentation built on Jan. 27, 2024, 11:46 a.m.