AvotrexPhylo: Avotrex phylo dataset

In avotrex: A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder

Avotrex phylo dataset

Description

The dataset provides instructions to graft extinct bird species from Sayol et al. (IN PREP) on to existing BirdTree phylogenies using the AvoPhylo function from the Avotrex package. Instructions are provided in various columns (see format).

Usage

data("AvotrexPhylo")

Format

A data frame with 610 rows and the following variables:

sp_id

a character vector detailing the order in which species are joined

phylo_id

a character vector detailing the order in which species are joined and whether a species is part of a group (see details)

per_fixed

a logical vector

time_fixed

a numeric vector detailing a specific time point for grafting or NA

group

a numeric vector detailing a group code or NA (see details)

species

a character vector detailing species name with an underscore

order

a character vector detailing species order

family

a character vector detailing species family

genus

a character vector detailing species genus

jetz_order

a character vector detailing species order within the Jetz phylogeny

jetz_family

a character vector detailing species family within the Jetz phylogeny

jetz_genus

a character vector detailing species genus within the Jetz phylogeny

type

a character vector of codes. The codes determine how and where the species is grafted to the tree. See details and function "AvoPhylo"

sister_order

a character vector. Provides the order within the BirdTree backbone tree to join the extinct species to, or randomly within, depending on the code within the column "type"

sister_clade

a character vector. Provides the clade within the BirdTree backbone tree to join the extinct species to, or randomly within, depending on the code within the column "type"

sister_family

a character vector. Provides the family within the BirdTree backbone tree to join the extinct species to, or randomly within, depending on the code within the column "type"

sister_genus

a character vector. Provides the genus within the BirdTree backbone tree to join the extinct species to, or randomly within, depending on the code within the column "type"

sister_species

a character vector. Provides the species within the BirdTree backbone tree to join the extinct species to depending on the code within the column "type"

sister_species_group

a character vector. Provides the group of species within the BirdTree backbone tree to join the extinct species to, or randomly within, depending on the code within the column "type"

Details

As certain species need to be grafted onto the tree before other species, a number of the species are grafted in a set order. This ordering is controlled through the “sp_id”, “phylo_id” and “group” columns in the extinct species phylogeny database. Before grafting, the database is ordered by the “sp_id” column, with the “phylo_id” and “group” columns used to filter out particular groups of species (i.e., those classified as "xS" in the "phylo_id" column) to be grafted in different orders (i.e., either a randomised order within groups, or a fixed order within groups). See the package vignette for further details.

Some species are grafted at specific time points along a branch (column "time_fixed").

As some of the codes within the column "type" (see table below) randomly place the given species within a group of species, a genus, or a family, and some species groups are randomised before grafting (see above), it is useful to run the grafting proceedure over a a number of trees to average out the randomisation (see function "AvoPhylo").

See the package vignette, and the help file for AvoPhylo() for more information.

References

Matthews et al. (IN REVIEW) The global loss of avian functional and phylogenetic diversity from extinctions in the Holocene and Late Pleistocene.

Sayol et al. (IN PREP) The global loss of avian functional and phylogenetic diversity from extinctions in the Holocene and Late Pleistocene

Examples

data(AvotrexPhylo)

avotrex documentation built on Sept. 12, 2024, 9:36 a.m.