FishPhyloMaker {FishPhyloMaker}

Obtaining fish phylogeny according to a local pool of species

Description

Obtaining fish phylogeny according to a local pool of species

Usage

FishPhyloMaker(
  data,
  insert.base.node = FALSE,
  return.insertions = TRUE,
  progress.bar = TRUE
)

Arguments

data

A data frame with three columns containing the name of species (s), the Family (f) and the Order (o). This data frame can be generated with tab_function function.

insert.base.node

Logical argument indicating if the species must be added automatically in the family and order (when needed) nodes. Default is FALSE

return.insertions

Logical, if TRUE (default) the output is a list of length two containing the phylogeny and a dataframe with a column indicating at which level each species was inserted.

progress.bar

Logical argument. If TRUE (default) a progress bar will be shown in console.

Value

A newick object containing the phylogeny with the species in data object. If return.insertions = TRUE the output will be a list of length two containing the newick phylogeny and a data frame equal that provided in data plus a column indicating at which level each species was inserted in the tree.

Examples

    data("taxon_data_PhyloMaker")
    res_phylo <- FishPhyloMaker(data = taxon_data_PhyloMaker,
    insert.base.node = TRUE, 
    return.insertions = TRUE, 
    progress.bar = TRUE)