Create a new phylogenetic flow collection object (pfc)

Create a new phylogenetic flow collection object (pfc)

Usage

pfc(
  pfn = character(),
  pfpp = pfp(),
  pfl = list(),
  is_tip = logical(),
  edge_names = character(),
  internal = logical(),
  node_ord = NULL,
  edge_ord = NULL,
  sparse_mat = NULL
)

pf_is_pfc(x)

Arguments

pfn

A character vector of names for each phylogenetic flow

pfpp

A vector of phylogenetic flow paths of class pfp

pfl

A list of phylogenetic flow feature. Should be numeric.

is_tip

A logical vector specifying whether the phylogenetic flow reaches the phylogeny's tips

edge_names

A character vector of names for the phylogeny's edges

internal

A logical vector specifying whether each edge is internal (not leading to a tip)

node_ord

An optional integer vector specifying an order for the nodes. Usually used to store ordering information from another tree format such as phylo so it is easier to match data up later.

edge_ord

An optional integer vector specifying an order for the edges. Usually used to store ordering information from another tree format such as phylo so it is easier to match data up later.

sparse_mat

A sparse matrix representation of the phylogenetic flow collection. Can be left NULL, in which case it is constructed from the other arguments.

x

An object to be tested

Value

A pfc object