PhyloDiv: PhyloDiv and PhyloDivOne classes

In ropensci/phylodiv: Phylogenetic Biodiversity Query Tools

Description

PhyloDiv and PhyloDivOne classes

PhyloDiv and PhyloDivOne classes

Public fields

trees

(list) list of phylogenetic trees

query

(character) query string

data

ignored for now

Methods

Public methods

• PhyloDiv$print()

• PhyloDiv$new()

• PhyloDiv$add_tree()

• PhyloDiv$fetch_hierarchies()

• PhyloDiv$to_list()

• PhyloDiv$to_json()

• PhyloDiv$clone()

---

Method print()

print method for 'PhyloDivOne' objects

Usage

PhyloDiv$print(x, ...)

Arguments

x

self

...

ignored

---

Method new()

Create a new 'PhyloDiv' object

Usage

PhyloDiv$new(...)

Arguments

...

any number of 'PhyloDivOne' objects

Returns

A new 'PhyloDiv' object

---

Method add_tree()

add a tree

Usage

PhyloDiv$add_tree(tree)

Returns

nothing, adds a tree

---

Method fetch_hierarchies()

fetch hierarchy data for all trees

Usage

PhyloDiv$fetch_hierarchies()

Returns

list

---

Method to_list()

coerce to a list

Usage

PhyloDiv$to_list()

Returns

list of lists

---

Method to_json()

coerce to JSON

Usage

PhyloDiv$to_json(...)

Returns

json/character

---

Method clone()

The objects of this class are cloneable with this method.

Usage

PhyloDiv$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## Not run: 
library(ape)
set.seed(132434)
tree <- rcoal(20)
pd1 <- PhyloDivOne$new(tree)
pd1
pd1$to_list()
pd1$to_json()

x <- "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);"
tree <- read.tree(text = x)

# xxx
x <- PhyloDiv$new(pd1, pd1, pd1)
x
x$to_list()
x$to_json()
x$to_json(pretty = TRUE)

## End(Not run)

ropensci/phylodiv documentation built on March 13, 2020, 3:14 p.m.