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ftolr

ftolr is an R package that provides access to the Fern Tree of Life (FTOL) and related datasets.

These data were originally compiled using methods described in this paper:

Installation

You can install ftolr from GitHub with:

# install.packages("devtools")
devtools::install_github("fernphy/ftolr")

Examples

Fern Tree of Life (FTOL)

The ft_tree() function loads FTOL into the current R session. There are several options available to control branch lengths, presence or absence of outgroup, and sampling scheme.

library(ftolr)
# Default: consensus tree with branchlengths in units of time
ft_tree()
#> 
#> Phylogenetic tree with 5868 tips and 5867 internal nodes.
#> 
#> Tip labels:
#>   Acrostichum_danaeifolium, Acrostichum_speciosum, Acrostichum_aureum, Ceratopteris_richardii, Ceratopteris_cornuta, Ceratopteris_pteridoides, ...
#> Node labels:
#>   100/100, 100/100, 100, 100/100, 100/100, 100/100, ...
#> 
#> Rooted; includes branch lengths.

# Maximum-likelihood (ML) tree with raw branchlengths and outgroup pruned
ft_tree(
  branch_len = "raw",
  consensus = FALSE,
  drop_og = TRUE
) 
#> 
#> Phylogenetic tree with 5850 tips and 5849 internal nodes.
#> 
#> Tip labels:
#>   Acrostichum_danaeifolium, Acrostichum_speciosum, Acrostichum_aureum, Ceratopteris_richardii, Ceratopteris_cornuta, Ceratopteris_pteridoides, ...
#> Node labels:
#>   100/100, 100/100, 100/100, 100/100, 80/100, 100, ...
#> 
#> Rooted; includes branch lengths.

DNA sequences

The DNA sequences used to build the tree are also available. These can be subset by locus (gene) name and can be formatted as a matrix (DNA alignment) or a list.

# Default: aligned Sanger sequences
ft_seqs()
#> 5869 DNA sequences in binary format stored in a matrix.
#> 
#> All sequences of same length: 13384 
#> 
#> Labels:
#> Acrostichum_danaeifolium
#> Actiniopteris_dimorpha
#> Actiniopteris_semiflabellata
#> Adenophorus_sarmentosus
#> Adenophorus_tenellus
#> Adiantopsis_alata
#> ...
#> 
#> More than 10 million bases: not printing base composition.
#> (Total: 78.55 Mb)

# Unaligned rbcL
ft_seqs(loci = "rbcL", aligned = FALSE)
#> 5068 DNA sequences in binary format stored in a list.
#> 
#> Mean sequence length: 1256.457 
#>    Shortest sequence: 214 
#>     Longest sequence: 1428 
#> 
#> Labels:
#> Acrostichum_danaeifolium
#> Actiniopteris_dimorpha
#> Actiniopteris_semiflabellata
#> Adenophorus_sarmentosus
#> Adenophorus_tenellus
#> Adiantopsis_alata
#> ...
#> 
#> Base composition:
#>     a     c     g     t 
#> 0.266 0.217 0.252 0.266 
#> (Total: 6.37 Mb)

FTOL data version

You can check the current version of the FTOL data included in ftolr with ft_data_ver():

ft_data_ver()
#> [1] "1.7.0"

Citing

If you use this package, please cite it!

Here is an example:

The example DOI above is for the overall package.

Here is the latest DOI, which you should cite if you are using the latest version of the package:

DOI

Please also cite the paper describing how the data were generated:

Licenses