In ropensci/phylocomr: Interface to 'Phylocom'

phylocomr

knitr::opts_chunk$set(
  comment = "#>",
  warning = FALSE,
  message = FALSE,
  fig.path = "man/figures/"
)

phylocomr gives you access to the Phylocom C library, licensed under BSD 2-clause

Package API

• ecovolve/ph_ecovolve - interface to ecovolve executable, and a higher level interface
• phylomatic/ph_phylomatic - interface to phylomatic executable, and a higher level interface
• phylocom - interface to phylocom executable
• ph_aot - higher level interface to aot
• ph_bladj - higher level interface to bladj
• ph_comdist/ph_comdistnt - higher level interface to comdist
• ph_comstruct - higher level interface to comstruct
• ph_comtrait - higher level interface to comtrait
• ph_pd - higher level interface to Faith's phylogenetic diversity

A note about files

As a convenience you can pass ages, sample and trait data.frame's, and phylogenies as strings, to phylocomr functions. However, phylocomr has to write these data.frame's/strings to disk (your computer's file system) to be able to run the Phylocom code on them. Internally, phylocomr is writing to a temporary file to run Phylocom code, and then the file is removed.

In addition, you can pass in files instead of data.frame's/strings. These are not themselves used. Instead, we read and write those files to temporary files. We do this for two reasons. First, Phylocom expects the files its using to be in the same directory, so if we control the file paths that becomes easier. Second, Phylocom is case sensitive, so we simply standardize all taxon names by lower casing all of them. We do this case manipulation on the temporary files so that your original data files are not modified.

Installation

Stable version:

install.packages("phylocomr")

Development version:

remotes::install_github("ropensci/phylocomr")

library("phylocomr")
library("ape")

ecovolve

ph_ecovolve(speciation = 0.05, extinction = 0.005, time_units = 50)

phylomatic

taxa_file <- system.file("examples/taxa", package = "phylocomr")
phylo_file <- system.file("examples/phylo", package = "phylocomr")
(taxa_str <- readLines(taxa_file))
(phylo_str <- readLines(phylo_file))
ph_phylomatic(taxa = taxa_str, phylo = phylo_str)

use various different references trees

library(brranching)
library(ape)

r2 <- ape::read.tree(text=brranching::phylomatic_trees[['R20120829']])
smith2011 <- ape::read.tree(text=brranching::phylomatic_trees[['smith2011']])
zanne2014 <- ape::read.tree(text=brranching::phylomatic_trees[['zanne2014']])

# R20120829 tree
taxa_str <- c(
  "asteraceae/bidens/bidens_alba",
  "asteraceae/cirsium/cirsium_arvense",
  "fabaceae/lupinus/lupinus_albus"
)
ph_phylomatic(taxa = taxa_str, phylo = r2)

# zanne2014 tree
taxa_str <- c(
  "zamiaceae/dioon/dioon_edule",
  "zamiaceae/encephalartos/encephalartos_dyerianus",
  "piperaceae/piper/piper_arboricola"
)
ph_phylomatic(taxa = taxa_str, phylo = zanne2014)

# zanne2014 subtree
zanne2014_subtr <- ape::extract.clade(zanne2014, node='Loganiaceae')
zanne_subtree_file <- tempfile(fileext = ".txt")
ape::write.tree(zanne2014_subtr, file = zanne_subtree_file)
taxa_str <- c(
  "loganiaceae/neuburgia/neuburgia_corynocarpum",
  "loganiaceae/geniostoma/geniostoma_borbonicum",
  "loganiaceae/strychnos/strychnos_darienensis"
)
ph_phylomatic(taxa = taxa_str, phylo = zanne2014_subtr)
ph_phylomatic(taxa = taxa_str, phylo = zanne_subtree_file)

aot

traits_file <- system.file("examples/traits_aot", package = "phylocomr")
phylo_file <- system.file("examples/phylo_aot", package = "phylocomr")
traitsdf_file <- system.file("examples/traits_aot_df", package = "phylocomr")
traits <- read.table(text = readLines(traitsdf_file), header = TRUE,
  stringsAsFactors = FALSE)
phylo_str <- readLines(phylo_file)
ph_aot(traits = traits, phylo = phylo_str)

bladj

ages_file <- system.file("examples/ages", package = "phylocomr")
phylo_file <- system.file("examples/phylo_bladj", package = "phylocomr")
ages_df <- data.frame(
  a = c('malpighiales','salicaceae','fabaceae','rosales','oleaceae',
        'gentianales','apocynaceae','rubiaceae'),
  b = c(81,20,56,76,47,71,18,56)
)
phylo_str <- readLines(phylo_file)
(res <- ph_bladj(ages = ages_df, phylo = phylo_str))
plot(ape::read.tree(text = res))

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for phylocomr in R doing citation(package = 'phylocomr')
• Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

ropensci/phylocomr documentation built on April 22, 2023, 8:36 p.m.