phylocomr
is an R
client for Phylocom - a C library for Analysis of Phylogenetic Community
Structure and Character Evolution.
Phylocom home page is at https://phylodiversity.net/phylocom/. The source code for Phylocom is at https://github.com/phylocom/phylocom/.
Phylocom is usually used either on the command line or through the R
package picante
, which has duplicated some of the Phylocom
functionality.
Phylocom has been cited nearly 1000 times according to Google
Scholar, so is clearly a very widely used piece of software. The goal
with this package is to make it even easier to use - and in particular,
to incorporate its use into a reproducible workflow entirely in R
instead of going to the shell/command line for Phylocom usage. (Yes,
some of Phylocom functionality is in picante
, but not
all.)
In terms of performance, some functionality will be faster here than
in picante
, but the maintainers of picante
have re-written some Phylocom functionality in C/C++, so performance
should be similar in those cases.
Install ape
for below examples:
Stable phylocomr
version from CRAN
Or, the development version from Github
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)
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)
if (requireNamespace("ape")) {
library(ape)
plot(read.tree(text = res))
}