ph_pd: pd - Faith's index of phylogenetic diversity

In phylocomr: Interface to 'Phylocom'

pd - Faith's index of phylogenetic diversity

Description

Calculates Faith’s (1992) index of phylogenetic diversity (PD) for each sample in the phylo.

Usage

ph_pd(sample, phylo)

Arguments

sample	(data.frame/character) sample data.frame or path to a sample file. required
phylo	(character/phylo) One of: phylogeny as a newick string (will be written to a temp file) - OR path to file with a newick string - OR a an ape phylo object. required.

Details

See phylocomr-inputs for expected input formats

Value

A single data.frame, with the colums:

• sample - community name/label

• ntaxa - number of taxa

• pd - Faith's phylogenetic diversity

• treebl - tree BL

• proptreebl - proportion tree BL

Taxon name case

In the sample table, if you're passing in a file, the names in the third column must be all lowercase; if not, we'll lowercase them for you. If you pass in a data.frame, we'll lowercase them for your. All phylo tip/node labels are also lowercased to avoid any casing problems

See Also

Other phylogenetic-diversity: ph_rao()

Examples

sfile <- system.file("examples/sample_comstruct", package = "phylocomr")
pfile <- system.file("examples/phylo_comstruct", package = "phylocomr")

# from data.frame
sampledf <- read.table(sfile, header = FALSE,
  stringsAsFactors = FALSE)
phylo_str <- readLines(pfile)
ph_pd(sample = sampledf, phylo = phylo_str)

# from files
sample_str <- paste0(readLines(sfile), collapse = "\n")
sfile2 <- tempfile()
cat(sample_str, file = sfile2, sep = '\n')
pfile2 <- tempfile()
phylo_str <- readLines(pfile)
cat(phylo_str, file = pfile2, sep = '\n')

ph_pd(sample = sfile2, phylo = pfile2)

phylocomr documentation built on April 22, 2023, 1:14 a.m.