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pd - Faith's index of phylogenetic diversity

Source: R/pd.R
ph_pd.Rd

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.

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

Details

See phylocomr-inputs for expected input formats

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)
#> # A tibble: 6 × 5
#>   sample  ntaxa    pd treebl proptreebl
#>   <chr>   <int> <dbl>  <dbl>      <dbl>
#> 1 clump1      8    16     62      0.258
#> 2 clump2a     8    17     62      0.274
#> 3 clump2b     8    18     62      0.29 
#> 4 clump4      8    22     62      0.355
#> 5 even        8    30     62      0.484
#> 6 random      8    27     62      0.435

# 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)
#> # A tibble: 6 × 5
#>   sample  ntaxa    pd treebl proptreebl
#>   <chr>   <int> <dbl>  <dbl>      <dbl>
#> 1 clump1      8    16     62      0.258
#> 2 clump2a     8    17     62      0.274
#> 3 clump2b     8    18     62      0.29 
#> 4 clump4      8    22     62      0.355
#> 5 even        8    30     62      0.484
#> 6 random      8    27     62      0.435