fpd

fpd calculates various alpha diversity metrics of placefiles.

usage: fpd [options] placefile[s]

Options

--pp	Use posterior probability for the weight.
-o	Specify the filename to write to.
--out-dir	Specify the directory to write files to.
--prefix	Specify a string to be prepended to filenames.
--csv	Output the results as csv instead of a padded matrix.
--theta	A comma-separated list of additional exponents to use for calculating bwpd.
--chao-d	A comma-separated list of additional exponents to use for calculating qD(T).
--include-pendant
	Consider pendant branch length in diversity calculations.

Details

By default, guppy fpd outputs a matrix containing in each row: the placefile name, the phylogenetic entropy (phylo_entropy, Allen 2009), the quadratic entropy (quadratic, Rao 1982, Warwick and Clark 1995) phylogenetic diversity (unrooted_pd, Faith 1992), phylogenetic diversity which only requires distal mass (rooted_pd, this is as oppposed to pd requiring both distal and proximal mass), and a new diversity metric generalizing PD to incorporate abundance: balance-weighted phylogenetic diversity (bwpd).

When passed a --theta flag and a comma-delimited list of values for theta, a one-parameter family of functions is used to calculate a diversity measure that scales the incorporation of abundance from traditional phylogenetic diversity (at theta = 0.0) to abundance-weighted phylogenetic diversity (at theta = 1.0). A column labeled bwpd_[theta] is added to the output for each.

When passed a --chao-d flag and a comma-delimited list of values for q, the qD(T) measure of Chao 2010 is added to the output for each value of q.