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
.