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r"""Alpha diversity measures (:mod:`skbio.diversity.alpha`)
=======================================================
.. currentmodule:: skbio.diversity.alpha
This package provides implementations of various alpha diversity [1]_ metrics,
including measures of richness, diversity, evenness, dominance, and coverage.
Some functions generate confidence intervals (CIs). These functions have the
suffix ``_ci``.
Richness metrics
----------------
**Richness** [2]_ measures the number of species (taxa) in a community.
Due to incomplete sampling, the number of observed species (``sobs``) in a
sample is usually lower than the true number of species in the community.
Metrics have been proposed to estimate the latter based on the distribution
of observed species in the sample.
.. autosummary::
:toctree:
ace
chao1
chao1_ci
doubles
faith_pd
margalef
menhinick
michaelis_menten_fit
observed_features
osd
singles
sobs
Diversity metrics
-----------------
**Diversity** [3]_ measures the number and relative abundances of species
(taxa) in a community. It combines richness and evenness.
Some diversity metrics describe the effective number of species (a.k.a., true
diversity) -- the number of equally-abundant species that produce the same
diversity measurement.
.. autosummary::
:toctree:
brillouin_d
enspie
fisher_alpha
hill
inv_simpson
kempton_taylor_q
phydiv
renyi
shannon
simpson
tsallis
Evenness metrics
----------------
**Evenness** [4]_ (or equitability) measures the closeness of species (taxa) in a
community in terms of abundance (number of individuals within the species). The
calculation of evenness involves the relative abundances of species.
.. autosummary::
:toctree:
heip_e
mcintosh_e
pielou_e
simpson_e
Dominance metrics
-----------------
**Dominance** [5]_ (or concentration) measures the degree that one or a few
most abundant species (taxa) represent the great majority of a community. It
can be considered as a measure of community unevenness.
It should be noted that higher dominance corresponds to lower biodiversity.
.. autosummary::
:toctree:
berger_parker_d
dominance
gini_index
mcintosh_d
simpson_d
strong
Coverage metrics
----------------
**Coverage** [6]_ measures the proportion of individuals of a community that
have been observed (or unobserved) in a sample. It describes the completeness
of sampling.
.. autosummary::
:toctree:
esty_ci
goods_coverage
lladser_ci
lladser_pe
robbins
References
----------
.. [1] https://en.wikipedia.org/wiki/Alpha_diversity
.. [2] https://en.wikipedia.org/wiki/Species_richness
.. [3] https://en.wikipedia.org/wiki/Species_diversity
.. [4] https://en.wikipedia.org/wiki/Species_evenness
.. [5] https://en.wikipedia.org/wiki/Dominance_%28ecology%29
.. [6] Good, I. J. (1953). The population frequencies of species and the
estimation of population parameters. Biometrika, 40(3-4), 237-264.
""" # noqa: D205, D415
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# ----------------------------------------------------------------------------
from ._base import (
berger_parker_d,
brillouin_d,
dominance,
doubles,
enspie,
esty_ci,
fisher_alpha,
goods_coverage,
heip_e,
hill,
inv_simpson,
kempton_taylor_q,
margalef,
mcintosh_d,
mcintosh_e,
menhinick,
michaelis_menten_fit,
observed_features,
osd,
pielou_e,
renyi,
robbins,
shannon,
simpson,
simpson_d,
simpson_e,
singles,
sobs,
strong,
tsallis,
)
from ._ace import ace
from ._chao1 import chao1, chao1_ci
from ._gini import gini_index
from ._lladser import lladser_pe, lladser_ci
from ._pd import faith_pd, phydiv
__all__ = [
"ace",
"chao1",
"chao1_ci",
"berger_parker_d",
"brillouin_d",
"dominance",
"doubles",
"enspie",
"esty_ci",
"faith_pd",
"fisher_alpha",
"gini_index",
"goods_coverage",
"heip_e",
"hill",
"inv_simpson",
"kempton_taylor_q",
"lladser_pe",
"lladser_ci",
"margalef",
"mcintosh_d",
"mcintosh_e",
"menhinick",
"michaelis_menten_fit",
"observed_features",
"osd",
"phydiv",
"pielou_e",
"renyi",
"robbins",
"shannon",
"simpson",
"simpson_d",
"simpson_e",
"singles",
"sobs",
"strong",
"tsallis",
]
from sys import modules
from skbio.util._decorator import register_aliases
register_aliases(modules[__name__])
|
