Tools for measuring heterogeneity
pip install git+https://github.com/abrahamnunes/diversity.git
Documentation is provided in the Jupyter notebooks located in the docs/
directory.
- Berger-Parker Diversity index:
berger_parker_diversity
- Berger-Parker Dominance index:
berger_parker_dominance
- Rényi heterogeneity (aka. Hill numbers):
renyi
- Includes decomposition (
renyi_decomp
) into$\alpha$ (renyi_alpha
) and$\beta$ components
- Includes decomposition (
- Rényi entropy:
renyi_entropy
- Coefficient of variation:
coef_variation
- Community weighted mean:
func_cwm
- Freeman index:
freeman_index
- Functional divergence:
func_div
- Generalized Entropy Index:
gei
- Gini coefficient (based on Lorenz curve):
gini_lorenz
- Gini-Simpson index:
gini_simpson
- Hartley heterogeneity:
hartley
- Hartley entropy:
hartley_entropy
- Lincoln index (base, Chapman, and Bayesian estimators):
lincoln_index
- Lorenz curves:
lorenz_curve
- Mean Log-Deviation:
mean_logdev
- ModVR (Variation around the Mode):
ModVR
- Pietra index (based on the Lorenz curve):
pietra_lorenz
- Range (simple):
range
- RanVR (Range around the Mode):
RanVR
- Rao's quadratic entropy:
rqe
- Rao's generalized quadratic entropy:
qrqe
- Shannon heterogeneity:
shannon
- Shannon entropy:
shannon_entropy
- Simpson index (aka Herfindahl index):
simpson
- Simpson dominance:
simpson_dominance
- Theil index:
theil
- Tsallis entropy:
tsallis_entropy
- Bootstrap sampling:
div.bootstrap.bootci
- State of the art approach is implemented: bias-corrected and accelerated [BCa] confidence intervals
- Note this currently only works for measures of Type I (richness) heterogeneity
- Methods for which we have closed form estimators have those implemented by default
-
Accumulation curves:
accumulation_curve
-
Amato's index:
amato
-
Atkinson index:
atkinson
-
Average deviation:
AvDev
-
Birthday paradox estimate:
bday_paradox_test
-
Brillouin's D:
brillouin_d
-
Brillouin's E:
brillouin_e
-
Chao & Lee 1:
chao_lee1
-
Chao & Lee 2:
chao_lee2
-
Chao Presence/Absence:
chao_pa
-
Chao Quantitative:
chao_quant
-
Convex hull volume:
hull_volume
-
Dalton index:
dalton
-
Equal shares coefficient:
equal_shares_coef
-
Fisher's
$\alpha$ :fisher_alpha
-
Functional Attribute Diversity:
fad
-
Functional Hill Numbers:
func_hill
-
Functional dendrogram:
func_dendrogram
-
Functional dispersion:
func_disp
-
Functional evenness:
func_eve
-
Functional logarithmic variance:
func_logvar
-
Functional unalikeability:
func_unalikeability
-
Functional Range:
func_range
-
Functional regularity:
func_reg
-
Functional richness:
func_ric
-
Functional variance:
func_var
-
Functional volume:
func_vol
-
Help index:
help_index
-
Huffman code length:
huffman
-
Leinster-Cobbold index:
leinster_cobbold
-
Lempel-Ziv code length:
lempel_ziv
-
Logarithmic variance:
logvar
-
Magurran-Henderson:
magurran_henderson
-
Margalef's index:
margalef
-
McIntosh's D:
mcintosh_d
-
McIntosh's E:
mcintosh_e
-
Michaelis-Menten:
michaelis_menten
-
Minimal majority:
min_majority
-
(MNDif) Mean absolute pairwise difference:
MNDif
-
Menhinick's index:
menhinick
-
Modified functional attribute diversity:
mfad
-
Pielou J:
pielou
-
Pooled Rarefaction:
pooled_rarefaction
-
Relative mean deviation:
rel_mean_dev
-
Numbers equivalent RQE:
rqe_neq
-
Rademacher complexity:
rademacher
-
Ricotta-Szeidl entropy:
ricotta_szeidl
-
Simpson's E:
simpson_evenness
-
Rarefaction (across samples):
rarefaction
-
Rarefaction (single sample):
rarefaction_single
-
Smith & Wilson B:
smith_wilson_b
-
Smith & Wilson 1D:
smith_wilson_1d
-
Smith & Wilson -lnD:
smith_wilson_lnd
-
StDev1 & StDev2:
StDev1
,StDev2
-
Strong's index:
strong_index
-
Variance of logarithms:
var_logs
-
VarNC:
VarNC
-
We will also add wrappers for existing functions to account for synonymous indices such as
- Hartley heterogeneity and "species richness":
species_richness
- and more
- Hartley heterogeneity and "species richness":