ent_allen {divent} | R Documentation |
Allen et al.'s Phylogenetic Entropy of a Community
Description
Estimate entropy (Allen et al. 2009) from abundance or probability data and a phylogenetic or functional dendrogram.
Usage
ent_allen(x, tree, ...)
## S3 method for class 'numeric'
ent_allen(
x,
tree,
q = 1,
normalize = TRUE,
prune = FALSE,
as_numeric = FALSE,
...,
check_arguments = TRUE
)
## S3 method for class 'species_distribution'
ent_allen(
x,
tree,
q = 1,
normalize = TRUE,
prune = FALSE,
gamma = FALSE,
as_numeric = FALSE,
...,
check_arguments = TRUE
)
Arguments
x |
An object, that may be a named numeric vector (names are species names) containing abundances or probabilities, or an object of class abundances or probabilities. |
tree |
an ultrametric, phylogenetic tree. May be an object of class phylo_divent, ape::phylo, ade4::phylog or stats::hclust. |
... |
Unused. |
q |
a number: the order of diversity. |
normalize |
if |
prune |
What to do when some species are in the tree but not in |
as_numeric |
if |
check_arguments |
if |
gamma |
if |
Details
Estimators to deal with incomplete sampling are not implemented. Use function ent_phylo with argument if they are needed.
The phylogenetic entropy is calculated following
Allen et al. (2009) for order q=1
and
Leinster and Cobbold (2012) for other orders.
The result is identical to the total entropy calculated by
ent_phylo.
It is much faster but no bias correction is available.
All species of the species_distribution
must be found in the tips of the
tree
.
Value
A tibble with the site names, the estimators used and the estimated entropy.
References
Allen B, Kon M, Bar-Yam Y (2009).
“A New Phylogenetic Diversity Measure Generalizing the Shannon Index and Its Application to Phyllostomid Bats.”
American Naturalist, 174(2), 236–243.
doi:10.1086/600101.
Leinster T, Cobbold C (2012).
“Measuring Diversity: The Importance of Species Similarity.”
Ecology, 93(3), 477–489.
doi:10.1890/10-2402.1.
Examples
# entropy of each community
ent_allen(paracou_6_abd, tree = paracou_6_taxo)
# gamma entropy
ent_allen(paracou_6_abd, tree = paracou_6_taxo, gamma = TRUE)