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Allen et al.'s Phylogenetic Entropy of a Community

Source: R/ent_allen.R
ent_allen.Rd

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 TRUE, phylogenetic is normalized: the height of the tree is set to 1.

prune

What to do when some species are in the tree but not in x? If TRUE, the tree is pruned to keep species of x only. The height of the tree may be changed if a pruned branch is related to the root. If FALSE (default), the length of branches of missing species is not summed but the height of the tree is never changed.

as_numeric

if TRUE, a number or a numeric vector is returned rather than a tibble.

check_arguments

if TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.

gamma

if TRUE, \(\gamma\) diversity, i.e. diversity of the metacommunity, is computed.

Value

A tibble with the site names, the estimators used and the estimated entropy.

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.

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)
#> # A tibble: 4 × 5
#>   site      weight estimator order entropy
#>   <chr>      <dbl> <chr>     <dbl>   <dbl>
#> 1 subplot_1   1.56 naive         1    3.60
#> 2 subplot_2   1.56 naive         1    3.83
#> 3 subplot_3   1.56 naive         1    3.74
#> 4 subplot_4   1.56 naive         1    3.63

# gamma entropy
ent_allen(paracou_6_abd, tree = paracou_6_taxo, gamma = TRUE)
#> # A tibble: 1 × 4
#>   site          estimator order entropy
#>   <chr>         <chr>     <dbl>   <dbl>
#> 1 Metacommunity naive         1    3.82