phylobeta_core

phylobeta

<code>phylobeta_core</code> computes efficiently for large community matrices and
trees the necessary quantities used by the betapart package to compute
pairwise and multiple-site phylogenetic dissimilarities.

phyloregion

Computational infrastructure for biogeography, community ecology,
and biodiversity conservation (Daru et al. 2020) <doi:10.1111/2041-210X.13478>.
It is based on the methods described in Daru et al. (2020) <doi:10.1038/s41467-020-15921-6>.
The original conceptual work is described in Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013>
on patterns and processes of biogeographical regionalization. Additionally, the package
contains fast and efficient functions to compute more standard conservation measures
such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness
and global endangerment, as well as compositional turnover (e.g., beta diversity).

Barnabas H. Daru

Biogeographic Regionalization and Macroecology

Piyal Karunarathne

Klaus Schliep

Xiaobei Zhao

Albin Sandelin

Luciano Pataro

phylobeta_core function

<dl><dt>x</dt>
<dd>an object of class Matrix, matrix or phyloseq</dd>
<dt>phy</dt>
<dd>a phylogenetic tree (object of class phylo)</dd>
<dt>index.family</dt>
<dd>family of dissimilarity indices, partial match of
"sorensen" or "jaccard".</dd></dl>

Arguments

Author

Phylogenetic beta diversity — phylobeta_core

<dl>

<dt>x</dt>
<dd>an object of class Matrix, matrix or phyloseq</dd>


<dt>phy</dt>
<dd>a phylogenetic tree (object of class phylo)</dd>


<dt>index.family</dt>
<dd>family of dissimilarity indices, partial match of
"sorensen" or "jaccard".</dd>

</dl>

phylobeta_core: Phylogenetic beta diversity

Description

Usage

Value

Arguments

Author

See Also

Examples