match_phylo_comm

match_phylo_comm compares taxa (species, labels, tips) present in a phylogeny
with a community matrix. Pruning, sorting and trying to add missing species
on genus level if possible to match in subsequent analysis.

bioregion

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

phyloregion

Biogeographic Regionalization and Macroecology

Piyal Karunarathne

Klaus Schliep

Xiaobei Zhao

Albin Sandelin

Luciano Pataro

match_phylo_comm function

<dl><dt>phy</dt>
<dd>A phylogeny</dd>
<dt>comm</dt>
<dd>A (sparse) community data matrix</dd>
<dt>delete_empty_rows</dt>
<dd>delete rows with no observation</dd></dl>

Arguments

Match taxa and in phylogeny and community matrix — match_phylo_comm

<dl>

<dt>phy</dt>
<dd>A phylogeny</dd>


<dt>comm</dt>
<dd>A (sparse) community data matrix</dd>


<dt>delete_empty_rows</dt>
<dd>delete rows with no observation</dd>

</dl>

match_phylo_comm: Match taxa and in phylogeny and community matrix

Description

Usage

Value

Arguments

Details

Examples