Calculate the sum of the total phylogenetic branch length for one or multiple samples.

univar

Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.

Steven W Kembel

picante

Integrating Phylogenies and Ecology

Helene Morlon

pd function

<dl> <dt>samp</dt>
<dd>Community data matrix</dd> <dt>tree</dt>
<dd>A phylo tree object</dd> <dt>include.root</dt>
<dd>Should the root node be included in all PD calculations (default = TRUE)</dd></dl>

Arguments

If the root is to be included in all calculations (<code>include.root=TRUE</code>), the PD of all samples will include the branch length connecting taxa in those samples and the root node of the supplied tree. The root of the supplied tree may not be spanned by any taxa in the sample. If you want the root of your tree to correspond to the most recent ancestor of the taxa actually present in your sample, you should prune the tree before running <code>pd</code>:
<code>prunedTree &lt;- prune.sample(sample,tree)</code>

Warning 

Matthew Helmus <a href="/link/mrhelmus%40gmail.com?package=picante&version=1.8.4" data-mini-rdoc="picante::mrhelmus@gmail.com">mrhelmus@gmail.com</a>, Jonathan Davies <a href="/link/davies%40nceas.ucsb.edu?package=picante&version=1.8.4" data-mini-rdoc="picante::davies@nceas.ucsb.edu">davies@nceas.ucsb.edu</a>, Steven Kembel <a href="/link/steve.kembel%40gmail.com?package=picante&version=1.8.4" data-mini-rdoc="picante::steve.kembel@gmail.com">steve.kembel@gmail.com</a>

Author

Calculate Faith's Phylogenetic Diversity — pd

<dl>

 <dt>samp</dt>
<dd>Community data matrix</dd>

 <dt>tree</dt>
<dd>A phylo tree object</dd>

 <dt>include.root</dt>
<dd>Should the root node be included in all PD calculations (default = TRUE)</dd>

</dl>

Matthew Helmus <a href='mailto:mrhelmus@gmail.com'>mrhelmus@gmail.com</a>, Jonathan Davies <a href='mailto:davies@nceas.ucsb.edu'>davies@nceas.ucsb.edu</a>, Steven Kembel <a href='mailto:steve.kembel@gmail.com'>steve.kembel@gmail.com</a>

pd: Calculate Faith's Phylogenetic Diversity

Description

Usage

Value

Arguments

Warning

Author

References

See Also

Examples