
recipe
rphylomeasures
¶ Given a phylogenetic tree T and an assemblage S of species represented as a subset of tips in T, we want to compute a measure of the diversity of the species in S with respect to T. The current package offers efficient algorithms that can process large phylogenetic data for several such measures. Most importantly, the package includes algorithms for computing efficiently the standardized versions of phylogenetic measures and their pvalues, which are essential for null model comparisons. Among other functions, the package provides efficient computation of richnessstandardized versions for indices such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of twosample measures. The package also introduces a new singlesample measure, the Core Ancestor Cost (CAC); the package provides functions for computing the value and the standardised index of the CAC and, more than that, there is an extra function available that can compute exactly any statistical moment of the measure. The package supports computations under different null models, including abundanceweighted models.
 Homepage
 License
GPL3 / GPL3
 Recipe

package
rphylomeasures
¶ 
 Versions
2.12, 2.11, 2.10
 Depends libgccng
>=7.3.0
 Depends libstdcxxng
>=7.3.0
 Depends rape
 Depends rbase
>=3.5.1,<3.5.2.0a0
 Requirements
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install rphylomeasures
and update with:
conda update rphylomeasures
or use the docker container:
docker pull quay.io/biocontainers/rphylomeasures:<tag>
(see rphylomeasures/tags for valid values for
<tag>
)
Link to this page¶
Render an badge with the following MarkDown:
[![install with bioconda](https://img.shields.io/badge/install%20withbiocondabrightgreen.svg?style=flat)](http://bioconda.github.io/recipes/rphylomeasures/README.html)