recipe r-phylomeasures

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 p-values, which are essential for null model comparisons. Among other functions, the package provides efficient computation of richness-standardized versions for indices such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of two-sample measures. The package also introduces a new single-sample 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 abundance-weighted models.

Homepage:

https://CRAN.R-project.org/package=PhyloMeasures

License:

GPL3 / GPL-3

Recipe:

/r-phylomeasures/meta.yaml

package r-phylomeasures

(downloads) docker_r-phylomeasures

versions:
2.1-9,  2.1-8,  2.1-7,  2.1-6,  2.1-5,  2.1-4,  2.1-3,  2.1-2,  2.1-1, 

2.1-9,  2.1-8,  2.1-7,  2.1-6,  2.1-5,  2.1-4,  2.1-3,  2.1-2,  2.1-1,  2.1-0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install r-phylomeasures

and update with::

   mamba update r-phylomeasures

To create a new environment, run:

mamba create --name myenvname r-phylomeasures

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/r-phylomeasures:<tag>

(see `r-phylomeasures/tags`_ for valid values for ``<tag>``)

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