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:
2.1-10,  2.1-9,  2.1-8,  2.1-7,  2.1-6,  2.1-5,  2.1-4,  2.1-3,  2.1-2, 

2.1-10,  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:

  • on libgcc >=13

  • on libstdcxx >=13

  • on r-ape

  • on r-base >=4.4,<4.5.0a0

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install r-phylomeasures

to add into an existing workspace instead, run:

pixi add r-phylomeasures

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install r-phylomeasures

Alternatively, to install into a new environment, run:

conda create -n envname r-phylomeasures

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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