Package Recipe 'r-abdiv'

recipe r-abdiv

Alpha and Beta Diversity Measures

Homepage:: https://github.com/kylebittinger/abdiv
License:: MIT
Recipe:: /r-abdiv/meta.yaml

'A collection of measures for measuring ecological diversity.: Ecological diversity comes in two flavors: alpha diversity measures the diversity within a single site or sample, and beta diversity measures the diversity across two sites or samples. This package overlaps considerably with other R packages such as ''vegan'', ''gUniFrac'', ''betapart'', and ''fossil''. We also include a wide range of functions that are implemented in software outside the R ecosystem, such as ''scipy'', ''Mothur'', and ''scikit-bio''. The implementations here are designed to be basic and clear to the reader.'

package r-abdiv¶

Versions:

0.2.0-3, 0.2.0-2, 0.2.0-1, 0.2.0-0

Depends:

on r-ape
on r-base >=4.4,<4.5.0a0
on r-testthat >=2.1.0
on r-vegan

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-abdiv

to add into an existing workspace instead, run:

pixi add r-abdiv

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-abdiv

Alternatively, to install into a new environment, run:

conda create -n envname r-abdiv

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-abdiv:<tag>

(see r-abdiv/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.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/r-abdiv/README.html)