rbiom

rbiom-package

A toolkit for working with Biological Observation Matrix (BIOM) files.
Features include reading/writing all BIOM formats, rarefaction, alpha
diversity, beta diversity (including UniFrac), summarizing counts by
taxonomic level, and sample subsetting. Standalone functions for
reading, writing, and subsetting phylogenetic trees are also provided.
All CPU intensive operations are encoded in C with multi-thread support.

internal

A toolkit for working with Biological Observation Matrix ('BIOM') files.
Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and
beta diversity (including 'UniFrac'). Summarize counts by taxonomic level.
Subset based on metadata. Generate visualizations and statistical analyses.
CPU intensive operations are coded in C for speed.

Daniel P. Smith

Read/Write, Analyze, and Visualize 'BIOM' Data

Alkek Center for Metagenomics and Microbiome Research 

rbiom-package function

Many rbiom functions support multithreading:
The default behavior of these function is to run on as many cores as are
available in the local compute environment. If you wish to limit the number
of simultaneous threads, set <code>RcppParallel</code>'s <code>numThreads</code> option.
For instance:
<pre><code>
 RcppParallel::setThreadOptions(numThreads = 4)
</code></pre>

Multithreading

Maintainer: Daniel P. Smith <a href="/link/dansmith01%40gmail.com?package=rbiom&version=2.1.2" data-mini-rdoc="rbiom::dansmith01@gmail.com">dansmith01@gmail.com</a> (<a href="https://orcid.org/0000-0002-2479-2044">ORCID</a>)
Other contributors:<ul>
<li>Alkek Center for Metagenomics and Microbiome Research [copyright holder, funder]</li>
</ul>

Author

rbiom: Read/Write, Transform, and Summarize BIOM Data — rbiom-package

Many rbiom functions support multithreading:
The default behavior of these function is to run on as many cores as are
available in the local compute environment. If you wish to limit the number
of simultaneous threads, set <code>RcppParallel</code>'s <code>numThreads</code> option.
For instance:
<pre><code>
 RcppParallel::setThreadOptions(numThreads = 4)
</code></pre>

Maintainer: Daniel P. Smith <a href='mailto:dansmith01@gmail.com'>dansmith01@gmail.com</a> (<a href='https://orcid.org/0000-0002-2479-2044'>ORCID</a>)
Other contributors:<ul>
<li>Alkek Center for Metagenomics and Microbiome Research [copyright holder, funder]</li>
</ul>

rbiom-package: rbiom: Read/Write, Transform, and Summarize BIOM Data

Description

Arguments

Multithreading

Author

See Also