ecodive - Parallel and Memory-Efficient Ecological Diversity Metrics

Computes alpha and beta diversity metrics in a parallel, memory-efficient manner using 'C' and 'pthreads'. Implements 51 classic, compositional, and phylogenetic indices including Shannon, Bray-Curtis, Faith, JSD, Hellinger, Robust Aitchison, and the UniFrac family. Provides random sub-sampling for table rarefaction and parses Newick trees into 'phylo' objects. Integrates with data structures from 'phyloseq', 'rbiom', and other common bioinformatics packages. Algorithms are described in Smith et al. (2026) <doi:10.21105/joss.09777>.

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8.58 score 7 stars 10 dependents 6 scripts 3.5k downloads

rbiom - Integrated Analysis and Visualization of Microbiome Data

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.

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7.45 score 18 stars 1 dependents 182 scripts 3.2k downloads

h5lite - Simplified 'HDF5' Interface

A user-friendly interface for the Hierarchical Data Format 5 ('HDF5') library designed to "just work." It bundles the necessary system libraries to ensure easy installation on all platforms. Features smart defaults that automatically map R objects (vectors, matrices, data frames) to efficient 'HDF5' types, removing the need to manage low-level details like dataspaces or property lists. Uses the 'HDF5' library developed by The HDF Group <https://www.hdfgroup.org/>.

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6.41 score 2 stars 13 scripts 534 downloads

fillpattern - Patterned Fills for 'ggplot2' and 'grid' Graphics

Provides geometric patterns to replace solid color fills in statistical graphics. These patterns ensure figures remain distinguishable when viewed by colorblind readers or when printed in black and white. The included patterns can be customized in terms of scale, rotation, color, fill, line type, and line width. Compatible with the 'ggplot2' package as well as 'grid' graphics.

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5.39 score 12 stars 2 dependents 16 scripts 2.1k downloads

interprocess - Mutexes, Semaphores, and Message Queues

Provides access to low-level operating system mechanisms for performing atomic operations on shared data structures. Mutexes provide shared and exclusive locks. Semaphores act as counters. Message queues move text strings from one process to another. All these interprocess communication (IPC) tools can optionally block with or without a timeout. Implemented using the cross-platform 'boost' 'C++' library <https://www.boost.org/doc/libs/release/libs/interprocess/>.

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cpp

4.92 score 11 stars 1 dependents 6 scripts 545 downloads

jobqueue - Run Interruptible Code Asynchronously

Takes an R expression and returns a job object with a $stop() method which can be called to terminate the background job. Also provides timeouts and other mechanisms for automatically terminating a background job. The result of the expression is available synchronously via $result or asynchronously with callbacks or through the 'promises' package framework.

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4.85 score 2 stars 14 scripts 528 downloads

hdf5lib - Headers and Static Libraries for 'HDF5'

Provides a self-contained, static build of the 'HDF5' (Hierarchical Data Format 5) 'C' library (release 2.1.1) for R package developers. Designed for use in the 'LinkingTo' field, it enables zero-dependency integration by building the library entirely from source during installation. Additionally, it compiles and internally links a comprehensive suite of advanced compression filters and their 'HDF5' plugins (Zstd, LZ4, Blosc/Blosc2, Snappy, ZFP, Bzip2, LZF, Bitshuffle, szip, and gzip). These plugins are integrated out-of-the-box, allowing downstream packages to utilize high-performance compression directly through the standard 'HDF5' API while keeping the underlying third-party headers fully encapsulated. 'HDF5' is developed by The HDF Group <https://www.hdfgroup.org/>.

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4.54 score 1 dependents 3 scripts 400 downloads

semaphore - Shared Memory Atomic Operations

Implements named semaphores from the 'boost' 'C++' library <https://www.boost.org/> for interprocess communication. Multiple 'R' sessions on the same host can block (with optional timeout) on a semaphore until it becomes positive, then atomically decrement it and unblock. Any session can increment the semaphore.

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cpp

3.00 score 2 stars 6 scripts 190 downloads