A High-Performance Taxonomic Database Interface

Provides fast access to many commonly used taxonomic authorities in a uniform Darwin Core format. Tables are read directly from versioned Parquet snapshots, streamed from cloud storage or from a local copy, and queried with familiar 'dplyr' verbs.

A General-Purpose Package for Dynamic Report Generation in R

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

Downloading Supplementary Data from Published Manuscripts

Downloads data supplementary materials from manuscripts, using papers' DOIs as references. Facilitates open, reproducible research workflows: scientists re-analyzing published datasets can work with them as easily as if they were stored on their own computer, and others can track their analysis workflow painlessly. The main function suppdata() returns a (temporary) location on the user's computer where the file is stored, making it simple to use suppdata() with standard functions like read.csv().

Interface to 'Phylocom'

Interface to 'Phylocom' (< https://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.

Parse Messy Geographic Coordinates

Parse messy geographic coordinates from various character formats to decimal degree numeric values. Parse coordinates into their parts (degree, minutes, seconds); calculate hemisphere from coordinates; pull out individually degrees, minutes, or seconds; add and subtract degrees, minutes, and seconds. C++ code herein originally inspired from code written by Jeffrey D. Bogan, but then completely re-written.

Network Analysis and Visualization

Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

Sparse and Dense Matrix Classes and Methods

A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.

Manage the Life Cycle of your Package Functions

Manage the life cycle of your exported functions with shared conventions, documentation badges, and user-friendly deprecation warnings.

Automatically Position Non-Overlapping Text Labels with 'ggplot2'

Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.

Fast and Versatile Argument Checks

Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.