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.

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.

Create Compact Hash Digests of R Objects

Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.

Update and Manipulate Rd Documentation Objects

Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.

Methods to Convert R Data to YAML and Back

Implements the 'libyaml' 'YAML' 1.1 parser and emitter (< https://pyyaml.org/wiki/LibYAML>) for R.