Interactive, Complex Heatmaps

Make complex, interactive heatmaps. 'iheatmapr' includes a modular system for iteratively building up complex heatmaps, as well as the iheatmap() function for making relatively standard heatmaps.

Control 'BEAST2'

'BEAST2' (< https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'.

Reproducible Data Science Environments with 'Nix'

Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) . The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools or programming languages such as Python or Julia. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.

Generate Raster Images from QuadKey-Identified Datasets

A set of functions of increasing complexity allows users to (1) convert QuadKey-identified datasets, based on 'Microsoft's Bing Maps Tile System', into Simple Features data frames, (2) transform Simple Features data frames into rasters, and (3) process multiple 'Meta' ('Facebook') QuadKey-identified human mobility files directly into raster files. For more details, see D’Andrea et al. (2024) .

'IUCN' Red List Client

'IUCN' Red List (< https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.

World Map Data from Natural Earth

Facilitates mapping by making natural earth map data from < https://www.naturalearthdata.com/> more easily available to R users.

Connector to 'CouchDB'

Provides an interface to the 'NoSQL' database 'CouchDB' (< https://couchdb.apache.org/>). Methods are provided for managing databases within 'CouchDB', including creating/deleting/updating/transferring, and managing documents within databases. One can connect with a local 'CouchDB' instance, or a remote 'CouchDB' database such as 'IBM Cloudant'. Documents can be inserted directly from vectors, lists, data.frames, and 'JSON'. Targeted at 'CouchDB' v2 or greater.

Generate 'CodeMeta' Metadata for R Packages

The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at < https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.

Querying and Managing Large Biodiversity Occurrence Datasets

Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.

Cast '(R)Markdown' Files to 'XML' and Back Again

Parsing '(R)Markdown' files with numerous regular expressions can be fraught with peril, but it does not have to be this way. Converting '(R)Markdown' files to 'XML' using the 'commonmark' package allows in-memory editing via of 'markdown' elements via 'XPath' through the extensible 'R6' class called 'yarn'. These modified 'XML' representations can be written to '(R)Markdown' documents via an 'xslt' stylesheet which implements an extended version of 'GitHub'-flavoured 'markdown' so that you can tinker to your hearts content.