R Client Package for Circle CI

Tools for interacting with the 'Circle CI' API (< https://circleci.com/docs/api/v2/>). Besides executing common tasks such as querying build logs and restarting builds, this package also helps setting up permissions to deploy from builds.

Tracer from R

'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. 'Tracer' (< https://github.com/beast-dev/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.

Print Maps, Draw on Them, Scan Them Back in

Enables preparation of maps to be printed and drawn on. Modified maps can then be scanned back in, and hand-drawn marks converted to spatial objects.

Mechanistic Metacommunity Simulator

Flexible, mechanistic, and spatially explicit simulator of metacommunities. It extends our previous package - 'rangr' (see < https://github.com/ropensci/rangr>), which implemented a mechanistic virtual species simulator integrating population dynamics and dispersal. The 'mrangr' package adds the ability to simulate multiple species interacting through an asymmetric matrix of pairwise relationships, allowing users to model all types of biotic interactions — competitive, facilitative, or neutral — within spatially explicit virtual environments. This work was supported by the National Science Centre, Poland, grant no. 2018/29/B/NZ8/00066 and the Poznań Supercomputing and Networking Centre (grant no. pl0090-01).

Deterministic Categorization of Items Based on External Code Data

Fast categorization of items based on external code data identified by regular expressions. A typical use case considers patient with medically coded data, such as codes from the International Classification of Diseases ('ICD') or the Anatomic Therapeutic Chemical ('ATC') classification system. Functions of the package relies on a triad of objects: (1) case data with unit id:s and possible dates of interest; (2) external code data for corresponding units in (1) and with optional dates of interest and; (3) a classification scheme ('classcodes' object) with regular expressions to identify and categorize relevant codes from (2). It is easy to introduce new classification schemes ('classcodes' objects) or to use default schemes included in the package. Use cases includes patient categorization based on 'comorbidity indices' such as 'Charlson', 'Elixhauser', 'RxRisk V', or the 'comorbidity-polypharmacy' score (CPS), as well as adverse events after hip and knee replacement surgery.

A Test Environment for Database Requests

Testing and documenting code that communicates with remote databases can be painful. Although the interaction with R is usually relatively simple (e.g. data(frames) passed to and from a database), because they rely on a separate service and the data there, testing them can be difficult to set up, unsustainable in a continuous integration environment, or impossible without replicating an entire production cluster. This package addresses that by allowing you to make recordings from your database interactions and then play them back while testing (or in other contexts) all without needing to spin up or have access to the database your code would typically connect to.

Interface to Species Occurrence Data Sources

A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist', 'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.

Interface with the United Nations Comtrade API

Interface with and extract data from the United Nations 'Comtrade' API < https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping data for a variety of commodities, these functions allow for easy API query and data returned as a tidy data frame.

Extract Tables from PDF Documents

Bindings for the 'Tabula' < https://tabula.technology/> 'Java' library, which can extract tables from PDF files. This tool can reduce time and effort in data extraction processes in fields like investigative journalism. It allows for automatic and manual table extraction, the latter facilitated through a 'Shiny' interface, enabling manual areas selection\ with a computer mouse for data retrieval.

Build Reproducible Analytical Pipelines with 'Nix'

Streamlines the creation of reproducible analytical pipelines using 'default.nix' expressions generated via the 'rix' package for reproducibility. Define derivations in 'R', 'Python' or 'Julia', chain them into a composition of pure functions and build the resulting pipeline using 'Nix' as the underlying end-to-end build tool. Functions to plot the pipeline as a directed acyclic graph are included, as well as functions to load and inspect intermediary results for interactive analysis. User experience heavily inspired by the 'targets' package.