Tools for Managing Classes on GitHub

Interface for the GitHub API that enables efficient management of courses on GitHub. It has a functionality for managing organizations, teams, repositories, and users on GitHub and helps automate most of the tedious and repetitive tasks around creating and distributing assignments.

Pain Assessment at Withdrawal Speeds (PAWS)

Automated pain scoring from paw withdrawal tracking data. Based on Jones et al. (2020) "A machine-vision approach for automated pain measurement at millisecond timescales" .

Gillespie's Stochastic Simulation Algorithm for Impatient People

A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended. Cannoodt and Saelens et al. (2021) .

String Distance Calculation with Tidy Data Principles

Calculation of string distance following the tidy data principles. Built on top of the 'stringdist' package.

Generate Fake Datasets for Prototyping and Teaching

Create fake datasets that can be used for prototyping and teaching. This package provides a set of functions to generate fake data for a variety of data types, such as dates, addresses, and names. It can be used for prototyping (notably in 'shiny') or as a tool to teach data manipulation and data visualization.

Lorem-Ipsum-Like Helpers for Fast Shiny Prototyping

Prototype your shiny apps quickly with these Lorem-Ipsum-like Helpers.

An R Interface to the JBrowse 2 Genome Browser

Provides an R interface to the JBrowse 2 genome browser. Enables embedding a JB2 genome browser in a Shiny app or R Markdown document. The browser can also be launched from an interactive R console. The browser can be loaded with a variety of common genomics data types, and can be used with a custom theme.

An API Client for the Environmental Data Initiative Repository

A client for the Environmental Data Initiative repository REST API. The 'EDI' data repository < https://portal.edirepository.org/nis/home.jsp> is for publication and reuse of ecological data with emphasis on metadata accuracy and completeness. It is built upon the 'PASTA+' software stack < https://pastaplus-core.readthedocs.io/en/latest/index.html#> and was developed in collaboration with the US 'LTER' Network < https://lternet.edu/>. 'EDIutils' includes functions to search and access existing data, evaluate and upload new data, and assist other data management tasks common to repository users.

Access Pinterest API

Get information (boards, pins and users) from the Pinterest < http://www.pinterest.com> API.

R Interface to Proximal Interior Point Quadratic Programming Solver

An embedded proximal interior point quadratic programming solver, which can solve dense and sparse quadratic programs, described in Schwan, Jiang, Kuhn, and Jones (2023) . Combining an infeasible interior point method with the proximal method of multipliers, the algorithm can handle ill-conditioned convex quadratic programming problems without the need for linear independence of the constraints. The solver is written in header only 'C++ 14' leveraging the 'Eigen' library for vectorized linear algebra. For small dense problems, vectorized instructions and cache locality can be exploited more efficiently. Allocation free problem updates and re-solves are also provided.