Optimizing Acoustic Signal Detection

Facilitates the automatic detection of acoustic signals, providing functions to diagnose and optimize the performance of detection routines. Detections from other software can also be explored and optimized. This package has been peer-reviewed by rOpenSci. Araya-Salas et al. (2022) .

Download and Explore Datasets from UCSC Xena Data Hubs

Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.

'Webdriver'/'Selenium' Binary Manager

There are a number of binary files associated with the 'Webdriver'/'Selenium' project. This package provides functions to download these binaries and to manage processes involving them.

Setup and connect to 'OpenTripPlanner'

Setup and connect to 'OpenTripPlanner' (OTP) < http://www.opentripplanner.org/>. OTP is an open source platform for multi-modal and multi-agency journey planning written in 'Java'. The package allows you to manage a local version or connect to remote OTP server to find walking, cycling, driving, or transit routes. This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).

A Binary Download Manager

Tools and functions for managing the download of binary files. Binary repositories are defined in 'YAML' format. Defining new pre-download, download and post-download templates allow additional repositories to be added.

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.

Sustainable Transport Planning

Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) , but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) . The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as < https://cyclestreets.net/> (Desjardins et al. 2021) ; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) and the 'OD jittering' method described in Lovelace et al. (2022) . Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) , and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) .

R Interface to 'Apache Tika'

Extract text or metadata from over a thousand file types, using Apache Tika < https://tika.apache.org/>. Get either plain text or structured XHTML content.

Residuals from Partial Regressions

Creates a data frame with the residuals of partial regressions of the main explanatory variable and the variable of interest. This method follows the Frisch-Waugh-Lovell theorem, as explained in Lovell (2008) .

Sports Physiology Analysis from Local 'Strava' Data

Tools for reproducible, offline analysis of endurance-training data exported from 'Strava'. Provides data import, quality-control, cohort-reference, and visualization helpers for sports-science indicators including acute:chronic workload ratio, aerobic efficiency, cardiovascular decoupling, exposure, and personal-best profiles.