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).

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 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.

Efficiently Retrieve and Process Satellite Imagery

Downloads spatial data from spatiotemporal asset catalogs ('STAC'), computes standard spectral indices from the Awesome Spectral Indices project (Montero et al. (2023) ) against raster data, and glues the outputs together into predictor bricks. Methods focus on interoperability with the broader spatial ecosystem; function arguments and outputs use classes from 'sf' and 'terra', and data downloading functions support complex 'CQL2' queries using 'rstac'.

Positron Emission Tomography Time-Activity Curve Analysis

To facilitate the analysis of positron emission tomography (PET) time activity curve (TAC) data, and to encourage open science and replicability, this package supports data loading and analysis of multiple TAC file formats. Functions are available to analyze loaded TAC data for individual participants or in batches. Major functionality includes weighted TAC merging by region of interest (ROI), calculating models including standardized uptake value ratio (SUVR) and distribution volume ratio (DVR, Logan et al. 1996 ), basic plotting functions and calculation of cut-off values (Aizenstein et al. 2008 ). Please see the walkthrough vignette for a detailed overview of 'tacmagic' functions.

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.

'OpenStreetMap' API

Interface to 'OpenStreetMap API' for fetching and saving data from/to the 'OpenStreetMap' database (< https://wiki.openstreetmap.org/wiki/API_v0.6>).

Convert European Regional Data

Motivated by changing administrative boundaries over time, the 'nuts' package can convert European regional data with NUTS codes between versions (2006, 2010, 2013, 2016 and 2021) and levels (NUTS 1, NUTS 2 and NUTS 3). The package uses spatial interpolation as in Lam (1983) based on granular (100m x 100m) area, population and land use data provided by the European Commission's Joint Research Center.