Rpadrino: an R package to access and use PADRINO, an open access database of Integral Projection Models

Journal article

Discrete time structured population projection models are an important tool for studying population dynamics. Within this field, integral projection models (IPMs) have become a popular method for studying populations structured by continuously distributed traits (e.g. height, weight). Databases of discrete time, discrete state structured population models, for example DATLife (life tables) and COMPADRE & COMADRE (matrix population models), have made quantitative syntheses straightforward to implement. These efforts allow researchers to address questions in both basic and applied ecology and evolutionary biology. Since their introduction in 2000, over 300 works containing IPMs have been published, offering opportunities for ecological synthesis too. We describe a novel framework to quickly reconstruct these models for subsequent analyses using Rpadrino R package, which serves as an interface to PADRINO, a new database of IPMs. We introduce an R package, Rpadrino, which enables users to download, subset, reconstruct, and extend published IPMs. Rpadrino makes use of recently created software, ipmr, to provide an engine to reconstruct a wide array of IPMs from their symbolic representations and conduct subsequent analyses. Rpadrino and ipmr are extensively documented to help users learn their usage. Rpadrino currently enables users to reconstruct 280 IPMs from 40 publications that describe the demography of 14 animal and 26 plant species. All of these IPMs are tested to ensure they reproduce published estimates. Rpadrino provides an interface to augment PADRINO with external data and modify parameter values, creating a platform to extend models beyond their original purpose while retaining full reproducibility. PADRINO and Rpadrino provide a toolbox for asking new questions and conducting syntheses with peer-reviewed published IPMs. Rpadrino provides a user-friendly interface so researchers do not need to worry about the database structure or syntax, and can focus on their research questions and analyses. Additionally, Rpadrino is thoroughly documented and provides numerous examples of how to perform analyses which are not included in the package's functionality.

Authors: Levin, SC; Evers, S; Potter, T; Guerrero, MP; Childs, DZ

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Wiley
• Journal: Methods in Ecology and Evolution
• Volume: 13
• Issue: 9
• Pages: 1923-1929
• Publication date: 2022-06-23
• Acceptance date: 2022-05-20
• DOI: 10.1111/2041-210X.13910
• EISSN: 2041-2096
• ISSN: 2041-210X
• Language: English
• Keywords: open access; database; elasticity; sensitivity; population dynamics; FFR; life history; demography