A standard protocol to report discrete stage‐structured demographic information
Authors: Gascoigne Samuel J. L. , Rolph Simon , Sankey Daisy , Nidadavolu Nagalakshmi , Stell Pičman Adrian S. , Hernández Christina M. , Philpott Matthew E. R. , Salam Aiyla , Bernard Connor , Fenollosa Erola , Lee Young Jun , McLean Jessica , Hetti Achchige Perera Shathuki , Spacey Oliver G. , Kajin Maja , Vinton Anna C. , Archer C. Ruth , Burns Jean H. , Buss Danielle L. , Caswell Hal , Che‐Castaldo Judy P. , Childs Dylan Z. , Capdevila Pol , Compagnoni Aldo , Crone Elizabeth , Ezard Thomas H. G. , Hodgson Dave , Knight Tiffany M. , Jones Owen R. , Jongejans Eelke , McDonald Jenni , Tenhumberg Brigitte , Thomas Chelsea C. , Tyre Andrew J. , Ramula Satu , Stott Iain , Tremblay Raymond L. , Wilson Phil , Vaupel James W. , Salguero‐Gómez Roberto 
Published: June 2023

Abstract

Stage‐based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open‐access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported.

Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs.

Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre‐db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open‐access repositories such as DRYAD, Figshare and Zenodo.

Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.