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biomonitoR: an R package for managing ecological data and calculating biomonitoring indices

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posted on 2022-11-15, 09:33 authored by Alex Laini, Simone GuareschiSimone Guareschi, Rossano Bolpagni, Gemma Burgazzi, Daniel Bruno, Cayetano Gutiérrez-Cánovas, Rafael Miranda, Cédric Mondy, Gábor Várbíró, Tommaso Cancellario
The monitoring of biological indicators is required to assess the impacts of environmental policies, compare ecosystems and guide management and conservation actions. However, the growing availability of ecological data has not been accompanied by concomitant processing tools able to facilitate data handling and analysis. Multiple common challenges limit the usefulness of biomonitoring information across ecosystems and biological groups. Biomonitoring data analysis is currently constrained by time-consuming steps for data preparation and a data processing environment with limited integration in terms of software, biological groups, and protocols. We introduce biomonitoR, a package for the R programming language that addresses technical challenges for the management of ecological data and metrics calculation. biomonitoR implements most of the biological indices currently used or proposed in different fields of ecology and water resource management. Its combination of customizable functions aims to support a transferable and comprehensive biomonitoring workflow in a user-friendly environment. biomonitoR represents a versatile toolbox with five main assets: (i) it checks taxonomic information against reference datasets allowing for customization of trait and sensitivity scores; (ii) it supports heterogeneous taxonomic resolution allowing computations at multiple taxonomic levels; (iii) it calculates multiple biological indices, including metrics for both broad and stressor-specific ecological assessments; (iv) it enables user-friendly data visualization, helping both decision-making processes and data interpretation; and (v) it allows working with an interactive web application straight from R. Overall, biomonitoR can benefit the wide biomonitoring community, including environmental private consultants, ecologists and natural resource managers.

Funding

COST (European Cooperation in Science and Technology) action CA15113 (Science and Management of Intermittent Rivers and Ephemeral Streams)

NOWATER-community responses and ecosystem processes in WATERcourses subject to hydrological intermittence

Ministry of Education, Universities and Research

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CSIC Interdisciplinary Thematic Platform (PTI) Síntesis de Datos de Ecosistemas y Biodiversidad (PTI-ECOBIODIV)

‘‘Juan de la Cierva—Incorporación’’: MINECO, IJC2018-036642-I

Royal Society-Newton International Fellowship at Loughborough University: (NIF R1 180346)

European Regional Development Fund (SUMHAL, LIFEWATCH-2019-09-CSIC-13, POPE 2014–2020) at Doñana Biological Station (2021–2022)

National Research, Development and Innovation Office: NKFIH FK 135 136

History

School

  • Social Sciences and Humanities

Department

  • Geography and Environment

Published in

PeerJ

Volume

10

Publisher

PeerJ

Version

  • VoR (Version of Record)

Rights holder

© The Authors

Publisher statement

This is an Open Access Article. It is published by PeerJ under the Creative Commons Attribution 4.0 International Licence (CC BY). Full details of this licence are available at: https://creativecommons.org/licenses/by/4.0/

Acceptance date

2022-09-14

Publication date

2022-10-14

Copyright date

2022

eISSN

2167-8359

Language

  • en

Depositor

Dr Simone Guareschi. Deposit date: 14 November 2022

Article number

e14183

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