| Abstract | The widespread use of species traits in basic and applied ecology, conservation and bio- geography has led to an exponential increase in functional diversity analyses, with > 10 000 papers published in 2010-2020, and > 1800 papers only in 2021. This interest is reflected in the development of a multitude of theoretical and methodological frame- works for calculating functional diversity, making it challenging to navigate the myri- ads of options and to report detailed accounts of trait-based analyses. Therefore, the discipline of trait-based ecology would benefit from the existence of a general guideline for standard reporting and good practices for analyses. We devise an eight-step pro- tocol to guide researchers in conducting and reporting functional diversity analyses, with the overarching goal of increasing reproducibility, transparency and comparabil- ity across studies. The protocol is based on: 1) identification of a research question; 2) a sampling scheme and a study design; 3-4) assemblage of data matrices; 5) data exploration and preprocessing; 6) functional diversity computation; 7) model fitting, evaluation and interpretation; and 8) data, metadata and code provision. Throughout the protocol, we provide information on how to best select research questions, study designs, trait data, compute functional diversity, interpret results and discuss ways to ensure reproducibility in reporting results. To facilitate the implementation of this template, we further develop an interactive web-based application (stepFD) in the form of a checklist workflow, detailing all the steps of the protocol and allowing the user to produce a final 'reproducibility report' to upload alongside the published paper. A thorough and transparent reporting of functional diversity analyses ensures that ecologists can incorporate others' findings into meta-analyses, the shared data can be integrated into larger databases for consensus analyses, and available code can be reused by other researchers. All these elements are key to pushing forward this vibrant and fast-growing field of research. |
| Text | 470691 2022 10.1111/ecog.06287 biological diversity ecosystem functioning open science replicability reproducibility standardised protocols trait based ecology A protocol for reproducible functional diversity analyses Facundo X. Palacio, Corey T. Callaghan, Pedro Cardoso, Emma J. Hudgins, Marta A. Jarzyna, Gianluigi Ottaviani, Federico Riva, Caio Graco Roza, Vaughn Shirey, Stefano Mammola F. X. Palacio, Division Zoologia Vertebrados, Museo de La Plata, Univ. Nacional de La Plata, La Plata, Argentina and Consejo Nacional de Investigaciones Cientificas y Tecnicas CONICET , La Plata, Argentina. C. T. Callaghan https //orcid.org/0000 0003 0415 2709 , German Centre for Integrative Biodiversity Research iDiv Leipzig, Halle, Jena, Leipzig, Germany. P. Cardoso https //orcid.org/0000 0001 8119 9960 and S. Mammola https // orcid.org/0000 0002 4471 9055 stefano.mammola@cnr.it , LIBRe Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History LUOMUS , Univ. of Helsinki, Helsinki, Finland. E. J. Hudgins https //orcid.org/0000 0002 8402 5111 and F. Riva https //orcid.org/0000 0002 1724 4293 , Dept of Biology, Carleton Univ., Ottawa, ON, Canada. M. A. Jarzyna https //orcid.org/0000 0002 6734 0566 , Dept of Evolution, Ecology and Organismal Biology, The Ohio State Univ., Columbus, OH, USA and Translational Data Analytics Inst., The Ohio State Univ., Columbus, OH, USA. G. Ottaviani https //orcid.org/0000 0003 3027 4638 , Inst. of Botany, The Czech Academy of Sciences, T ebo , Czech Republic. C. Graco Roza https //orcid.org/0000 0002 0353 9154 , Dept of Geosciences and Geography, Univ. of Helsinki, Helsinki, Finland. V. Shirey https //orcid. org/0000 0002 3589 9699 , Dept of Biology, Georgetown Univ., Washington, DC, USA. SM also at Molecular Ecology Group MEG , Water Research Inst. IRSA , National Research Council of Italy CNR , Verbania Pallanza, Italy. The widespread use of species traits in basic and applied ecology, conservation and bio geography has led to an exponential increase in functional diversity analyses, with > 10 000 papers published in 2010 2020, and > 1800 papers only in 2021. This interest is reflected in the development of a multitude of theoretical and methodological frame works for calculating functional diversity, making it challenging to navigate the myri ads of options and to report detailed accounts of trait based analyses. Therefore, the discipline of trait based ecology would benefit from the existence of a general guideline for standard reporting and good practices for analyses. We devise an eight step pro tocol to guide researchers in conducting and reporting functional diversity analyses, with the overarching goal of increasing reproducibility, transparency and comparabil ity across studies. The protocol is based on 1 identification of a research question; 2 a sampling scheme and a study design; 3 4 assemblage of data matrices; 5 data exploration and preprocessing; 6 functional diversity computation; 7 model fitting, evaluation and interpretation; and 8 data, metadata and code provision. Throughout the protocol, we provide information on how to best select research questions, study designs, trait data, compute functional diversity, interpret results and discuss ways to ensure reproducibility in reporting results. To facilitate the implementation of this template, we further develop an interactive web based application stepFD in the form of a checklist workflow, detailing all the steps of the protocol and allowing the user to produce a final reproducibility report to upload alongside the published paper. A thorough and transparent reporting of functional diversity analyses ensures that ecologists can incorporate others findings into meta analyses, the shared data can be integrated into larger databases for consensus analyses, and available code can be reused by other researchers. All these elements are key to pushing forward this vibrant and fast growing field of research. Published version https //doi.org/10.1111/ecog.06287 Published version 2022_PALACIO ET AL Ecography.pdf Articolo in rivista Blackwell 0906 7590 Ecography Cop. Ecography Cop. Ecography Cop. Ecography. Cop. stefano.mammola MAMMOLA STEFANO |
