A workflow to integrate ecological monitoring data from different sources

Wicquart, Jérémy; Gudka, Mishal; Obura, David; Logan, Murray; Staub, Francis; Souter, David; Planes, Serge

doi:10.1016/j.ecoinf.2021.101543

Cited by 6 publications

(5 citation statements)

References 38 publications

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“…Advances in data management and data standardization may also enable more efficient data synthesis projects like meta‐analysis (Sansone et al., 2019). In addition, newly emerging data standardization tools and reporting formats (Bond‐Lamberty et al., 2021) are being created that allow researchers to upload their data to be harmonized in a central data repository (Wicquart et al., 2022). Our work benefited from these positive trends in science.…”

Section: Discussionmentioning

confidence: 99%

Soil Respiration Response to Simulated Precipitation Change Depends on Ecosystem Type and Study Duration

et al. 2022

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Section: Discussionmentioning

confidence: 99%

Soil Respiration Response to Simulated Precipitation Change Depends on Ecosystem Type and Study Duration

et al. 2022

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“…While some of the analysis may be suboptimal in the context of resilience, if the data are accessible and available for use, they can be re-analysed to improve the accuracy of resilience potential assessments or contribute to broader assessments, such as systematic conservation planning and RLE assessments. The coral reef community has made significant strides in sharing data in recent years, with networks like the Global Coral Reef Monitoring Network bringing together data for regional and global initiatives (Wicquart et al, 2022), and we encourage assessors to continue this trend by making underlying data accessible to a wider audience. • Articulate a clear purpose of the assessment, include a resilience definition and state the relevant disturbance(s)/threat(s) being considered.…”

Section: Management Applicationmentioning

confidence: 99%

Strengthening resilience potential assessments for coral reef management

Gudka,

Obura,

Treml

et al. 2024

Methods Ecol Evol

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The persistence of diverse yet threatened ecosystems like coral reefs will require urgent action underpinned by effective assessments of resilience. Resilience potential assessments are commonly used to identify coral reefs likely to be more resilient to disturbances, based on indicators of state and function. Assessments are intended to support decision‐making, therefore, using principles from decision‐science and indicator design theory, we evaluated the selection, design and analysis of indicators from 68 resilience potential assessments conducted between 2008 and 2022. These principles include justifying and testing indicators and aggregation approaches, representing key parts of the ecosystem, considering uncertainty and meaningful normalisation of indicators. Although a broad range of indicators were typically evaluated, assessments rarely present structured processes to guide and justify indicator selection, such as selection criteria and conceptual models of ecosystem function. We also found that certain key ecosystem components that confer resilience were represented by indicators in almost all assessments, such as corals, herbivory, competition and reef structure. Other factors were rarely considered, such as abundance and diversity of key fish trophic groups other than herbivores, for example groupers and corallivores, other aspects of biodiversity and competitive interactions with corals. Reference points used to translate variables into resilience indicators were typically derived from the data, such as the highest indicator value of assessed sites. Ecologically meaningful thresholds, such as collapse or historic levels, were used less often as references. In most cases, indicators were not tested or validated against independent data, uncertainties were not presented, and there was a tendency to simplify results into composite indices to rank sites, without justifying aggregation methods. Despite resource constraints, most resilience potential assessments collect quantitative data that are useful for coral reef management. However, the shortcomings identified can make indicator interpretation difficult, limiting the capacity to predict the resilience of the system and support decisions. Implementation of robust approaches drawn from indicator design and selection theory can help strengthen resilience potential assessments of coral reefs and other ecosystems, ultimately improving the prospects of conservation.

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“…Users may need to make upfront data harmonisation and integration of the fields, if their data comes from other sources of information (e.g. iDigBio, BIEN, Paleobiology Database and Neotoma) or compilations of different sources (Wicquart et al., 2022).…”

Section: Advantages and Limitations Of Occur Application Compared To ...mentioning

confidence: 99%

“…Yet, little detail on data curation procedures is provided in many published papers using occurrence records from biodiversity databases. Such heterogeneity and poor reporting of data selection steps prevent from tracking the entire curation process, thus compromising the reproducibility of studies (Wicquart et al., 2022). However, to date, there has been no comprehensive review that guides researchers through all the information required for data curation, and the large array of modules and strategies already available to assess different aspects of data quality.…”

Section: Introductionmentioning

confidence: 99%

OCCUR Shiny application: A user‐friendly guide for curating species occurrence records

Ronquillo,

Stropp,

Hortal

2024

Methods Ecol Evol

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Ecology increasingly relies on a massive volume of biodiversity occurrence records to draw insights into large‐scale biogeographical, ecological and evolutionary phenomena. This often involves defining a set of criteria that guides the collection, filtering and standardising of available records. These curation processes are often neither described in detail nor well documented. This hampers the comparability and reproducibility of studies and thus undermines the robustness of any ecological result. Yet, to date, there is no guide providing a friendly way to reason and document a complete data curation process. We reviewed the available literature on data curation, including tools such as R packages and workflows. From this assessment, we created a complete guide organised into five modules that allows users to consciously select and validate occurrence records based on these curation criteria. This is presented in the user‐friendly Shiny R OCCUR application, available at https://ecoinformatic.shinyapps.io/OCCUR/. OCCUR application provides a guide for researchers to deal with the trade‐off between data certainty and coverage generated in each data curation step. An interactive graph of these changes is provided within each module. OCCUR also produces a custom‐made final report including all steps used for data filtering. This report helps to streamline the writing of the methods section of manuscripts and technical reports, thus promoting the reproducibility of data curation processes. This Shiny application provides an interactive overview of the data curation methods and their use for handling occurrence records from public repositories. It brings together the taxonomic, temporal and spatial dimensions of data and also the identification of duplicates of the records. OCCUR can be applied for multiple purposes, such as teaching R to ecologists or enhancing reproducibility of macroecology and biogeography.

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A workflow to integrate ecological monitoring data from different sources

Cited by 6 publications

References 38 publications

Soil Respiration Response to Simulated Precipitation Change Depends on Ecosystem Type and Study Duration

Soil Respiration Response to Simulated Precipitation Change Depends on Ecosystem Type and Study Duration

Strengthening resilience potential assessments for coral reef management

OCCUR Shiny application: A user‐friendly guide for curating species occurrence records

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