Use and misuse of trait imputation in ecology: the problem of using out‐of‐context imputed values Article Swipe
Lucas D. Gorné
,
Jesús Aguirre‐Gutiérrez
,
Fernanda C. Souza
,
Nathan G. Swenson
,
Nathan J. B. Kraft
,
Beatriz Schwantes Marimon
,
Timothy R. Baker
,
Renato A. Ferreira de Lima
,
Emilio Vilanova
,
Esteban Álvarez‐Dávila
,
Abel Monteagudo Mendoza
,
Gerardo Flores Llampazo
,
Rubens Manoel dos Santos
,
Gerhard Boenisch
,
Alejandro Araujo‐Murakami
,
Gonzalo Rivas‐Torres
,
Hirma Ramírez‐Angulo
,
Nayane Cristina Candida dos Santos Prestes
,
Paulo S. Morandi
,
Sabina Cerruto Ribeiro
,
Wesley Jonatar Alves da Cruz
,
Mathias Disney
,
Anthony Di Fiore
,
Ben Hur Marimon
,
Ted R. Feldpausch
,
Yadvinder Malhi
,
Oliver L. Phillips
,
David Galbraith
,
Sandra Díaz
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1111/ecog.07520
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1111/ecog.07520
Despite the progress in the measurement and accessibility of plant trait information, acquiring sufficiently complete data from enough species to answer broad‐scale questions in plant functional ecology and biogeography remains challenging. A common way to overcome this challenge is by imputation, or ‘gap‐filling' of trait values. This has proven appropriate when focusing on the overall patterns emerging from the database being imputed. However, some applications force the imputation procedure out of its original scope, using imputed values independently from the imputation context, and specific trait values for a given species are used as input for computing new variables. We tested the performance of three widely used imputation methods (Bayesian hierarchical probabilistic matrix factorization, multiple imputation by chained equations with predictive mean matching, and Rphylopars) on a database of tropical tree and shrub traits. By applying a leave‐one‐out procedure, we assessed the accuracy and precision of the imputed values and found that out‐of‐context use of imputed values may bias the estimation of different variables. We also found that low redundancy (i.e. low predictability of a new value on the basis of existing values) in the dataset, not uncommon for empirical datasets, is likely the main cause of low accuracy and precision in the imputed values. We therefore suggest the use of a leave‐one‐out procedure to test the quality of the imputed values before any out‐of‐context application of the imputed values, and make practical recommendations to avoid the misuse of imputation procedures. Furthermore, we recommend not publishing gap‐filled datasets, publishing instead only the empirical data, together with the imputation method applied and the corresponding script to reproduce the imputation. This will help avoid the spread of imputed data, whose accuracy, precision, and source are difficult to assess and track, into the public domain.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1111/ecog.07520
- OA Status
- gold
- Cited By
- 5
- References
- 26
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4407120989
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4407120989Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1111/ecog.07520Digital Object Identifier
- Title
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Use and misuse of trait imputation in ecology: the problem of using out‐of‐context imputed valuesWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-02-03Full publication date if available
- Authors
-
Lucas D. Gorné, Jesús Aguirre‐Gutiérrez, Fernanda C. Souza, Nathan G. Swenson, Nathan J. B. Kraft, Beatriz Schwantes Marimon, Timothy R. Baker, Renato A. Ferreira de Lima, Emilio Vilanova, Esteban Álvarez‐Dávila, Abel Monteagudo Mendoza, Gerardo Flores Llampazo, Rubens Manoel dos Santos, Gerhard Boenisch, Alejandro Araujo‐Murakami, Gonzalo Rivas‐Torres, Hirma Ramírez‐Angulo, Nayane Cristina Candida dos Santos Prestes, Paulo S. Morandi, Sabina Cerruto Ribeiro, Wesley Jonatar Alves da Cruz, Mathias Disney, Anthony Di Fiore, Ben Hur Marimon, Ted R. Feldpausch, Yadvinder Malhi, Oliver L. Phillips, David Galbraith, Sandra DíazList of authors in order
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https://doi.org/10.1111/ecog.07520Publisher landing page
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
- OA URL
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https://doi.org/10.1111/ecog.07520Direct OA link when available
- Concepts
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Imputation (statistics), Trait, Ecology, Context (archaeology), Geography, Statistics, Biology, Computer science, Missing data, Mathematics, Programming language, ArchaeologyTop concepts (fields/topics) attached by OpenAlex
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5Total citation count in OpenAlex
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2025: 5Per-year citation counts (last 5 years)
- References (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.imputation. | 266 |
| abstract_inverted_index.measurement | 5 |
| abstract_inverted_index.performance | 101 |
| abstract_inverted_index.procedures. | 239 |
| abstract_inverted_index.Furthermore, | 240 |
| abstract_inverted_index.applications | 64 |
| abstract_inverted_index.biogeography | 28 |
| abstract_inverted_index.challenging. | 30 |
| abstract_inverted_index.gap‐filled | 245 |
| abstract_inverted_index.hierarchical | 109 |
| abstract_inverted_index.information, | 11 |
| abstract_inverted_index.sufficiently | 13 |
| abstract_inverted_index.accessibility | 7 |
| abstract_inverted_index.broad‐scale | 21 |
| abstract_inverted_index.corresponding | 261 |
| abstract_inverted_index.independently | 77 |
| abstract_inverted_index.probabilistic | 110 |
| abstract_inverted_index.factorization, | 112 |
| abstract_inverted_index.predictability | 171 |
| abstract_inverted_index.recommendations | 232 |
| abstract_inverted_index.leave‐one‐out | 136, 211 |
| abstract_inverted_index.‘gap‐filling' | 42 |
| abstract_inverted_index.out‐of‐context | 151, 223 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 97 |
| corresponding_author_ids | https://openalex.org/A5058817731 |
| countries_distinct_count | 11 |
| institutions_distinct_count | 29 |
| corresponding_institution_ids | https://openalex.org/I151201029, https://openalex.org/I166401450 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/15 |
| sustainable_development_goals[0].score | 0.6499999761581421 |
| sustainable_development_goals[0].display_name | Life in Land |
| citation_normalized_percentile.value | 0.99159707 |
| citation_normalized_percentile.is_in_top_1_percent | True |
| citation_normalized_percentile.is_in_top_10_percent | True |