Evidence map›Paper›PMID 30058746›Full record

ArticleGlobal change biology2018

Extending the Latent Dirichlet Allocation model to presence/absence data: A case study on North American breeding birds and biogeographical shifts expected from climate change.

Denis Valle, Pedro Albuquerque, Qing Zhao, Albert Barberan, Robert J Fletcher

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Global change biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

18 citing papers in PubMed.

  1. Article
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  4. Global mapping of interventions to improve quality of life of patients with depression during 1990-2018.Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation · 2020
    Review
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  9. Modeling the Research Landscapes of Artificial Intelligence Applications in Diabetes (GAPInternational journal of environmental research and public health · 2020
    Article
  10. Global Mapping of Interventions to Improve Quality of Life of People with Diabetes in 1990-2018.International journal of environmental research and public health · 2020
    Review
  11. Article
  12. Article
  13. Characterizing Obesity Interventions and Treatment for Children and Youths During 1991-2018.International journal of environmental research and public health · 2019
    Article
  14. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Denis ValleSchool of Forest Resources and Conservation, University of Florida, Gainesville, Florida.ORCID 0000-0002-9830-8876
Pedro AlbuquerqueSchool of Forest Resources and Conservation, University of Florida, Gainesville, Florida.
Qing ZhaoSchool of Forest Resources and Conservation, University of Florida, Gainesville, Florida.
Albert BarberanDepartment of Soil, Water and Environmental Science, University of Arizona, Tucson, Arizona.
Robert J FletcherDepartment of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida.ORCID 0000-0003-1717-5707

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Understanding how species composition varies across space and time is fundamental to ecology. While multiple methods having been created to characterize this variation through the identification of groups of species that tend to co-occur, most of these methods unfortunately are not able to represent gradual variation in species composition. The Latent Dirichlet Allocation (LDA) model is a mixed-membership method that can represent gradual changes in community structure by delineating overlapping groups of species, but its use has been limited because it requires abundance data and requires users to a priori set the number of groups. We substantially extend LDA to accommodate widely available presence/absence data and to simultaneously determine the optimal number of groups. Using simulated data, we show that this model is able to accurately determine the true number of groups, estimate the underlying parameters, and fit with the data. We illustrate this method with data from the North American Breeding Bird Survey (BBS). Overall, our model identified 18 main bird groups, revealing striking spatial patterns for each group, many of which were closely associated with temperature and precipitation gradients. Furthermore, by comparing the estimated proportion of each group for two time periods (1997-2002 and 2010-2015), our results indicate that nine (of 18) breeding bird groups exhibited an expansion northward and contraction southward of their ranges, revealing subtle but important community-level biodiversity changes at a continental scale that are consistent with those expected under climate change. Our proposed method is likely to find multiple uses in ecology, being a valuable addition to the toolkit of ecologists.

Indexed as

Animal DistributionBiodiversityClimate ChangeAnimalsBirdsCanadaModels, BiologicalUnited Statesbiodiversitybreeding bird groupsclimate changecluster analysiscommunity ecologymixed-membership modelmultivariate statisticspresence/absence data

Identifiers

PMID30058746
PMCPMC7165608

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.