The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models.
Null models exploring species co-occurrence and trait-based limiting similarity are increasingly used to explore the influence of competition on community assembly; however, assessments of common models have not thoroughly explored the influence of variation in matrix size on error rates, in spite o...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4778770?pdf=render |
| _version_ | 1819242286639218688 |
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| author | Thomas Michael Lavender Brandon S Schamp Eric G Lamb |
| author_facet | Thomas Michael Lavender Brandon S Schamp Eric G Lamb |
| author_sort | Thomas Michael Lavender |
| collection | DOAJ |
| description | Null models exploring species co-occurrence and trait-based limiting similarity are increasingly used to explore the influence of competition on community assembly; however, assessments of common models have not thoroughly explored the influence of variation in matrix size on error rates, in spite of the fact that studies have explored community matrices that vary considerably in size. To determine how smaller matrices, which are of greatest concern, perform statistically, we generated biologically realistic presence-absence matrices ranging in size from 3-50 species and sites, as well as associated trait matrices. We examined co-occurrence tests using the C-Score statistic and independent swap algorithm. For trait-based limiting similarity null models, we used the mean nearest neighbour trait distance (NN) and the standard deviation of nearest neighbour distances (SDNN) as test statistics, and considered two common randomization algorithms: abundance independent trait shuffling (AITS), and abundance weighted trait shuffling (AWTS). Matrices as small as three × three resulted in acceptable type I error rates (p < 0.05) for both the co-occurrence and trait-based limiting similarity null models when exclusive p-values were used. The commonly used inclusive p-value (≤ or ≥, as opposed to exclusive p-values; < or >) was associated with increased type I error rates, particularly for matrices with fewer than eight species. Type I error rates increased for limiting similarity tests using the AWTS randomization scheme when community matrices contained more than 35 sites; a similar randomization used in null models of phylogenetic dispersion has previously been viewed as robust. Notwithstanding other potential deficiencies related to the use of small matrices to represent communities, the application of both classes of null model should be restricted to matrices with 10 or more species to avoid the possibility of type II errors. Additionally, researchers should restrict the use of the AWTS randomization to matrices with fewer than 35 sites to avoid type I errors when testing for trait-based limiting similarity. The AITS randomization scheme performed better in terms of type I error rates, and therefore may be more appropriate when considering systems for which traits are not clustered by abundance. |
| first_indexed | 2024-12-23T14:37:24Z |
| format | Article |
| id | doaj.art-a9078b69051246608df5229405b95d7e |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T14:37:24Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a9078b69051246608df5229405b95d7e2022-12-21T17:43:18ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01113e015114610.1371/journal.pone.0151146The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models.Thomas Michael LavenderBrandon S SchampEric G LambNull models exploring species co-occurrence and trait-based limiting similarity are increasingly used to explore the influence of competition on community assembly; however, assessments of common models have not thoroughly explored the influence of variation in matrix size on error rates, in spite of the fact that studies have explored community matrices that vary considerably in size. To determine how smaller matrices, which are of greatest concern, perform statistically, we generated biologically realistic presence-absence matrices ranging in size from 3-50 species and sites, as well as associated trait matrices. We examined co-occurrence tests using the C-Score statistic and independent swap algorithm. For trait-based limiting similarity null models, we used the mean nearest neighbour trait distance (NN) and the standard deviation of nearest neighbour distances (SDNN) as test statistics, and considered two common randomization algorithms: abundance independent trait shuffling (AITS), and abundance weighted trait shuffling (AWTS). Matrices as small as three × three resulted in acceptable type I error rates (p < 0.05) for both the co-occurrence and trait-based limiting similarity null models when exclusive p-values were used. The commonly used inclusive p-value (≤ or ≥, as opposed to exclusive p-values; < or >) was associated with increased type I error rates, particularly for matrices with fewer than eight species. Type I error rates increased for limiting similarity tests using the AWTS randomization scheme when community matrices contained more than 35 sites; a similar randomization used in null models of phylogenetic dispersion has previously been viewed as robust. Notwithstanding other potential deficiencies related to the use of small matrices to represent communities, the application of both classes of null model should be restricted to matrices with 10 or more species to avoid the possibility of type II errors. Additionally, researchers should restrict the use of the AWTS randomization to matrices with fewer than 35 sites to avoid type I errors when testing for trait-based limiting similarity. The AITS randomization scheme performed better in terms of type I error rates, and therefore may be more appropriate when considering systems for which traits are not clustered by abundance.http://europepmc.org/articles/PMC4778770?pdf=render |
| spellingShingle | Thomas Michael Lavender Brandon S Schamp Eric G Lamb The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models. PLoS ONE |
| title | The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models. |
| title_full | The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models. |
| title_fullStr | The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models. |
| title_full_unstemmed | The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models. |
| title_short | The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models. |
| title_sort | influence of matrix size on statistical properties of co occurrence and limiting similarity null models |
| url | http://europepmc.org/articles/PMC4778770?pdf=render |
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