| Evaluating the relative importance of phylogeny and predictors in phylogenetic generalized linear models using the phylolm.hp R package | |
Lai, Jiangshan1,2; He, Yan1; Hou, Mi1; Zhang, Aiying1; Wang, Gang3 ; Mao, Lingfeng1
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| 2025 | |
| Source Publication | PLANT DIVERSITY
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| ISSN | 2096-2703 |
| Volume | 47Issue:5Pages:709-717 |
| Abstract | Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry (phylogeny) from those of ecological or trait-based predictors on species traits. Phylogenetic Generalized Linear Models (PGLMs) address this issue by integrating phylogenetic relationships into statistical models. However, accurately partitioning explained variance among correlated predictors remains challenging. The phylolm.hp R package tackles this problem by extending the concept of average shared variance to PGLMs, enabling nuanced quantification of the relative importance of phylogeny and other predictors. The package calculates individual likelihood-based R2 contributions of phylogeny and each predictor, accounting for both unique and shared explained variance. This approach overcomes limitations of traditional partial R2 methods, which often fail to sum the total R2 due to multicollinearity. We demonstrate the functionality of phylolm.hp through two case studies: one involving continuous trait data (maximum tree height in Californian species) and another focusing on binary trait data (species invasiveness in North American forests). The phylolm.hp package offers researchers a powerful tool to disentangle the contributions of phylogenetic and ecological predictors in comparative analyses. Copyright (c) 2025 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY |
| Keyword | Average shared variance Comparative analysis Hierarchical portioning Phylogenetic signal Variation partitioning |
| Subject Area | Plant Sciences |
| DOI | 10.1016/j.pld.2025.06.003 |
| Indexed By | SCI |
| Language | 英语 |
| WOS ID | WOS:001600651000001 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | https://ir.xtbg.ac.cn/handle/353005/15693 |
| Collection | 2012年后新成立研究组 |
| Affiliation | 1.Nanjing Forestry Univ, Coll Ecol & Environm, Coinnovat Ctr Sustainable Forestry Southern China, Nanjing 210037, Peoples R China 2.Nanjing Forestry Univ, Res Ctr Quantitat Ecol, Nanjing 210037, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Chinese Acad Sci, Yunnan Key Lab Forest Ecosyst Stabil & Global Chan, Xishuangbanna Trop Bot Garden, Mengla 666303, Peoples R China |
| Recommended Citation GB/T 7714 | Lai, Jiangshan,He, Yan,Hou, Mi,et al. Evaluating the relative importance of phylogeny and predictors in phylogenetic generalized linear models using the phylolm.hp R package[J]. PLANT DIVERSITY,2025,47(5):709-717. |
| APA | Lai, Jiangshan,He, Yan,Hou, Mi,Zhang, Aiying,Wang, Gang,&Mao, Lingfeng.(2025).Evaluating the relative importance of phylogeny and predictors in phylogenetic generalized linear models using the phylolm.hp R package.PLANT DIVERSITY,47(5),709-717. |
| MLA | Lai, Jiangshan,et al."Evaluating the relative importance of phylogeny and predictors in phylogenetic generalized linear models using the phylolm.hp R package".PLANT DIVERSITY 47.5(2025):709-717. |
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| Evaluating the relat（4388KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Download | |
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