| Title: |
Data from: A phylogeny-informed characterisation of global tetrapod traits addresses data gaps and biases |
| Authors: |
Moura, Mario R.; Ceron, Karoline; Guedes, Jhonny J. M.; Chen-Zhao, Rosana; Sica, Yanina; Hart, Julie; Dorman, Wendy; Portmann, Julia M.; Gonzalez-del-Pliego, Pamela; Ranipeta, Ajay; Catenazzi, Alessandro; Werneck, Fernanda; Toledo, Luis Felipe; Upham, Nathan; Tonini, Joao F. R.; Colston, Timothy J.; Guralnick, Robert; Bowie, Rauri C. K.; Pyron, R. Alexander; Jetz, Walter |
| Publisher Information: |
Zenodo Digital Repository |
| Publication Year: |
2024 |
| Collection: |
Zenodo |
| Subject Terms: |
Tetrapoda; Multiple Imputation; Trait data; Global Ecology; Amphibia; Reptilia; Aves; Mammalia; Zoology; Big Data; Comparative Biology; Macroecology; Conservation; Biodiversity Shortfall |
| Description: |
Description Raw data and R-code for the research approach on phylogenetic multiple imputation of natural history traits for tetrapod species. In brief, the code computes the phylogenetic filters, reproduces the grid search procedure to tune XGBoost hyperparameters; compute phylogenetic multiple imputations for traits related to body length, body mass, activity time, and microhabitat; and build the figures used in the main text and supplementary material. The original code was executed on a private cloud-processing service, which may limit is reproducibility by external users. However, the code provided here has been adapted to ensure reproducibility on local machines, using a subset of the data. The complete TetrapodTraits database is available at 10.5281/zenodo.10530617. The modelling framework was built using the directory structure informed in the README.pdf file. The R-code provided have steps designed to replicate the directory structure as informed, but understanding it is a good starting point to navigate the outputs produced. Updates October 19, 2024: the file Tetrapoda_prunedToFamily.tree has been updated to remove a duplicate entry for the tip label "Phasianidae". File content Datasets.zip: this zip file represents the "Datasets" folder directory, as illustrated in the README.pdf. This zip file contains 17 CSV files, encompassing outputs at the genus- and family-level (measures of trait completeness, relative change in average trait values per taxon), assemblage-level outputs (measures of richness, trait completeness, and relative change in average trait values per 110 x 110 km grid cell), tuned hyperparameters of XGBoost models, summary statistics of model performance across the 10,000 multiple phylogenetic imputations computed, and a table with data source and respective reference type. All csv files are loaded from within the R scripts provided. PhylogenySets.zip: this zip file represents the "PhylogenySets" folder directory. It includes subsets of 100 fully-sampled phylogenetic tree published for ... |
| Document Type: |
text |
| Language: |
English |
| Relation: |
https://zenodo.org/records/13909811; oai:zenodo.org:13909811; https://doi.org/10.5281/zenodo.13909811 |
| DOI: |
10.5281/zenodo.13909811 |
| Availability: |
https://doi.org/10.5281/zenodo.13909811; https://zenodo.org/records/13909811 |
| Rights: |
Creative Commons Attribution 4.0 International ; cc-by-4.0 ; https://creativecommons.org/licenses/by/4.0/legalcode |
| Accession Number: |
edsbas.5E3CDBE4 |
| Database: |
BASE |