Code and data for: Traits, threats, and popularity explain extinction risk of bird
Notice bibliographique
Résumé
README for Supplementary Materials<b>Title of Paper:</b> Traits, threats, and popularity explain extinction risk of birds globally<br><b>Authors:</b> Janaina Serrano, Lars Iversen, Laura Pollock<br>DescriptionThis README file provides an overview of the dataset, columns, and code files included in the supplementary materials for the paper titled <i>Traits, threats, and popularity explain extinction risk of birds globally</i>. The dataset contains information on bird species, their traits, threats they face, habitat characteristics, and popularity metrics. The associated code files are provided to facilitate reproducibility and further exploration.Files in Supplementary Materials1. <b>Dataset File</b><b>Filename:</b> dat<b>Format:</b> CSVDataset DescriptionColumns in the Dataset<b>Column Name</b><b>Description</b><b>species</b>Scientific name of the bird species.<b>threatened</b>Binary indicator of whether the species is classified as threatened (1/0).<b>Habitat</b>Primary habitat type for the species.<b>Order1</b>Taxonomic order to which the species belongs.<b>total_threats</b>Total number of threats affecting the species.<b>Migration</b>Migration status of the species (e.g., migratory or non-migratory).<b>HabitatBreadth</b>Breadth of habitat types the species can occupy (numerical value).<b>Range.Size</b>Geographical range size of the species (in square kilometers).<b>Mass</b>Body mass of the species (in grams).<b>gbif_mean</b>Mean number of GBIF records indicating species' data availability.<b>mean</b>Mean number of Google search hits for the species (popularity metric).<b>pollution</b>Impact of pollution threats on the species.<b>logging</b>Impact of logging threats on the species.<b>invasive</b>Impact of invasive species threats on the species.<b>agriculture</b>Impact of agricultural activities on the species.<b>climate_change</b>Impact of climate change threats on the species.<b>hunting</b>Impact of hunting threats on the species.<b>Mass.log</b>Log-transformed body mass.<b>Range.Size.log</b>Log-transformed range size.<b>gbif_mean.log</b>Log-transformed GBIF mean value.<b>HabitatBreadth.log</b>Log-transformed habitat breadth.<b>google.log</b>Log-transformed Google search popularity.<b>Migration1</b>Categorical indicator of migration type.<b>Mass.log.cs</b>Centered and scaled log-transformed body mass.<b>Range.Size.log.cs</b>Centered and scaled log-transformed range size.<b>gbif_mean.log.cs</b>Centered and scaled log-transformed GBIF mean value.<b>HabitatBreadth.log.cs</b>Centered and scaled log-transformed habitat breadth.<b>google.log.cs</b>Centered and scaled log-transformed Google popularity.<br>2. <b>Code Files</b>Descriptions of the provided code files:<b>Filename</b><b>Description</b><b>dataprep_birdtraits</b>Script for preparing and cleaning the bird trait dataset. Includes processes like data wrangling, standardization of column names, log-transformations of variables, and preparation of final input data for analysis.<b>model_figures_script</b>Script to generate the main figures from the paper. This includes plotting extinction risk models, trait relationships, and visualizations of the species' threats and popularity metrics.<b>model_evaluation_bivmap</b>Script for model evaluation and bivariate mapping. Evaluates the predictive performance of models and creates spatial maps to visualize overlaps modeled extinction risk and observed conservation status of birds.<b>gtrends</b>Script for collecting and processing Google Trends data related to species' popularity. Retrieves search hit data, processes it for analysis, and calculates summary metrics like mean hits and log-transformed values.<b>GBIF_download</b> Script for collecting and processing GBIF number of observations for birds globally from 2004-2021. Retrieves GBIF data, processes it for analysis, and calculates average species observations per year.Data Usage and CitationThe dataset is provided as supplementary material for the paper and can be used for academic purposes. If you use this dataset, please cite the paper as follows:<i>Serrano J., Iversen L., Pollock L. (2025). Traits, threats, and popularity explain extinction risk of birds globally.</i>Contact InformationFor questions about the dataset or paper, please contact:<b>Janaina Serrano</b>: janaina.serrano@mail.mcgill.ca<b>Lars Iversen</b>: lars.iversen@mcgill.ca<b>Laura Pollock</b>: laura.pollock@mcgill.ca<br>
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,002 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,001 |
| Méta-épidémiologie (sens large) | 0,002 | 0,000 |
| Bibliométrie | 0,002 | 0,001 |
| Études des sciences et des technologies | 0,001 | 0,001 |
| Communication savante | 0,001 | 0,002 |
| Science ouverte | 0,006 | 0,010 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; les deux têtes enseignantes s’accordent sur ce qui est montré ici.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».