Data and code supporting "Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses"
Notice bibliographique
Résumé
About this repositoryCitation:This repository can be cited as:Cormier, T., Barychka, T., Beaumont, M., Burt, T. B., English, M. D., Giacinti, J. A., Giroux, J-F., Guillemette, M., Hargan, K. E., Jones, M., Lair, S., Lang, A. S., Lepage, C., Montevecchi W. A., Rahman, I., Rail, J-F., Robertson, G. J., Ronconi, R. A., Seyer, Y., Taylor, L. U., Ward, C. R. E., Wight, J., Wilhelm, S. I., Avery-Gomm, S. 2024. Data and Code supporting "Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses". FigShare. https://doi.org/10.6084/m9.figshare.25492693 This repository contains all data and code necessary to generate manuscript results associated with the following peer-reviewed publication: Cormier, T., Barychka, T., Beaumont, M., Burt, T. B., English, M. D., Giacinti, J. A., Giroux, J-F., Guillemette, M., Hargan, K. E., Jones, M., Lair, S., Lang, A. S., Lepage, C., Montevecchi W. A., Rahman, I., Rail, J-F., Robertson, G. J., Ronconi, R. A., Seyer, Y., Taylor, L. U., Ward, C. R. E., Wight, J., Wilhelm, S. I., Avery-Gomm, S. 2024. Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses. Bird Study, Vol. 71, No. 4. https://doi.org/10.1080/00063657.2024.2415161 InstructionsDataThis repository contains the complete collated dataset of reported wild bird mortalities in eastern Canada for October 1, 2022 to September 30, 2023 with anonymized personal information. See the manuscript above for details. Metadata describing the data is provided in Sheet: Metadata. Instructions for how to use the dataset are provided in Instructions for DataS1.txt Data S1. Reported mortalities and morbidities in Eastern Canada.xlsxInstructions for DataS1.txtPlease note: All data in DataS1 from April 1 to September 2022 were obtained from the Complete_Mortality_Dataset published by Avery-Gomm et al., (2024) and accessed from the data repository where that study published their data: https10.6084/m9.figshare.24856869.This repository also contains three .xlsx files with information on colony surveys from 2023 for Common Eiders (Data S2), Northern Gannets (Data S3) and Common Murres (Data S4). Also included in Data S2-4 are the best available information on recent breeding pair numbers and locations for all known colonies in eastern Canada, for each species, but this should not be construed or used as the official records on colony locations for Common Eiders or Common Mures. References are provided in Sheet: References. Metadata describing the data is provided in Sheet: Metadata. Data S2. American Common Eider (ACOEI) colony survey information.xlsxData S3. Northern Gannet (NOGA) colony survey information.xlsxData S4. Common Murre (COMU) colony survey information.xlsxCodeThe code required to reproduce the double count analysis is in Scenario_Analysis.Rmd.Scenario_Analysis.Rmd (input files are Data S1.csv and SpeciesAlphaCode_KEY.csv)Please note: This code was adapted from the Scenario_Analysis.Rmd provided by Avery-Gomm et al., (2024), accessed from the data repository where that study published their data: https10.6084/m9.figshare.24856869. Software RequirementsScripts are written for R version 4.2.2 (2022-10-31 ucrt). See scripts and the manuscript for packages and software citations.Required R packages can be installed in R with: install.packages(c("tidyverse", "dplyr", "data.table", "fossil", "DataCombine", "janitor", "here", "formattable", "openxlsx"]] Terms of Use: CC-BYYou are free to:Share — copy and redistribute the material in any medium or format for any purpose, even commercially.Adapt — remix, transform, and build upon the material for any purpose, even commercially.The licensor cannot revoke these freedoms as long as you follow the license terms.Under the following terms:Attribution — You must give appropriate credit , provide a link to the license, and indicate if changes were made . You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.
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 machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,001 | 0,017 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,001 |
| Méta-épidémiologie (sens large) | 0,002 | 0,002 |
| Bibliométrie | 0,008 | 0,021 |
| Études des sciences et des technologies | 0,002 | 0,001 |
| Communication savante | 0,004 | 0,002 |
| Science ouverte | 0,004 | 0,003 |
| Intégrité de la recherche | 0,002 | 0,002 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,292 | 0,113 |
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; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».