Supporting data for "Controlling avian influenza with public health measures"

This dataset contains the data collected and generated during the PhD. 
The avian human infections folder contains a dataset from a collection of avian influenza human infections from the published literature and publicly available reports from the WHO, between 1996 to 2021. Information on date of report, age, gender, outcome, exposure, and source (as a DOI or URL to the document providing this information) is available. 

The avian interventions folder contains a dataset from a collection of estimates of public health interventions and their practical applications on avian influenza outbreaks, retreived from the published literature. For each intervention estimate, I provide the source (URL or DOI), target of the intervention, location, dates, pathogenicity of the virus at the origin of the outbreak (when available), subtype of the virus at the origin of the outbreak (when available), details of the periods used for comparison, kind of estimate (relative risk, odds ratio, hazard ratio, reproductive number ratio, incidence ratio, etc), type of unit used (environmental samples, human incidence, poultry flock, poultry farm, etc), raw data (if available), estimate information (point estimate, confidence interval, adjusted or not), and type of interventions used (LPM closure, rest days, cleaning, disinfection, culling, prophylaxis vaccination, emergency vaccination, ban of quail, ban of keeping poultry overnight, ban of restocking, controlled traffic, prophylaxis antivirals, personal protective equipment use, biosecurity improvements and/or training). 

The folder avian poultry network contains two subfolders: models, containing the script used on the free software GAMA platform to simulate an agent based model of avian influenza transmission and public health interventions on a poultry network, and
generated, containing a synthesis of the outputs of seven scenarios applied during my thesis, as R datasets.

本数据集收录了博士研究期间收集和生成的数据。禽类人感染文件夹中包含了一组源自已发表文献及世界卫生组织公开报告的禽流感人感染数据集，时间跨度为1996年至2021年。其中，报告日期、年龄、性别、结局、暴露情况以及信息来源（以DOI或URL形式提供相关文档的链接）等信息均有详细记录。

禽类干预文件夹中收录了来自已发表文献的关于公共卫生干预及其在禽流感爆发中的实际应用的数据集。对于每个干预措施的评估，我提供了来源（URL或DOI）、干预目标、地点、日期、爆发起源病毒的原生致病性（如有）、爆发起源病毒的原生亚型（如有）、用于比较的时期细节、估计类型（相对风险、比值比、风险比、繁殖数比、发病率比等）、所使用的单位类型（环境样本、人类发病率、家禽群、家禽农场等）、原始数据（如有）、估计信息（点估计、置信区间、是否调整）、以及所采用的干预类型（LPM关闭、休息日、清洁、消毒、扑杀、预防性疫苗接种、紧急疫苗接种、禁止饲养鹧鸪、禁止夜间饲养家禽、禁止补种、交通控制、预防性抗病毒药物、个人防护设备使用、生物安全改进及/或培训）。

禽类家禽网络文件夹包含两个子文件夹：模型文件夹，其中包含在GAMA免费软件平台上用于模拟基于智能体的禽流感传播和家禽网络公共卫生干预的脚本；生成文件夹，其中包含我在论文中应用的七个场景的输出综合，以R数据集的形式呈现。