Giayetto et al, 2023 - Ecological and life-history traits and their relationship with West Nile virus and Saint Louis Encephalitis virus exposure risk.

Code and data to accompany: Giayetto et al., 2023 -  Ecological and life-history traits and their relationship with West Nile virus and Saint Louis Encephalitis virus exposure risk.

We combined a dataset of ecological and life-history traits that were potentially relevant to explain West Nile virus (WNV) and Saint Louis Encephalitis  virus (SLEV) birds’ exposure risk. We selected the following six traits: body mass, clutch size, nest height, nest type, diet type and migratory status, and we combined it with data obtained in the field on the serological status of 3502 birds against the aforementioned viruses.  We used the serological state against WNV and SLEV (presence/absence of neutralizing antibodies) data from free-ranging birds, obtained between 2004 and 2019 in 5 different Argentinean provinces and compiled the traits of the 130 represented species in our dataset of de sampled free-ranging birds.

Both, body mass and clutch size data were mainly complied from Cooke et al 2019, that includes these following databases:  PanTHERIA (Jones et al., 2009), Pacifici database (Pacifici et al., 2013), EltonTraits database (Wilman et al., 2014) and Amniote database (Myhrvold et al., 2015). We supplemented missing species traits using data from Aráoz et al 2016.  Information referring to nest characteristics, diet and migratory status was extracted mainly from The Cornell Lab of Ornithology website (https://birdsoftheworld.org).

Nest height was classified in three categories, as ground, understory (nests predominantly found above ground and below 3m) or canopy/sub-canopy (nests predominantly found above 3m).

Nest type was classified in three categories, as open cup, closed cup or cavity.

Diet type was categorized into 7 groups according to the primary diet of each species: Folivore-Frugivore, Frugivore-Insectivore, Granivore, Granivore-Insectivore, Insectivore, Insectivore-Carnivore and Omnivore.

Migratory status was categorized as resident or migrant.

# FILESET

nmds-traits.csv - Dataframe for NMDS analysis according birds seroprevalence and their ecological and life history traits.

nmds.R - Scripts for the visualization of birds’ species according their seroprevalence and their ecological and life history traits via NMDS 

Graf_WNV_SLEV_CoefData.R - Codes for plotting model-averaged parameter estimates and their CIs.

database.csv -  Compiled trait data and serological state of Argentinean birds against WNV and SLEV.  Imputed data of Argentinean birds tested for WNV and SLEV neutralizing antibodies and their compiled traits by specie (body mass, clutch size, migratory status, diet type, nest type, nest, height).

WN-traits.R - Codes for WNV model averaging analysis

SLE-traits.R -  Codes for SLEV model averaging analysis

本数据集配套代码与数据源自Giayetto等人2023年发表的研究——《生态与生活史特征及其与西尼罗河病毒（West Nile virus, WNV）和圣路易斯脑炎病毒（Saint Louis Encephalitis virus, SLEV）暴露风险的关联》。

我们整合了一套生态与生活史特征数据集，用于阐释西尼罗河病毒（WNV）与圣路易斯脑炎病毒（SLEV）的鸟类暴露风险机制。本次研究选取了六项核心特征：体重、窝卵数、巢高、巢型、食性以及迁徙状态，并结合2004至2019年间在阿根廷5个省份采集的3502只野生鸟类的血清学检测数据（即针对上述两种病毒的中和抗体存在/缺失情况），为本次采样涉及的130个鸟类物种整理了上述特征数据。

体重与窝卵数数据主要来源于Cooke等人2019年的研究，该研究整合了以下数据库：PanTHERIA（Jones等人2009年）、Pacifici数据库（Pacifici等人2013年）、EltonTraits数据库（Wilman等人2014年）以及Amniote数据库（Myhrvold等人2015年）。对于数据缺失的物种，我们补充了Aráoz等人2016年的研究数据。巢型特征、食性与迁徙状态信息主要提取自康奈尔鸟类学实验室官网（https://birdsoftheworld.org）。

巢高被划分为三类：地面巢、下层灌丛巢（巢体主要位于地面以上3米以下区域）以及冠层/亚冠层巢（巢体主要位于3米以上区域）。
巢型被划分为三类：开放式杯状巢、封闭式杯状巢以及树洞巢。
食性依据各物种的主要摄食对象分为7类：植食-果食性、果食-食虫性、谷食性、谷食-食虫性、食虫性、食虫-肉食性以及杂食性。
迁徙状态被划分为留鸟与候鸟两类。

# 数据集文件清单
- nmds-traits.csv：用于非度量多维尺度分析（NMDS）的数据集，包含鸟类血清阳性率及其生态与生活史特征。
- nmds.R：用于通过非度量多维尺度分析（NMDS）可视化鸟类物种与其血清阳性率、生态及生活史特征关联关系的脚本。
- Graf_WNV_SLEV_CoefData.R：用于绘制模型平均参数估计值及其置信区间的代码。
- database.csv：整合了阿根廷鸟类针对WNV与SLEV的血清学状态与相关特征的数据集，包含经插补的阿根廷鸟类WNV与SLEV中和抗体检测数据，以及各物种的整理特征（体重、窝卵数、迁徙状态、食性、巢型、巢高）。
- WN-traits.R：用于西尼罗河病毒（WNV）模型平均分析的代码。
- SLE-traits.R：用于圣路易斯脑炎病毒（SLEV）模型平均分析的代码。