Factors influencing survival of female eastern wild turkeys in northeastern South Dakota

# Factors Influencing Survival of Female Eastern Wild Turkeys in Northeastern South Dakota: Open Source Data ## **Metadata for The Hen (Female) Survival Analysis Prior Distribution Calculation** Files needed to calculate Hen Survival Analysis Prior Distributions: * beta.txt – JAGS model code for survival probability estimation * gaussian.txt – JAGS model code for age-class specific survival probability estimation * Prior_Distribution.RMD – R Markdown file used to run prior distribution calculation * Prior_Estimates.xlsx – Excel Workbook (2 sheets) containing published estimates of hen annual survival from studies of turkeys in the Midwest used to calculate prior distributions for the hen survival analysis Description of variables within “Prior_Estimates.xlsx” * Sheet = Combined * Estimate – published annual hen survival estimates where hen age was pooled * Source – the published study each estimate originated from * Sheet = Age * Adult – published annual survival estimates for adult hens * Juv – published annual survival estimates for juvenile/yearling hens * Source – the published study each estimate originated from ## **Metadata for Hen (Female) Survival Analysis** Files needed to run the Hen Survival Analysis: * HenObservations.csv – observation history for each hen monitored over the course of the study * HenSurvival_InputData.RData – R object containing all hen survival model input data * HenSurvivalAnalysis_DataSetUp.R – R code used to develop hen survival model input data * HenSurvivalModel.R – R code used to run hen survival analysis * hensurvmodel.txt – JAGS model code for hen survival analysis * IncubationData.csv – incubation history for each nest attempt * MilbankDailySumm2016to2019.csv – raw temperature and precipitation from NOAA NCEI CDO (Menne, M. J., I. Durre, B. Korzeniewski, S. McNeal, K. Thomas, X. Yin, S. Anthony, R. Ray, R. S. Vose, B. E. Gleason, and T. G. Houston. 2012. Global Historical Climatology Network - Daily (GHCN-Daily), Version 3.26. NOAA National Climatic Data Center. [http://doi.org/10.7289/V5D21VHZ](http://doi.org/10.7289/V5D21VHZ). Accessed March 5, 2020.) To run the hen survival analysis, start by opening the “HenSurvivalModel.R” file. Ensure the “Hen Survival” folder is set as the working directory. Ensure all required packages (i.e., jagsUI & ggplot2) are installed and loaded. Execute code. Description of variables within “HenObservations.csv” * Band_ID – the identification number on leg bands of individually marked eastern wild turkey hens. A factor with 122 levels where each level is a unique identification number (and unique individual hen). * Age – the age of the hen at the time of capture. A factor with 2 levels: adult or juvenile (i.e., yearling). * Date_Captured – the date each hen was captured. * Last_Obs_Date – the last date the hen was observed alive. If the hen was still alive at the end of the study period, then no date is entered into this column for that hen. * Date_Mortality – the date the hen was found to have died (i.e., mortality signal was detected) (if applicable). Description of variables within “IncubationData.csv” * Band_ID – the identification number on leg bands of individually marked eastern wild turkey hens that reached incubation of at least one nest during at least one year of the study. A factor with 89 levels where each level is a unique identification number (and unique individual hen). * Incubation_Date – the start date of the incubation period (i.e., first day the hen was known to be incubating a nest). * Fate_Date – the day after the end of the incubation period (i.e., first day the hen was known to be no longer incubating a nest). Description of variables within “MilbankDailySumm2016to2019.csv” * STATION – the station identification code. Please see [http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-stations.txt](http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-stations.txt) for a complete list of stations and their metadata. * NAME – the name of the station (usually city/airport name). Optional output field. * LATITUDE – decimated degrees w/ northern hemisphere values > 0 * LONGITUDE – decimated degrees w/ western hemisphere values < 0 * ELEVATION – elevation above mean sea level (tenths of meters) * DATE – the date of the record * PRCP – precipitation in mm * SNOW – snowfall in mm * SNWD – snow depth in mm * TMAX – maximum temperature in Celsius * TMIN – minimum temperature in Celsius * TOBS – temperature at time of observation in Celsius ## **Metadata for Winter Weather Comparison Figure creation** Files needed to create the Winter Weather Comparison figure: * MilbankDailySummary1990to2019.csv – raw temperature and precipitation from NOAA NCEI CDO (Menne, M. J., I. Durre, B. Korzeniewski, S. McNeal, K. Thomas, X. Yin, S. Anthony, R. Ray, R. S. Vose, B. E. Gleason, and T. G. Houston. 2012. Global Historical Climatology Network - Daily (GHCN-Daily), Version 3.26. NOAA National Climatic Data Center. [http://doi.org/10.7289/V5D21VHZ](http://doi.org/10.7289/V5D21VHZ). Accessed March 5, 2020.) * WinterWeatherCompare.png - image illustrating the total snow accumulation (cm) during the winter months (1-January to 31-March) and mean January air temperature (Celsius) recorded in Milbank, South Dakota, USA during the study years compared to 30-year normals. Included as a figure in the manuscript. * WinterWeatherComparison.R – R code used to create “WinterWeatherCompare.png” Description of variables within “MilbankDailySumm2016to2019.csv” * STATION – the station identification code. Please see [http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-stations.txt](http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-stations.txt) for a complete list of stations and their metadata. * NAME – the name of the station (usually city/airport name). Optional output field. * LATITUDE – decimated degrees w/ northern hemisphere values > 0 * LONGITUDE – decimated degrees w/ western hemisphere values < 0 * ELEVATION – elevation above mean sea level (tenths of meters) * DATE – the date of the record * PRCP – precipitation in mm * SNOW – snowfall in mm * SNWD – snow depth in mm * TMAX – maximum temperature in Celsius * TMIN – minimum temperature in Celsius * TOBS – temperature at time of observation in Celsius

# 美国南达科他州东北部东部野生雌火鸡存活影响因素：开源数据集
## **雌性（雌火鸡）存活分析先验分布计算元数据**
用于计算雌火鸡存活分析先验分布所需文件：
* beta.txt：用于存活概率估计的JAGS模型代码
* gaussian.txt：用于年龄组特异性存活概率估计的JAGS模型代码
* Prior_Distribution.RMD：用于运行先验分布计算的R Markdown文件
* Prior_Estimates.xlsx：包含2个工作表的Excel工作簿，收录了中西部地区火鸡研究中已发表的雌火鸡年存活估计值，用于构建雌火鸡存活分析的先验分布

### Prior_Estimates.xlsx内变量说明
* 工作表：Combined（合并表）
* Estimate：将雌火鸡年龄合并后的已发表年存活估计值
* Source：该估计值源自的已发表研究
* 工作表：Age（年龄表）
* Adult：已发表的成年雌火鸡年存活估计值
* Juv：已发表的幼体/亚成体雌火鸡年存活估计值
* Source：该估计值源自的已发表研究

## **雌火鸡（雌性）存活分析元数据**
运行雌火鸡存活分析所需文件：
* HenObservations.csv：研究期间监测的每只雌火鸡的观测历史文件
* HenSurvival_InputData.RData：包含所有雌火鸡存活模型输入数据的R对象文件
* HenSurvivalAnalysis_DataSetUp.R：用于构建雌火鸡存活模型输入数据的R代码文件
* HenSurvivalModel.R：用于运行雌火鸡存活分析的R代码文件
* hensurvmodel.txt：用于雌火鸡存活分析的JAGS模型代码文件
* IncubationData.csv：每一次筑巢孵卵的孵卵历史文件
* MilbankDailySumm2016to2019.csv：来自美国国家海洋和大气管理局国家环境信息中心国家气候数据中心（NOAA NCEI CDO）的原始气温与降水数据（引用来源：Menne, M. J., I. Durre, B. Korzeniewski, S. McNeal, K. Thomas, X. Yin, S. Anthony, R. Ray, R. S. Vose, B. E. Gleason, 及 T. G. Houston. 2012. 全球历史气候学网络-每日数据集（GHCN-Daily），版本3.26。NOAA国家气候数据中心。[http://doi.org/10.7289/V5D21VHZ](http://doi.org/10.7289/V5D21VHZ)，2020年3月5日访问。）

运行雌火鸡存活分析的步骤：请先打开`HenSurvivalModel.R`文件，将“Hen Survival”文件夹设置为工作目录，确认已安装并加载所有所需包（如`jagsUI`与`ggplot2`），随后执行代码即可。

### HenObservations.csv内变量说明
* Band_ID：个体标记的东部野生雌火鸡腿环标识号，为具有122个水平的因子变量，每个水平对应唯一标识号与唯一雌火鸡个体
* Age：捕获时雌火鸡的年龄，为具有2个水平的因子变量：成年或幼体（即亚成体）
* Date_Captured：每只雌火鸡的捕获日期
* Last_Obs_Date：最后一次观测到雌火鸡存活的日期。若雌火鸡在研究期结束时仍存活，则该列无对应日期
* Date_Mortality：被发现死亡的雌火鸡的死亡日期（即检测到死亡信号的日期，若适用）

### IncubationData.csv内变量说明
* Band_ID：研究期间至少有1年完成至少1次筑巢孵卵的个体标记东部野生雌火鸡腿环标识号，为具有89个水平的因子变量，每个水平对应唯一标识号与唯一雌火鸡个体
* Incubation_Date：孵卵期开始日期（即已知雌火鸡开始孵巢的首日）
* Fate_Date：孵卵期结束后的次日（即已知雌火鸡不再孵巢的首日）

### MilbankDailySumm2016to2019.csv内变量说明
* STATION：站点标识码，完整站点列表及元数据请参见[http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-stations.txt](http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-stations.txt)
* NAME：站点名称（通常为城市/机场名称），为可选输出字段
* LATITUDE：以十进制度表示的纬度，北半球数值大于0
* LONGITUDE：以十进制度表示的经度，西半球数值小于0
* ELEVATION：平均海平面以上海拔（单位为0.1米）
* DATE：记录日期
* PRCP：降水量（单位：毫米）
* SNOW：降雪量（单位：毫米）
* SNWD：积雪深度（单位：毫米）
* TMAX：最高气温（单位：摄氏度）
* TMIN：最低气温（单位：摄氏度）
* TOBS：观测时气温（单位：摄氏度）

## **冬季天气对比图制作元数据**
制作冬季天气对比图所需文件：
* MilbankDailySummary1990to2019.csv：来自NOAA NCEI CDO的原始气温与降水数据（引用来源同MilbankDailySumm2016to2019.csv）
* WinterWeatherCompare.png：展示美国南达科他州米尔班克市研究年份冬季（1月1日至3月31日）总积雪量（厘米）与1月平均气温（摄氏度），并与30年气候平均值对比的图像，已收录于论文手稿中
* WinterWeatherComparison.R：用于生成`WinterWeatherCompare.png`的R代码文件

### MilbankDailySumm2016to2019.csv内变量说明
* STATION：站点标识码，完整站点列表及元数据请参见[http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-stations.txt](http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-stations.txt)
* NAME：站点名称（通常为城市/机场名称），为可选输出字段
* LATITUDE：以十进制度表示的纬度，北半球数值大于0
* LONGITUDE：以十进制度表示的经度，西半球数值小于0
* ELEVATION：平均海平面以上海拔（单位为0.1米）
* DATE：记录日期
* PRCP：降水量（单位：毫米）
* SNOW：降雪量（单位：毫米）
* SNWD：积雪深度（单位：毫米）
* TMAX：最高气温（单位：摄氏度）
* TMIN：最低气温（单位：摄氏度）
* TOBS：观测时气温（单位：摄氏度）