Northern royal albatross demography, JAGS model

Files necessary to run the Bayesian multi-state capture-recapture model to analyse the demography of northern royal albatross at Taiaroa Head, New Zealand. The model is used for the article at https://peerj.com/preprints/712/, submitted for peer-reviewed publication. The files consist of: - <strong>model.bug</strong> - the Bayesian multi-state capture-recapture model, written in the BUG language, - <strong>data.txt</strong> - Data, in R raw format (readable in R using the source function), -<strong> inits.txt</strong> - Initialisation values for the model, - <strong>jags.cmd</strong> - JAGS command file to run the model, containing the names of the parameters to monitor, and to specify the length of the burnin period and of the total number of iterations. To run the model, assuming that JAGS is installed, simply run "jags jags.cmd". The data consist of 11 objects: - <strong>age</strong>: matrix of 355 x 23 values being the age in years for all 355 individuals and 23 years. - <strong>atcol</strong>: matrix of 355 x 23 values, with 1 indicating that an individual was at the colony, 0 otherwise, in each of the 23 years. - <strong>bsucc</strong>: matrix of 355 x 23 values, with 2 if an individual produced a fledgling, 1 otherwise, for each of the 23 years. - <strong>firstcap:</strong> vector of 355 values, representing the first year each individual was seen during the studied period, with 1 being the start of the period (1988-89). - <strong>k.R</strong><strong></strong>: minimum recruitment age, single value. - <strong>k.B</strong>: minimum age at first reproduction, single value. - <strong>N</strong>: number of individuals, single value. - <strong>sex</strong>: vector of 355 values, containing the gender of each individual: 1 for female, 2 for male, NA for unknown. - <strong>state</strong>: matrix of 355 x 23 values, being the state of each individual each year: 1: breeding adult, 2: non-breeding adult, 3: pre-breeder, 4: juvenile, 5: dead, NA: unknown. - <strong>T</strong>: number of years considered in the dataset, single value. - <strong>Tstar</strong>: maximum individual age in the dataset, single value.

本数据集包含运行贝叶斯多状态捕获-再捕获模型（Bayesian multi-state capture-recapture model）所需的全部文件，用于分析新西兰泰亚罗阿角（Taiaroa Head）北部皇家信天翁的种群动态。该模型对应已提交同行评审的学术论文，其预印本链接为https://peerj.com/preprints/712/。
本次提供的文件包括：
- **model.bug**：采用BUG语言编写的贝叶斯多状态捕获-再捕获模型代码文件；
- **data.txt**：以R原生格式存储的数据集，可通过R的`source()`函数读取；
- **inits.txt**：模型初始化参数文件；
- **jags.cmd**：JAGS运行命令文件，用于指定待监控的模型参数、预烧期（burn-in period）长度及总迭代次数。若已安装JAGS，直接执行命令`jags jags.cmd`即可启动模型运行。
本数据集共包含11个数据对象：
1. **age**：355×23的矩阵，记录了355只研究个体在23年研究周期内的年龄（单位：年）；
2. **atcol**：355×23的矩阵，取值为1代表对应年份个体处于繁殖群中，取值为0则代表未处于该区域，覆盖全部23年研究周期；
3. **bsucc**：355×23的矩阵，取值为2代表对应年份个体成功繁育出离巢幼鸟，取值为1则代表未成功繁殖，覆盖全部23年研究周期；
4. **firstcap**：长度为355的向量，记录了每只个体在研究期间首次被观测到的年份，其中取值为1代表研究起始年度（1988-1989年度）；
5. **k.R**：最小招募年龄，为单数值变量；
6. **k.B**：首次繁殖最小年龄，为单数值变量；
7. **N**：研究个体总数，为单数值变量；
8. **sex**：长度为355的向量，记录每只个体的性别：1代表雌性，2代表雄性，NA代表性别未知；
9. **state**：355×23的矩阵，记录每只个体每年的状态：1=繁殖成体，2=非繁殖成体，3=繁殖前亚成体，4=幼体，5=死亡，NA代表状态未知；
10. **T**：研究涵盖的总年数，为单数值变量；
11. **Tstar**：数据集内记录的个体最大年龄，为单数值变量。