Supplement 1. R code and data to run spatial mark–resight model for raccoon camera trap and telemetry data.

File List Raccoon_data.R: R list object with following slots $n: matrix with unmarked photo-counts for each trap (rows) and sampling period (columns) $yknown: 3-dimensional array with individual photographic encounter histories (counts) of all tagged and radio-collared individuals (rows) at each camera (columns) and each sampling period (3rd dimension) $X: matrix with X and Y coordinates (columns) of each camera trap (rows), in UTM scaled to km $mi: vector with total number of photos of marked individuals that could be identified to individual level for each sampling period $mall: vector with total number of photos of marked individuals, identified and unidentified, for each sampling period $M: size of the augmented data set $Eff: 3-dimensional array with information on how many days each camera trap (column) was functional during each sampling period (3rd dimension), expanded to hold the same information for each individual in the augmented data set (row), for easier array multiplication in the MCMC algorithm $collar: vector of length M with “TRUE” for individuals with radio-collars and “FALSE” for individuals without collars, tagged or unmarked $locs: list of length sum(collar) with 2-dimensional matrices containing X and Y coordinates of radio telemetry locations for each of the collard individuals SSp.dbf, SSp.shp, SSp.shx: Shapefile with outline of South Core Banks (which comprises the state-space for the raccoon analysis) Rscript_Raccoons.R: R code to load data and run raccoon analysis MCMC_algorithm.txt: R code for MCMC algorithm for spatial mark-resight analysis of raccoon data Description Data files and code are set up to repeat the spatial mark–resight analysis of raccoon camera trapping and telemetry data from South Core Bank, NC, as presented in the Application example in the manuscript.

文件列表
Raccoon_data.R：R列表对象，包含以下成员槽：
$n：矩阵，行代表每个相机诱捕位点，列代表每个采样周期，存储未标记个体的照片计数
$yknown：三维数组，行对应所有佩戴无线电项圈的标记个体，列对应每个相机位点，第三维度对应每个采样周期，存储各个体的摄影捕获历史（以计数形式呈现）
$X：矩阵，行对应每个相机诱捕位点，列存储其通用横轴墨卡托（Universal Transverse Mercator, UTM）投影下的X、Y坐标，坐标已缩放至千米单位
$mi：向量，每个元素对应一个采样周期内可识别至个体级别的标记个体照片总数量
$mall：向量，每个元素对应一个采样周期内标记个体（含已识别与未识别个体）的照片总数量
$M：扩增数据集的规模
$Eff：三维数组，为便于MCMC算法执行数组乘法操作，已将原信息扩展为：行对应扩增数据集中的每个个体，列对应每个相机诱捕位点，第三维度对应每个采样周期，存储各相机位点在对应采样周期内的有效工作天数
$collar：长度为$M的向量，其中"TRUE"代表佩戴无线电项圈的个体（无论是否标记），"FALSE"代表未佩戴项圈的个体（标记或未标记）
$locs：长度为sum($collar)的列表，每个元素为二维矩阵，存储对应佩戴无线电项圈个体的无线电遥测位点的X、Y坐标
SSp.dbf、SSp.shp、SSp.shx：北卡罗来纳州南核心岸（South Core Banks）的矢量形状文件，该区域为本次浣熊分析的状态空间
Rscript_Raccoons.R：用于加载数据并运行浣熊种群分析的R脚本
MCMC_algorithm.txt：用于浣熊数据空间标记重捕分析的马尔可夫链蒙特卡洛（Markov Chain Monte Carlo, MCMC）算法的R代码

说明
本数据集文件与代码可复现论文应用示例中，针对北卡罗来纳州南核心岸浣熊相机诱捕与无线电遥测数据开展的空间标记重捕分析。