Mechanistic home range capture–recapture models for the estimation of population density and landscape connectivity

Spatial capture–recapture models (SCRs) provide an integrative statistical tool for analyzing animal movement and population patterns. Although incorporating home range formation with a theoretical basis of animal movement into SCRs can improve the prediction of animal space use in a heterogeneous landscape, this approach is challenging owing to the sparseness of recapture events.
In this study, we developed an advection–diffusion capture–recapture model (ADCR), which is an extension of SCRs incorporating home range formation with advection–diffusion formalism, providing a new framework to estimate population density and landscape permeability. we tested the unbiasedness of the estimator using simulated capture–recapture data generated by a step selection function. We also compared accuracy of population density estimates and home range shapes with those from an SCR incorporating the least-cost path. In addition, ADCR was applied to real dataset of Asiatic black bear in Japan to demonst..., Study site
              Our survey was conducted in the eastern Toyama prefecture, Japan. Our study site locates at the western foot of Tateyama mountains and partly overlapped to the Chubusangaku National Park. It contains a wide range of topography from lowland, hill to mountains. In the hilly area, agricultural lands along the rivers divide the forest landscape. The deciduous coniferous trees (Fagus crenata, Quercus crispula and Q. serrata) which offer food for bears in autumn are dominant species of the forest (Arimoto et al. 2011). As in other parts of Japan, a hard crop of acorns causes behavioral changes in black bears that increase conflicts with human (Ohnishi et al. 2011).
Survey design
              From 2013 to 2015, we conducted a camera trap capture-recapture survey at 86 locations in the forest (Fig. S1). The survey were conducted from May to October, which is active season for bears. In each location, we set a camera trap (Trophycam ; Bushnell Outdoor Products, Overland..., , # Data from: Mechanistic home range capture–recapture models for the estimation of population density and landscape connectivity

[https://doi.org/10.5061/dryad.ksn02v7bq](https://doi.org/10.5061/dryad.ksn02v7bq)

Capture recapture dataset of Asiatic black bear (*Ursus thibetanus*) in eastern Toyama Prefecture, Japan in 2013-2015, and a shp file of 0.5km grid cells with the area ratio of agricultural land and water surface as factors affecting permeability of bears.

## Description of the data and file structure

The capture recapture data of Asiatic black bears were obtained by authors using video-recording camera traps set to 86 locations. ID of individuals were given by matching shapes of body marks such as ring marks. The dataset consists of the following two .csv files and one shapefile:

### 1. Deployments (**effort\_231225.csv**)

This is a data table defining location IDs (`trapid`), camera-working days (`effort`), years (`year`), decimal longitudes (`Lon`) and latitudes (`Lat`)...

空间捕获-再捕获模型（Spatial capture–recapture models, SCRs）是一类用于分析动物运动与种群格局的整合性统计工具。尽管将基于动物运动理论基础的家域形成机制纳入SCRs，能够提升异质景观中动物空间利用模式的预测精度，但由于再捕获事件较为稀疏，该方法的实施颇具挑战。
本研究构建了平流扩散捕获-再捕获模型（advection–diffusion capture–recapture model, ADCR），该模型为纳入平流扩散形式主义的家域形成机制的SCRs扩展模型，为种群密度与景观渗透性的估算提供了全新框架。本研究通过步选择函数生成的模拟捕获-再捕获数据，检验了该估计器的无偏性；同时将种群密度估计精度与家域形态的估算结果，与纳入最小成本路径的SCRs所得结果进行了对比。此外，本研究将ADCR应用于日本亚洲黑熊的真实数据集以验证……
### 研究样地
本调查于日本富山县东部开展。研究样地位于立山山脉西麓，部分区域与中部山岳国立公园重叠。样地内涵盖从低地、丘陵到山地的多样地形。丘陵区域内，沿河分布的农田分割了森林景观。秋季可为黑熊提供食物的落叶针叶林（日本山毛榉*Fagus crenata*、槲栎*Quercus crispula*及锐齿栎*Q. serrata*）为该区域森林的优势树种（Arimoto等，2011）。与日本其他区域类似，当地丰富的橡子产量会导致黑熊行为改变，进而加剧与人的冲突（Ohnishi等，2011）。
### 调查设计
2013年至2015年，本研究在86处森林样点开展了红外相机（camera trap）捕获-再捕获调查（图S1）。调查时段为5月至10月，这是黑熊的活动旺季。每个样点均布设了红外相机（Trophycam；Bushnell Outdoor Products, Overland...）。
# 数据来源：用于种群密度与景观连通性估算的机制性家域捕获-再捕获模型
[https://doi.org/10.5061/dryad.ksn02v7bq](https://doi.org/10.5061/dryad.ksn02v7bq)

本数据集包含日本富山县东部2013-2015年的亚洲黑熊（*Ursus thibetanus*）捕获-再捕获数据，以及一套0.5km网格单元的形状文件，该网格以农田面积占比与水面占比作为影响黑熊景观连通性的因子。

## 数据与文件结构说明
亚洲黑熊的捕获-再捕获数据由研究团队通过布设86个点位的红外相机录制获取。个体ID通过匹配个体体表斑纹（如环状斑纹）的形态进行判定。本数据集包含2个.csv文件与1个形状文件：
### 1. 布设信息（**effort_231225.csv**）
该数据表包含样点ID（`trapid`）、相机有效工作日（`effort`）、调查年份（`year`）、十进制经度（`Lon`）与十进制纬度（`Lat`）等信息。