Land cover preferences and spatiotemporal associations of ungulates within a Scottish mammal community

In the degraded and modified environment of the Scottish Highlands, novel ungulate communities have arisen following local extinctions, reintroductions, and the introduction of non-native species. An understanding of the dynamics and interactions within these unique mammal communities is important as many of these mammals represent keystone species with disproportionate impacts on the environment. Using a camera trap survey, we investigated land cover preferences and spatiotemporal interactions within a Scottish ungulate community: the sika deer (Cervus nippon), the roe deer (Capreolus capreolus), the red deer (Cervus elaphus), and the wild boar (Sus scrofa). We used generalised linear models to assess land cover preferences and the effect of human disturbance; spatiotemporal interactions were characterised using time interval modelling. We found sika deer and roe deer preferred coniferous plantations and grasslands, with sika deer additionally preferring woodland. For red deer, we foun..., These data are the results of a camera trapping survey on the Bunloit estate, as detailed in the manuscript Lovell et al. 2023 titled \"Habitat preferences and spatiotemporal associations of ungulates within a Scottish mammal community\". 
Datasets
contact_data contains the raw data set extracted from the tagged camera trap images
count_data is the number of independent contacts at each camera trap site, and the duration each camera trap was deployed for
 
Code
Summary stats.R was used to calculate various summary statistics for the dataset
Habitat Posson models.R was used to run the negative binomial habitat poisson models, and conduct associated emmeans comparisons and plots
Time diff analysis.R was used to conduct the time interval analysis to assess spatiotemporal associations/avoidance
Plotting time difference analysis.R was used to create the plot associated with the spatiotemporal analysis, Camera trap metadata was extracted using Exifpro, and all analysis was undertaken in R. , # Land cover preferences and spatiotemporal associations of ungulates within a Scottish mammal community

These data are the results of a camera trapping survey on the Bunloit rewilding project in Inverness-shire, as detailed in the manuscript Lovell et al. 2023 titled \"Habitat preferences and spatiotemporal associations of ungulates within a Scottish mammal community\". 

Datasets

contact_data contains the raw data set extracted from the tagged camera trap images. Each row represents an independent ungulate contact as detailed in the associated manuscript. Variables in this dataset utilised in future analysis are the 'placeID' (the ID number for the camera trap), the 'Date' and 'Time' each independent contact was recorded at, the 'Tag' (the species present in the image), and the location of each camera trap through longitude ('Long') and lattitude ('Lat') variables.

count_data is the number of independent contacts at each camera trap site, and the duration each camera trap was deplo...

## 苏格兰哺乳动物群落内有蹄类的生境偏好与时空关联
在苏格兰高地退化且经人为改造的生境中，随着本地物种灭绝、种群再引入以及外来物种的引入，已形成全新的有蹄类动物群落。理解这类独特哺乳动物群落的动态变化与种间相互作用至关重要，因为其中多数物种均为对生态环境具有不成比例影响的关键物种（keystone species）。

本研究借助红外相机陷阱（camera trap）调查，探究了苏格兰某有蹄类群落的生境偏好与时空相互作用，涉及的物种包括梅花鹿（*Cervus nippon*）、狍（*Capreolus capreolus*）、马鹿（*Cervus elaphus*）以及野猪（*Sus scrofa*）。研究采用广义线性模型（generalised linear models）评估生境偏好与人类干扰的影响，并通过时间间隔建模表征群落内的时空相互作用。

研究结果显示，梅花鹿与狍偏好针叶人工林与草原生境，梅花鹿还额外偏好林地；针对马鹿，本研究发现……。本数据集源自本洛特庄园（Bunloit estate）的红外相机陷阱调查结果，详见Lovell等人2023年发表的题为"苏格兰哺乳动物群落内有蹄类的生境偏好与时空关联"的学术手稿。

### 数据集
1. `contact_data`：包含从标记完成的红外相机陷阱图像中提取的原始数据集，每一行对应关联手稿中定义的一次独立有蹄类动物触发事件。本研究后续分析所用变量包括：相机陷阱编号（"placeID"）、每次独立触发事件的记录日期（"Date"）与时间（"Time"）、图像中出现的物种标签（"Tag"），以及通过经度（"Long"）与纬度（"Lat"）变量记录的每台相机陷阱的布设位置。
2. `count_data`：包含每个红外相机陷阱站点的独立触发事件数量，以及每台相机陷阱的布设时长（原文此处截断）。

### 代码
1. `Summary stats.R`：用于计算数据集的各类汇总统计量
2. `Habitat Posson models.R`：用于运行负二项分布生境泊松模型，并开展相关的`emmeans`比较与绘图
3. `Time diff analysis.R`：用于开展时间间隔分析，以评估物种间的时空关联或种间回避行为
4. `Plotting time difference analysis.R`：用于生成与时空分析相关的可视化图表

红外相机陷阱元数据通过`Exifpro`工具提取，所有分析均在R语言环境中完成。

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这些数据源自因弗内斯郡（Inverness-shire）本洛特再野化项目的红外相机陷阱调查结果，详见Lovell等人2023年发表的题为"苏格兰哺乳动物群落内有蹄类的生境偏好与时空关联"的学术手稿。

### 数据集补充说明
`contact_data`包含从标记完成的红外相机陷阱图像中提取的原始数据集，每一行代表关联手稿中定义的一次独立有蹄类动物触发事件。本研究后续分析所用的变量包括：相机陷阱ID（"placeID"）、每次独立接触事件的记录日期（"Date"）与时间（"Time"）、图像中出现的物种标签（"Tag"），以及通过经度（"Long"）与纬度（"Lat"）变量记录的每台相机陷阱的布设位置。

`count_data`包含每个红外相机陷阱站点的独立触发事件数量，以及每台相机陷阱的布设时长（原文此处截断）