Data and R code for "Land-use change reshapes host community composition and erodes biodiversity-mediated dilution of hantavirus exposure"

This repository contains the serological and community-composition dataset and the R analytical code supporting the manuscript "Land-use change reshapes host community composition and erodes biodiversity-mediated dilution of hantavirus exposure" by Vigueras-Galván et al. Study context. Small mammals (rodents and bats) were sampled between 2021 and 2023 at 12 localities across the Yucatán Peninsula (Mexico), distributed along an anthropization gradient encompassing four habitat types: conserved, diversified, rural and urban (n = 3 localities per type). Hantavirus IgG antibodies were detected by indirect ELISA using a recombinant Sin Nombre virus (SNV) nucleocapsid antigen. Data file. Vertebrados_2024_CURADA.xlsx contains three sheets: INFORMACIÓN GENERAL: metadata on the dataset. Claves: codebook describing variable codes used in the Registro sheet. Registro: individual-level capture records (one row per captured individual) including locality, habitat, date, taxonomic identification (Class, Order, Family, Genus, Species), morphometric measurements, sample collection metadata, and serological/molecular results for several pathogens. The column SH corresponds to hantavirus serology (ELISA), used as the primary exposure variable in the manuscript. R scripts. Three R scripts reproduce the main figures of the manuscript from the raw dataset. They expect the Excel file in a subfolder named data/ and write outputs to a figures_article/ folder: fig1_overview.R — sampling effort, host species richness, Jaccard community similarity and hantavirus seroprevalence by habitat type (overview panel). fig2_dilution.R — habitat-stratified binomial GLM relating community-level seroprevalence to host species richness; forest plot of slopes by habitat type. fig3_-_amplifier-diluters.R — leave-one-out classification of host species as amplifiers or diluters of community-level hantavirus exposure, by habitat type. Reproducibility. Scripts are written in R and rely on the packages dplyr, tidyr, purrr, broom, readxl, stringr, ggplot2, scales, patchwork and forcats. Missing packages are installed automatically on first run.本仓库包含支持Vigueras-Galván等人发表的题为《土地利用变化重塑宿主群落组成并削弱生物多样性介导的汉坦病毒（hantavirus）暴露稀释效应》的论文所需的血清学与群落组成数据集，以及R语言分析代码。 ## 研究背景 2021至2023年间，研究人员在墨西哥尤卡坦半岛的12个采样点对小型哺乳动物（啮齿类与蝙蝠）开展采样。采样点沿涵盖4种生境类型的人为干扰梯度分布：原生保育生境、多样化农作生境、乡村生境与城市生境，每种生境类型设置3个采样点。研究采用重组辛诺柏病毒（Sin Nombre virus, SNV）核衣壳抗原，通过间接酶联免疫吸附试验（indirect ELISA）检测汉坦病毒IgG抗体。 ## 数据文件 Vertebrados_2024_CURADA.xlsx包含3个工作表： 1. INFORMACIÓN GENERAL：数据集元数据。 2. Claves：代码簿，用于说明Registro工作表中使用的变量编码规则。 3. Registro：个体水平捕获记录（每个捕获个体对应一行），包含采样点、生境类型、采样日期、分类学鉴定信息（纲、目、科、属、种）、形态测量数据、样本采集元数据，以及多种病原体的血清学/分子检测结果。其中SH列对应汉坦病毒血清学检测（ELISA）结果，为本论文的核心暴露变量。 ## R语言脚本 共3个R脚本可基于原始数据集复现论文中的主要图表。脚本预设将Excel文件放置于名为data/的子文件夹中，并将输出结果保存至figures_article/文件夹： 1. fig1_overview.R：绘制按生境类型分组的采样强度、宿主物种丰富度、雅卡尔群落相似度（Jaccard community similarity）以及汉坦病毒血清阳性率概览面板。 2. fig2_dilution.R：构建按生境分层的二项式广义线性模型（binomial GLM），探究群落水平血清阳性率与宿主物种丰富度的关联，并生成按生境类型划分的斜率森林图。 3. fig3_-_amplifier-diluters.R：基于留一法分类（leave-one-out classification），按生境类型将宿主物种划分为群落水平汉坦病毒暴露的扩增因子或稀释因子。 ## 可复现性说明 本脚本采用R语言编写，依赖dplyr、tidyr、purrr、broom、readxl、stringr、ggplot2、scales、patchwork及forcats等R包。首次运行时，缺失的依赖包将自动完成安装。