Data and supporting R script for: Tissue Tropism and Transmission Ecology Predict Virulence of Human RNA Viruses

Ecological trait data for human RNA viruses, supporting R scripts and supporting analytical output values used to generate figures/tables.Virulence_data_Brierley_et_al_21_6_19.xlsx: Data file describes known virulence and fatalities, transmission routes, tissue tropisms, and host range for each of 214 human virus species. Data was compiled via structured literature searches following Woolhouse & Brierley (2018). Full data dictionary is provided in-file.Brierley_et_al_main_script_23_6_19.R: Supporting R script for classification tree analysis, calling random forest analyses and generating model visualisations.Brierley_et_al_random_forest_23_6_19.R: Supporting R script for conducting random forest analysis and extracting model outputs.Brierley_et_al_fig1_data.csv - Brierley_et_al_tableS5_data.xlsx: Supporting output value data for respective figures and tables. fig1_data contains counts of viruses by severity rating and taxonomic family. All other data contains values of either performance diagnostics (table1_data, tableS3_data, tableS5_data), variable importances (fig3_data, figS1_data, figS3_data), or partial dependence (fig4_data, figS2_data, figS4_data) extracted from random forest models using 200 training/test partitions. Sheet tab titles in Excel files denote data subset or virulence definition used.

人类RNA病毒生态特征数据集，包含R脚本支持及用于生成图表/表格的辅助分析输出值。数据文件Virulence_data_Brierley_et_al_21_6_19.xlsx描述了214种人类病毒物种的已知致病性和死亡率、传播途径、组织嗜性和宿主范围。数据通过遵循Woolhouse和Brierley（2018）的结构化文献检索进行汇编。完整的数据字典在文件中提供。Brierley_et_al_main_script_23_6_19.R为分类树分析提供支持性R脚本，调用随机森林分析并生成模型可视化。Brierley_et_al_random_forest_23_6_19.R为进行随机森林分析和提取模型输出的支持性R脚本。Brierley_et_al_fig1_data.csv - Brierley_et_al_tableS5_data.xlsx提供了相应图表和表格的辅助输出值数据。fig1_data包含按严重程度评级和分类家族计算的病毒数量。所有其他数据包含性能诊断（table1_data、tableS3_data、tableS5_data）、变量重要性（fig3_data、figS1_data、figS3_data）或部分依赖（fig4_data、figS2_data、figS4_data）的值，这些值是通过使用200个训练/测试分区从随机森林模型中提取得到的。Excel文件中的工作表标签标题表示数据子集或致病性定义。