Thesis on Global Patterns of Sampling Bias in Molecular Sequences of Vertebrate Viruses: Supplementary Data and Code

Supplementary Data and Code from my thesis on "Global Patterns of Sampling Bias in Molecular Sequences of Vertebrate Viruses". Virus family data was attained from NCBI Virus. GDP and population size data was attained from World Bank. Total number of animal species (biodiversity proxy) data was attained from IUCN Red List. NCBI Virus information per family can be found as .csv files in format "NCBI_VirusFamily_09042026.csv". For data on Coronaviridae, Orthomyxoviridae and Retroviridae, refer to .fst files which can be read into R; how these files were processed can be seen in the code; they contain the same information as the other virus families but just in different format for more efficient processing. Code files: loading_NCBI_Virus_datasets (needs to be run first, before any of the other code files); once run, the other code files can be run explorations_of_geographic_bias (code for maps, country-level data, log-log models, k-means clustering) explorations_of_taxonomic_bias (code for virus family bar chart, distinct vertebrate host species information, phylogenetic heatmap) explorations_of_temporal_bias (code for cumulative discovery curves, discovery rates, Kruskal-Wallis tests) For the pipeline used to attain taxonomy information via Taxonkit, "Taxonkit Taxonomic Information.txt". Contains the lines of code used and short description of code. GDP, population and biodiversity (IUCN_species_info) data are saved as .csv.本学位论文《脊椎动物病毒分子序列采样偏差的全球模式》附带的补充数据与代码。 病毒科相关数据源自NCBI病毒数据库（NCBI Virus）。 国内生产总值（GDP）与种群规模数据源自世界银行（World Bank）。 用以作为生物多样性替代指标的动物物种总数数据源自国际自然保护联盟红色名录（IUCN Red List）。 各病毒科的NCBI Virus相关信息以.csv格式文件存储，文件命名格式为"NCBI_VirusFamily_09042026.csv"。 关于冠状病毒科（Coronaviridae）、正黏病毒科（Orthomyxoviridae）以及反转录病毒科（Retroviridae）的数据，请参阅可在R语言中读取的.fst格式文件；此类文件的处理流程可参见对应代码，其包含的信息与其他病毒科完全一致，仅采用了更便于高效处理的不同存储格式。 代码文件如下： 1. loading_NCBI_Virus_datasets：需作为前置代码优先运行，执行完成后方可运行其余代码文件； 2. explorations_of_geographic_bias：用于绘制地图、处理国家层面数据、构建双对数模型以及K-means聚类的代码； 3. explorations_of_taxonomic_bias：用于绘制病毒科柱状图、统计不同脊椎动物宿主物种信息以及构建系统发育热图的代码； 4. explorations_of_temporal_bias：用于绘制累计发现曲线、计算发现速率以及开展Kruskal-Wallis检验的代码。 通过Taxonkit获取分类学信息的相关流程存储于"Taxonkit Taxonomic Information.txt"文件中，该文件包含所用代码片段及代码简要说明。 国内生产总值、种群规模以及生物多样性数据（对应文件标识为IUCN_species_info）均以.csv格式保存。