Data and supporting R script for: Tissue Tropism and Transmission Ecology Predict Virulence of Human RNA Viruses
2019-10-18T11:00:35Z (GMT) by
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.