Huanan Analysis

Folder Contents

• 1.0 Import shapedata.do
• 1.1 Import Huanan Market confirmed cases.do
• 1.2 Import environmental tests.do
• 1.3 Import raccoon dog readings.do
• 1.4 Import genomic sample data.do
• 2.1 Tabulate characteristics of market stalls.do
• 2.2 Tabulate incidence of cases by vendor type.do
• 2.3 Tabulate RT-qPCR tests by date & vendor.do
• 2.4 Tabulate BOLD data.do
• 2.5 Tabulate SARS-CoV-2 genomic data.do
• 3.1 Map first week of Huanan cases (13-20dec).do
• 3.2 Map second week of Huanan cases (21-31dec).do
• 3.3 Map number of environmental tests per shop.do
• 3.4 Map environmental tests vs. cases.do
• 4.1 Compute vendor distances to initial cases.do
• 4.2 Compute vendor distances to raccoon dogs.do
• 5.1 Analyze RT-qPCR tests & raccoon dog shops.do
• 5.2 Make scatterplot of RT-qPCR tests & distances to RD shops.do
• 5.3 Analyze spatiotemporal pattern of cases.do
• 5.4 Compare spatiotemporal Bayesian results.do
• 5.5 Map spatiotemporal Bayesian results.do
• S1. Tabulate NCBI data.do
• S2. Compute vendor distances to primary raccoon dog shop.do
• S3. Analyze RT-qPCR tests & primary RD shop.do
• S4. Make scatterplot of RT-qPCR tests & distance to primary RD shop.do

Subfolders

• Temp
• Shapedata
• Estimates
• Figures
• RawData
• Maps
• Datasets