Supporting R code for the manuscript "SARS-CoV-2 vaccine breakthrough by Omicron and Delta variants: comparative assessments with New York State genomic surveillance data"
00_Delta_Prelim_Settings.R: Settings for Delta analysis 00_Omicron_Prelim_Settings.R: Settings for Omicron analysis 00_Descriptive_Omicron.R: Basic descriptive analysis of the data set 01_ConditionalLogistic_Omicron.R: Main Omicron analysis 02_ConditionalLogistic_AGE_Omicron.R: Omicron analysis without age matching 03_ConditionalLogistic_VACCINATED_Omicron.R: Omicron analysis, restricted to vaccinated only 04_Overview_Figure_CondLogistic.R Creates the stacked bar chart that shows regional and temporal distribution 05_Descriptive_Delta.R Basic descriptive analysis of the Delta data set 06_ConditionalLogistic_Delta.R Main Delta analysis 07_ConditionalLogistic_AGE_Delta.R Delta analysis without age matching 08_PowerAnalysis.R Power analysis for Delta analysis DOH_COVID_hlpr.R File with helper functions