ZIP folder containing supplementary files to the article entitled Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022 and published in Emerging Infectious Diseases with doi 10.3201/eid2807.220033 Script_EID_1.R is the R script analysing the data_EID1.csv screening test data file (Figure 1 and Suppl Figure F1, and Tables 1 and 3). Script_EID_2.R is the R script analysing the data_EID2.csv screening test data file (Figures 2, 3, 5, and Suppl Figure F2, and Table 2). Script_EID_sequencing_raw.R is the R script analysing the data_EID_sequencing.csv sequencing data file (Figures 4, 5, and Suppl Figure F3).