population_immunity_predicting_flu

Kangchon Kim contributed most of the code. Marcos Vieira contributed changes during revisions.

Data

• Data/sera/data contains HA and NA titers
• Data/sequences/data contains HA and NA reference virus sequences

Analyses

Genealogy of HA and NA

Analyses/genealogy

• tree_201718_shaded.R makes plots of HA genealogy for season 16-17 and 17-18.
• na_tree_201718_shaded.R makes plots of NA genealogy for season 16-17 and 17-18.

Forecasting susceptibilities

Analyses/forecasting/src

• binning.R As pre-processing before calculating susceptibility, ages are binned and the age bins are saved as age_bin_ha.rds and age_bin_na.rds using this code.
• call_susceptibility.R sets the options for calculating relative susceptibility and calls susceptibility.R, which calculates and saves the results of relative susceptibility according to the options.
• plot_susceptibility_rank.R takes the results of relative susceptibility using cutoff and makes susceptibility plots such as Figure 2.
• plot_susceptibility_gmt_rank.R takes results of relative susceptibility using GMT and makes susceptibility plots.
• titer_distribution.R makes plots of titer distribution.

Frequency and age distribution of clades

Analyses/frequency/src

• make_plot_frequency.R takes “clade_assigned_season.csv” files and makes plots of frequencies by clade.
• difference_in_proportion_test.R performs chi-square test to test the difference in the proportion of 3C.2A2 between children and adults.

Analyses/age_distribution_of_clades/src

• age_distribution.R takes “clade_assigned_season.csv” files in frequency/data_clade_assigned folders and makes age distribution plots.

Correlation between pairs of viruses

Analyses/correlation_and_clustering/src

• correlation_analysis_boot_rmv_all_undetectable.R calculates correlation coefficients for each reference virus pairs in each age group. It also tests significant difference of the correlations using bootstrapping. This code uses analysis_uitl.R, correlation_functions.R, and correlation_function_bootstrap.R.
• plot_correlation.R takes the results from correlation_analysis_boot_rmv_all_undetectable.R and make heat maps.
• correlation_analysis_boot_equal_bin.R calculates correlation coefficients for each reference virus pairs in each age group which is binned with equal number of years. It also draws plot of this result.
• correlation_analysis_detail_plot.R makes plots showing correlation between titers to different reference viruses.

Cosine similarity between pairs of people

Analyses/correlation_and_clustering/src

• cosine_similarity_continuous_1000.R calculates cosine similarity between pairs of people using HA titer vectors and makes result plots.
• cosine_similarity_continuous_hana_1000.R calculates cosine similarity between pairs of people using HA-NA titer vectors and makes result plots.

Clustering analysis

Analyses/correlation_and_clustering/src

• clustering_analysis_using_cosine_smilarity.R performs clustering analysis and makes result plots.
• correlation_analysis_using_clusters.R calculate correlation coefficient for each clustering group and make result plots.
• larger_effect_in_targeting.R performs ANOVA to test if between-age-group titer difference is larger than within-age-group titer difference.

HA NA analysis

Analyses/ha_na_analysis

• hana_distribution_analysis.R makes plot of age distribution of HA and NA detectable titers. Performs logistic regression to test if fraction of detectable titers change by age.
• ha_na_correlation.R, ha_na_correlation_by10years.R make plots of correlation between HA and NA titers.