Analyses of the first wave of data from the CoMix social contact survey conducted in the UK during COVID-19 outbreak

data.table ggplot2 socialmixr patchwork ggthemr

remotes::install_github("Rdatatable/data.table")
install.packages("ggplot2)
remotes::install_github("sbfnk/socialmixr")
install.packages("patchwork/ggplot2)
devtools::install_github('cttobin/ggthemr')

data/ - for the data data/contact_matrices - For contact matrices r/ - for r scripts r/functions/ - for functions created for this analysis reports/ - For markdown documents outputs/ - For any graphs or output of data for public use admin/ - documents such as the survey protocol

scripts with dm_ are for data management scripts with an_ are for analysis and creating figures

• dm_setup_contact_matrix - Create contact matrices based on the survey data and polymod and save in data/contact_matrices/
• dm_scale_contact_matrix - Scale the contact matrices to impute age and reduction in R.
• dm_scale_boot_matrices - repeat what dm_scale_contact_matrix does but for bootstrapped matrices
• an_figure_one - Figure for paper
• an_figure_two - Figure of contact matrices for different locations
• an_descriptive_stats_tables - descriptive stats that go into tables in the analysis.
• an_table_two - Table overview of the characterstics of participants and contacts
• an_eigenvalues - Create data and look at change in R based on the eigenvalue scalings.