README.md
In jarvisc1/CoMix: Functions for running the CoMix analyses

CoMix

This repository contains the functions and analysis used to reproduce the CoMix survey results. The data is not currently available but dummy data will be added so that the code can be seen and checked.

# install.packages("remotes")
remotes::install_github("jarvisc1/CoMix")

Run Analysis

The inst/scripts folder contains code to run the social mixing matrices analysis for CoMix using POLYMOD as a baseline for imputation and comparison and imputation.

Choose from the following:
- Option 1: Fork the CoMix package repository
- Option 2: Copy the inst/ folder to another repository
  - For either option, set your .gitignore preferences before pushing any code or date to github (see the gitignore documentation for details)
Create panel and wave specific folders in data and outputs using the following structure (refer to inst/scripts/000_run_all.R)
- each panel and wave will need the following folders:
  - inst/data/panel_[LETTER]/wave_[NUMBER]/data
  - inst/outputs/panel_[LETTER]/wave_[NUMBER]/contact_matrices
  - inst/outputs/panel_[LETTER]/wave_[NUMBER]/contact_matrices_online
  - inst/outputs/combined
Add the following data:
- clean data for participants and contacts from the CoMix survey to the panel and wave specific data folder created in the previous step (clean_participants.rds and clean_contacts.rds from the CoMix survey)
- polymod participant and contacts data (named polymod_contacts.rds, polymod_participants.rds, and polymod_contacts_part.rds)
Run the inst/scripts/000_run_all.R file. By default it will bootstrap 5000 samples, which can be changed in aaa_create_contact_matrices

Outputs by script

Contact matrices

aaa_create_contact_matrices.R
- comix_survey.rds
- polymod_survey.rds
- comix_cm.rds
- polymod_cm.rds
- comix_cms.RData
- comix_phys_cms.RData
- boots_cms.RData
- boots_phys_cms.RData
aaa_scale_contact_matrices.R
- comix_cm_imputed.rds