Transvir SARS-CoV-2 Incidence

Description

Analysis for TransVIR Sars-CoV-2 Incidence Paper

Contents

The directory contains the code required to perform analyses:

• 📁 scripts: R scripts to be run in number order.

The raw and modified data required to replicate analyses is available upon request.

How to replicate analysis

This analysis requires R software and RStudio Desktop to be pre-installed.

1. Clone this repository
2. Open RStudio and create new project associated with this directory See here for details.
3. Open each script in ./scripts and run in number order

##To replicate incidence based analyses (i.e. Anderson-Gill Modelling)

1. Run 01_Data_cleaning.R
2. Import code to produce PCR negative dates (02_PCR_negative_dates.R)
3. Identify all infection episodes (incidence_data_base.R) - this is the default PCR neg definition
4. Convert into a lexis format 04_lexis_code
5. Run Anderson Gill Modelling 05_AG_Results

To run sensitivity analyses, repeat steps 3-5 with difference incidence_data_XX versions of the code 6. Summaryresults_sensitivity.R provides overall numbers for each scenario.

##To replicate symptom results

1. Run 01_Data_cleaning.R
2. Import code to produce PCR negative dates (02_PCR_negative_dates.R)
3. Identify all infection episodes (incidence_data_base.R) - this is the default PCR neg definition
4. Convert into a lexis format 04_lexis_code
5. Run symptom analysis - 05_symptomcode_V3.R
6. Produce summary description of symptoms - 06_symptom_summarycode.R

#To replicate cluster analysis

1. Run 01_data_cleaning.R
2. Run 02_cluster_code_final.R to produce cluster data sets for analysis
3. Run either 03_HCIR_analysis.R or 03_SAR_analysis.R for HCIR and SAR analyses respectively.