asthma-after-RI

Repository for the paper "Differential asthma risk following respiratory infection in children from three minority populations."
This paper was published in PLoS One on May 5, 2020
A preprint was also made available on MedRxiv on Novemenber 22, 2019

Analysis

This repository contains all the analysis scripts needed to reproduce all results and figures in the paper "Differential asthma risk following respiratory infection in children from three minority populations." Specifically you will find the following:

asthma-after-RI
|-- README.md
|-- LICENSE
|-- analysis
| |-- run_analysis.sh           # user friendly button to push for running all analysis steps
| |-- env.sh                    # a script for populating the environment variables
| 
| |--bin
| | |-- OddsRatioplot_func.R    # function to source to create the Odds Ratio Plot
| | |-- Prevalenceplot_func.R   # function to source to create the Prevalence Plot
| | |-- RSVseason_func.R        # function to source to create the RSV Season Plot **see Notes below
|
| |-- src
| | |-- run_AssocTests.R        # performs the association tests
| | |-- run_FigCreations.R      # sources all figure functions to generate figures
| | |-- run_PairwiseP.R         # performs the pairwise P-value analysis
| | |-- set_R_environment.R     # installs and loads all packages needed for the analysis 

Notes

Please contact the authors of the following paper for access to the data used to make the RSV season figure:

McGuiness CB, Boron ML, Saunders B, Edelman L, Kumar VR, Rabon-Stith KM. Respiratory syncytial virus surveillance in the United States, 2007-2012: results from a national surveillance system. Pediatr Infect Dis J. 2014;33(6):589-94. Epub 2014/01/22. doi: 10.1097/INF.0000000000000257. PubMed PMID: 24445835; PMCID: PMC4025589