Study Repository
This repository contains the data and statistical analyses of the study COVID-19 vaccine effectiveness against in-hospital mortality in immunocompromised older adults: a Brazilian hospital surveillance study, 2024.
Check the results at analysis.html.
Files
The repository contains the following files:
- SIVEP-Gripe data: SRAG 2024_DOWNLOAD 29_3_25 IMUNODEPRE_RT_PCR OU ANTIGENO%20POSITIVO.xlsx
- Data dictionary (in Portuguese): Dicionario_de_Dados_SRAG_Hospitalizado_19.09.2022.pdf
- R notebook source: analysis.Rmd
- R notebook result as HTML: analysis.html
- Table with versions of R packages for reproducibility: installed_packages.csv
- Project README (this): README.md
How to run
We performed the statistical analyses in R (version 4.5.0) using a single R notebook. The notebook is divided into sections and produces the results we included in the study.
It is possible to run and edit the notebook source ([analysis.Rmd]) with RStudio and use it to invoke knit to generate the results as HTML.
You may need to install some additional R libraries to run it. Use the following commands on R console:
install.packages("openxlsx")
install.packages("dplyr")
install.packages("lubridate")
install.packages("purrr")
install.packages("tidyr")
install.packages("prettyR")
install.packages("scales")
install.packages("DescTools")
install.packages("ggplot2")
install.packages("pROC")
install.packages("ResourceSelection")
For specific versions of the libraries, check installed_packages.csv. This file was created using the following commands:
ip = as.data.frame(installed.packages()[,c(1,3:4)])
ip = ip[is.na(ip$Priority),1:2,drop=FALSE]
write.csv(ip, "installed_packages.csv")
Authors
- Rodrigo P. V. Rezende MD PhD1
- João Felipe Pimentel PhD2,
- Bruno S. Caxias MD1,
- Caio M. Salgueiro MD1,
- Lucas T. Oliveira MD1,
- Luís Fernando A. Santos MD1,
- Caroline P. Pessanha MD1
- Vitoria Xavier Tracierra MD1
- Michael G. Simão MD1
- Mario Gustavo A. Pacheco MD1
- Vitor A. Cruz MD PhD3
- Luiz Eduardo C. Oliveira MD MSc1