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HTD Dengue Severity Profile (69DX)

This repository contains Rscript for the descriptive analysis for Dengue severity profile

Trinh Dong, 2024

Prerequisites

RStudio >= 2024.04

R >= 4.4.0

How to run

Warning

This code is tailored for RStudio. It is required to change the code to run in other environment/IDE. See below for instructions.

You have to create a directory data/raw/ and input your raw data inside. Additionally: data/raw/BirthDataFix.xlsx contains fixed age demographic info.

mkdir('data')
mkdir('data/raw')
install.package('renv')
renv::restore()

Given all datasets are in data/raw, to generate report, open in Rstudio 69DX.Rproj

  1. Open analysis/01_import.R, click on Source
  2. Open analysis/02_create_VAR.R, click on Source
  3. Open 69DX.Rmd, click on Knit

In case of failure in 1 or 2 (or not Rstudio), comment out this line

setwd(dirname(rstudioapi::getActiveDocumentContext()$path))

in both files, then change the working directory to analysis

setwd('analysis')

and run 1, 2 again.

Project tree

  • 69DX.Rmd: report generation file, requiring data generated for 02_create_VAD.R
  • analysis/: analysis code
  • analysis/01_import.R: code for importing data
  • analysis/02_create_VAD.R: generate processed data for 69DX
  • data/: data
  • data/raw: raw data
  • data/imported: imported data, generated by analysis/01_import.R
  • data/vad: processed data, generated by analysis/02_create_VAD.R