Bacterial Infections: temporal trends in the children population

Analysis of the bacterial infection trends in the children population.

Data

Analysis developed with the aim of using the 2.2 4CE consortium data

Repo organization

R/: contains the files carrying out the analysis
public-data/ICD_bacterial4.csv: mapping of ICD codes to bacterial infection categories
output: location of the files saved with by the analysis

How to run this code?

First, clone the repository: git clone https://github.com/covidclinical/Phase2.2.bacterial_infections

Then open the folder 'data_extraction' and open the file bacterialInfection.Rmd and go to the section “Variables that need to be checked/modified by each site”:

change the folder_4ce_files to the directory where your phase 2.2 AllAdm cohort data is located
determine the obfuscation threshold:
- obfuscation = FALSE if no obfuscation
- the numeric value of the obfuscation threshold if any; e.g. obfuscation = 3 Make sure you comment the existing obfuscation line, set up as FALSE
change the dateFormat to the one followed in your site (e.g., if your date looks like 03-AUG-20 follows the format "%d-%b-%y"). Further details about how to specificy the format below:

%d day as a number (0-31) 01-31 %a abbreviated weekday (e.g., Mon ) %A unabbreviated weekday (e.g, Monday) %m month (00-12) 00-12 %b abbreviated month (e.g, Jan) %B unabbreviated month (e.g, January) %y 2-digit year (e.g., 07) %Y 4-digit year (e.g., 2007)

After all these changes are done, run the bacterialInfection.Rmd. As an output the next files will be generated in the output folder:

an html file named: bacterialInfection.html
two RData files with ICD codes summary for QC