Kawasaki Disease and Autoimmune Disorders: exploratory analysis temporal trends in the children population

Analysis of the Kawasaki and autoimmune disease 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
kawasaki-disease-exploration/: contains the R code to get the counts and generate table 1 for Kawasaki disease patients
public-data/: mapping of ICD codes to the disease of interest

How to run this code?

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

Then open the folder kawasaki-disease-exploration/ and open the file temporalVariabilityExploration.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 temporalVariabilityExploration.Rmd.