Mental Health temporal trends in the children population

Analysis of the mental health trends in the children population admitted to an hospital site (inpatients and outpatients).

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/pediatric_psychiatric_ICD-10 codes_adjusted.csv: mapping of ICD codes to mental health 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.psy_peds_trends

Then open the file psy_peds_3.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 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
• specify if the race information is collected or not at your site (raceAvailable: set up as TRUE or 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 psy_peds_3.Rmd, as an output an html file named: psy_peds_3.Rmd.html and four png files will be generated in the output folder.