epicodr

Import, primary coding and export functions for data of the National Pandemic Cohort Network NAPKON.

💾 Versions & Download

The latest versions of epicodr can be found here: Releases

🔨 How to use this package

Using this package, you can import SÜP, HAP and POP data exported from SecuTrial by the Transfer-Office, set variable and value labels, format date variables, perform primary coding, as well as export the data, e.g. in SPSS format.

Tutorial

You can find a tutorial on how to use this package on YouTube at NUKLEUS ECU.

Step-by-Step Guide

  1. Install a R runtime environment and git on your computer. Provide Internet access.
  2. Create a R file and put the following code inside:
# Install package remotes
if(!require(remotes)) install.packages("remotes")

# Install package epicodr
# replace "release" with a specific version, if necessary
# See section *Versions* for more details
remotes::install_github("nukleus-ecu/epicodr@*release")

# Load package epicodr
library(epicodr)

# Specifiy location where to find data zip file
zip_file_path <- "data/import/NAME_OF_EXPORT_FILE.zip"

# Import the zip file data
data <- zip_file_path %>% 
  read_tsExport(separator = ";", decimal = ",")

# Execute primary coding on data
data_primary_coded <- data %>% 
  # place coding function accordingly, e.g., primary_coding_suep() or primary_coding_hap() or primary_coding_pop()
  primary_coding_suep()
  
# Execute Post-COVID-Syndrom Score (PCS score) for SUEP data
# if you only want to use the primary-coding function for the PCS score, use line 49
# if you already primary-coded your data using lines 40-42, use line 51
# please specify if you want the PCS score with (prom = "Yes") or without (prom = "No") patient reported outcome measures (PROMs)
# for detailed information abou PCS score with and without PROMs see primary-coding manual for SUEP (link below)
data_primary_coded_pcs <- primary_coding_suep_pcs_score(data, prom = "No")

data_primary_coded_pcs <- primary_coding_suep_pcs_score(data_primary_coded, prom = "No")
  
# Prepare data for SPSS export (remove .factor variables, add value labels, 
# optionally remove original date variables and set default missing values)
# - Set rm_stdates = FALSE if you want to keep original secutrial date variables
# - set_missings = TRUE, assign general missing values for the whole data set. 
#   Type "missing_labels_default" into console (without quotes) in order to 
#    check default values that are set to missing.
# - Additional Options: 
#   - keep_date_vars: character vector of date variable names that should be 
#     kept when rm_stdates = TRUE. Default: "birthdate_score"
#   - missing_labels: character vector that defines variable labels that should 
#     be set as missing value. Default: missing_labels_default
#   - missing_values: numeric vector that defines variable values that should be 
#     set as missing value. Default: NULL
data_spss_export_prepared <- prepare_spss_export(data_primary_coded, 
                                                 rm_stdates = TRUE, 
                                                 set_missings = TRUE)

# Export the prepared data in R to formats of other statistical software e.g. SPSS (sav) to export folder
# For other formats replace 'data_spss_export_prepared' with 'data_primary_coded' and "sav" with (one of "dta", "sas", "sav", "xpt")
write_tsExport(data_spss_export_prepared, format = "sav", path = "data/export/", metadata = TRUE)
  1. Run the script.
  2. Data is exported to folder data/export.

Alternative: Clone this Repository

  1. Install a R runtime environment and git on your computer. Provide Internet access.
  2. Clone this repository: git clone https://github.com/nukleus-ecu/epicodr.git
  3. Export data from secuTrial and place the *.zip file in data/import/.
  4. Create a new R script and add previously shown code for sample import, primary coding and SPSS export or create a new R script by yourself.
  5. Data is exported to folder data/export.

✏️ Supported data structure

Descriptions of the primary codings of the NAPKON cohort platforms SÜP, POP and HAP are available at the following link:

https://cloud.napkon.de/s/kgSLW7gkBExBYfC?path=%2F06_Prim%C3%A4rkodierung%20Datenauswertung__Primary%20coding%20Data%20analysis

Additionally, there are manuals that include variable categorizations, aids for calculating scores, defining normal ranges of laboratory parameters and clinical parameters. Further explanations are also available in the tutorial presentation.

Repository structure

This repository is structured as follows: - R contains all R code - man contains all manuals to ecu-functions

💻 R code structure

The R code is structured as follows: - R contains platform independent and platform specific implementations: - read-tsExport.R contains import functions - write-tsExport.R contains export functions, e.g. for export to SPSS (.sav) - primary-coding.R contains platform independent helper functions used in platform specific primary coding scripts - primary-coding-suep.R contains platform specific functions for primary coding for platform SUEP - primary-coding-hap.R contains platform specific functions for primary coding for platform HAP - primary-coding-pop.R contains platform specific functions for primary coding for platform POP