doc/02_redcap.md

In jlucasmckay/motionTools: Miscellaneous tools for human movement data and statistics

Redcap

This tutorial describes how to access Redcap datasets using functionality in motionTools.

Managing secrets

1. Request an API token from the Redcap instance.
   • The API token is essentially a password. It should never be synced to github or similar.
2. Store the API token in an .Renviron file in your project directory. The .gitignore file in motionTools is configured so that this file is ignored by any sync requests.
3. When downloading reports, the report ID can be obtained in the API playground section of the Redcap instance:
   • 
4. Supply your API token and this report ID to the ReadRedcapReport() function.

An example .Renviron file

Store secrets in an .Renviron file in the project directory. Add this plain text file to .gitignore. Here are the contents of a sample .Renviron:

fog_redcap_token=1XXXXDXXXX5XXXXGXXXXBXXXXCXXXX0C
clinic_redcap_token=1XXXXCXXXX4XXXXFXXXXAXXXXCXXXX0D

Note that the .Renviron file is only read at RStudio launch; if you create this file while developing a project restart the program prior to using it. Make sure that Sys.getenv("name_of_your_token") returns your token properly if you run into problems.

Reading a report into R

Again, your Redcap token should be stored in .Renviron within the project directory.

library(motionTools)
library(tidyverse)

redcap_data = ReadRedcapReport(token = Sys.getenv("clinic_redcap_token"), url = "https://redcap.emory.edu/api/", report_id = 31759) |> 
  group_by(record_id) |> 
  fill(first_name) |> 
  fill(last_name) |> 
  fill(dw_icd) |> 
  filter(redcap_repeat_instrument == "capture_session") |> 
  select(record_id,first_name,last_name,dw_icd,patient_fullpath_neurology) |> 
  mutate(directory = paste0("/Volumes/",patient_fullpath_neurology))

jlucasmckay/motionTools documentation built on Feb. 25, 2022, 7:53 a.m.