Content of review 1, reviewed on February 07, 2023
This Technical Note describes the software tool Ricu, which is "R's Interface to Intensive Care Data". The core objective of this software tool and its accompanying study is "to develop a unified framework for analyzing data from five large, publicly available ICU datasets." The manuscript is well written, and the code for Ricu is made publicly available from GitHub (https://github.com/eth-mds/ricu). Importantly, this repository has been ascribed an OSI-approved GPL-3.0 license which encourages reuse. An alternative CRAN link is also provided in the manuscript (https://CRAN.R-project.org/package=ricu).
For the supporting data, AmsterdamUMCdb is Restricted Access and reviewers must first complete the Data or Specimens Only Research (DSOR) course from CITI. Likewise, the complete MIMIC-III, eICU, HiRID and MIMIC-IV datasets can be accessed by registering and setting up a credentialed account at PhysioNet (https://physionet.org/). Only credentialed users who sign the Data Use Agreement can access the files.
Minor comment
I initially encountered difficulty in running Ricu using RStudio. I used the MIMIC-III and eICU demo datasets to test the Ricu software tool, and I was unable to run the command explain_dictionary(). However, the troubleshooting guidelines that the authors provided were very helpful and I am now able to run Ricu on macOS Ventura. The troubleshooting guidelines are below:
You just need to run
library(ricu)
before running the explain_dictionary() function. Also, note that the line
remotes::install_github("eth-mds/ricu")
resulted in an error due to the remotes package not being installed (to fix this, you can just run install.packages("remotes"), or alternatively use the ricu version from CRAN which is installed with install.packages("ricu")).
I request that the authors add these troubleshooting details to the Ricu documentation.
Source
© 2023 the Reviewer.
References
Nicolas, B., Drago, P., Ida-Fong, U., Nicolai, M., Peter, B. 2023. ricu: R's interface to intensive care data. GigaScience.