humbertomtzbta / medicaldata

Data Package for Medical Datasets

medicaldata

Overview

This is a data package with 17 medical datasets for teaching Reproducible Medical Research with R. The link to the pkgdown reference website for {medicaldata} is here and in the links at the right. This package will be useful for anyone teaching R to medical professionals, including doctors, nurses, trainees, and students.

These datasets range from reconstructed versions of James Lind’s scurvy dataset (1757) and the original Streptomycin for Tuberculosis trial (1948), a 2012 RCT of indomethacin to prevent post-ERCP pancreatitis that I was involved in, to cohort data on SARS-CoV2 testing results (2020). Many of the datasets come from the American Statistical Association’s TSHS (Teaching Statistics in the Health Sciences) Resources Portal, maintained by Carol Bigelow at the University of Massachusetts (with permission). A growing number of datasets in the dev version were generously donated by Frank Harrell from his website here. These datasets are currently only in the dev version of the package on github.com, which should make it to CRAN in January 2022.

How to Install and Use {medicaldata} Datasets

1. Install the stable, current CRAN version with install.packages("medicaldata"). If you want to try out the in-development version (which may have new datasets and vignettes, but which may also be intermittently wonky), install with: remotes::install_github("higgi13425/medicaldata")

2. Then load the package with library(medicaldata)

3. Then you can list the datasets available with data(package = "medicaldata")

4. Then assign a particular dataset to a named object in your environment with:
   covid <- medicaldata::covid_testing
   where covid is the name of the new object, and covid_testing is the name of the dataset.
   

5. Articles (vignettes) on how to use the datasets can be found at the pkgdown website under the Articles tab.

6. You can click on the links below to view the description document and/or codebook for each dataset. This information is also available under the Reference tab above, or within R by using help(dataset_name).
   

Please Donate Datasets

If you have access to data from a randomized, controlled clinical trial, or a prospective cohort study, or even a case-control study, please consider obtaining the appropriate permissions, anonymizing the data, and donating the dataset for teaching purposes to add to this package. Open an issue on the github page (source code link at the top right) to open the discussion of a data donation. I am happy to help with anonymization.

List of Datasets

Click on links below for more details about the dataset itself in the Description Document, and more details about the variables included in the dataset in the Codebook. Note that each dataset also has a help file that you can use within R or RStudio, by entering help("dataset_name") in the Console pane.

Dataset	Description document	Codebook
strep_tb	strep_tb_desc	strep_tb_codebook
scurvy	scurvy_desc	scurvy_codebook
indo_rct	indo_rct_desc	indo_rct_codebook
polyps	polyps_desc	polyps_codebook
covid_testing	covid_desc	covid_codebook
blood_storage	blood_storage_desc	blood_storage_codebook
cytomegalovirus	cytomegalovirus_desc	cytomegalovirus_codebook
esoph_ca	esoph_ca_desc	esoph_ca_codebook
laryngoscope	laryngoscope_desc	laryngoscope_codebook
licorice_gargle	licorice_gargle_desc	licorice_gargle_codebook
opt	opt_desc	opt_codebook
cath (dev)	cath_desc	cath_codebook
smartpill	smartpill_desc	smartpill_codebook
supraclavicular	supraclavicular_desc	supraclavicular_codebook
indometh	indometh_desc	indometh_codebook
theoph	theoph_desc	theoph_codebook