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Description

Data Package for Medical Datasets.

Provides access to well-documented medical datasets for teaching. Featuring several from the Teaching of Statistics in the Health Sciences website <https://www.causeweb.org/tshs/category/dataset/>, a few reconstructed datasets of historical significance in medical research, some reformatted and extended from existing R packages, and some data donations.

medicaldata

Overview

This is a data package with 15 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).

How to Install and Use {medicaldata} Datasets

  1. 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` <br> 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 codebook and/or description document for each dataset. This information is also available under the Reference tab above, or within R by using help(dataset_name).

Data Donations

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 to open the discussion of a data donation.

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.

DatasetDescription documentCodebook
strep_tbstrep_tb_descstrep_tb_codebook
scurvyscurvy_descscurvy_codebook
indo_rctindo_rct_descindo_rct_codebook
polypspolyps_descpolyps_codebook
covid_testingcovid_desccovid_codebook
blood_storageblood_storage_descblood_storage_codebook
cytomegaloviruscytomegalovirus_desccytomegalovirus_codebook
esoph_caesoph_ca_descesoph_ca_codebook
laryngoscopelaryngoscope_desclaryngoscope_codebook
licorice_garglelicorice_gargle_desclicorice_gargle_codebook
optopt_descopt_codebook
smartpillsmartpill_descsmartpill_codebook
supraclavicularsupraclavicular_descsupraclavicular_codebook
indomethindometh_descindometh_codebook
theophtheoph_desctheoph_codebook.

R-CMD-check

Metadata

Version

0.2.0

License

Unknown

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