cthist

This package provides functions for mass-downloading historical clinical trial registry entry data.

How to install

To install the stable version of cthist through CRAN:

install.packages("cthist")
library(cthist)

If you want the most recent development version of cthist, you will need to install devtools first, and then install via git:

install.packages("devtools")
library(devtools)
install_github("bgcarlisle/cthist")
library(cthist)

This package provides 3 for downloading historical clinical trial data from ClinicalTrials.gov

ClinicalTrials.gov functions

Download clinical trial version dates:

## Get all the dates and status updates when the registry entry for
## NCT02110043 changed

clinicaltrials_gov_dates("NCT02110043")
##  A tibble: 8 × 3
##  version date       status               
##     <int> <chr>      <chr>                
## 1       0 2014-04-08 RECRUITING
## 2       1 2014-09-22 RECRUITING
## 3       2 2014-10-13 RECRUITING
## 4       3 2016-03-15 RECRUITING
## 5       4 2016-12-20 RECRUITING
## 6       5 2017-07-04 RECRUITING
## 7       6 2017-07-26 ACTIVE_NOT_RECRUITING
## 8       7 2021-05-20 COMPLETED

## Get all the dates when NCT02110043 had a change in overall status

clinicaltrials_gov_dates("NCT02110043", status_change_only=TRUE)
##   A tibble: 3 × 3
##   version date       status               
##     <int> <chr>      <chr>                
## 1       0 2014-04-08 RECRUITING
## 2       6 2017-07-26 ACTIVE_NOT_RECRUITING
## 3       7 2021-05-20 COMPLETED

Download clinical trial registry entry version data:

## Get the 4th version of NCT02110043

version_data <- clinicaltrials_gov_version("NCT02110043", 4)

## Get the 2nd item (enrolment) for that version
version_data$enrol
## [1] 22

## Get the 3rd item (enrolment type) for that version
version_data$enroltype
## [1] "ESTIMATED"

Mass-download clinical trial registry entry versions:

## Download all data for all versions of NCT02110043 and store in
## variable `versions`

versions <- clinicaltrials_gov_download("NCT02110043")

Mass-download clinical trial registry entry versions for many trials and save to disk:

## Download all data for all versions of NCT02110043 and NCT03281616
## and save to versions.csv

clinicaltrials_gov_download(c("NCT02110043", "NCT03281616"), "versions.csv")

What data is extracted?

• Version number (1, 2, 3, etc.)
• Version date (ISO-8601)
• Overall status
• Start date
• Primary completion date
• Enrolment
• Enrolment type
• Inclusion and exclusion criteria
• Outcome measures
• Overall contacts
• Cetral contacts
• Responsible party
• Lead sponsor
• Collaborators
• “Why stopped?”
• Results reported
• References
• Organization study ID
• Secondary IDs

Note regarding ClinicalTrials.gov July 2023 website re-write

For cthist v >= 2.0.0, the method for downloading has been updated to reflect the new version of ClinicalTrials.gov. Because the data on the updated website are presented differently from the way they were scraped from the old version, there will be some changes. E.g. the overall status field is now in all-caps.

DRKS.de

Update as of 2022-12-11

DRKS.de has recently been updated in a manner that makes scraping data more difficult and so the functions related to DRKS.de have been deprecated, at least temporarily while I assess the changes.

Note on use

Please note that this script is provided under AGPL v 3, and so you may use it for any purpose, however if you modify it, you must provide access to your modified version or you are in violation of the terms of the license.

Citing cthist

@Manual{bgcarlisle-cthist,
  title          = {Analysis of Clinical Trial Registry Entry Histories Using the Novel {{R}} Package cthist},
  author         = {Carlisle, Benjamin Gregory},
  date           = {2022-07-01},
  journaltitle   = {PLOS ONE},
  shortjournal   = {PLOS ONE},
  volume         = {17},
  number         = {7},
  pages          = {e0270909},
  publisher      = {{Public Library of Science}},
  issn           = {1932-6203},
  doi            = {10.1371/journal.pone.0270909},
  url            = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0270909}
}

Please open an issue in the issue tracker above if you find a bug, need this package to download some historical trial data that it currently does not capture, or if you would like to collaborate on a project that uses this tool.

If you used my package in your research and you found it useful, I would take it as a kindness if you cited it.

Best,

Benjamin Gregory Carlisle PhD