ctcovidstop: Clinical trials that stopped during the Covid-19 pandemic

This R package provides two databases of ClinicalTrials.gov NCT Numbers corresponding to clinical trials that were "stopped" (had their overall status changed to "Terminated," "Suspended," or "Withdrawn"). The c19stoppedtrials dataset contains NCT numbers for all trials that stopped between 2019-12-01 (the month of the first human cases of SARS-CoV-2) and 2022-11-30 (three-year data cutoff). Trials that stopped during the pandemic were checked for whether they started again in December 2023, to allow at least one year of follow-up for the restart_date and restart_status columns. The comparator dataset contains NCT numbers for trials that stopped in the three years prior to the bounds for the c19stoppedtrials dataset (2016-12-01 to 2019-11-30).

The c19stoppedtrials dataset indicates the date that a trial was stopped, whether it was started again and on what date, and the contents of the "why stopped?" field on the date the trial stopped. This dataset also includes columns with manually coded data for whether the "why stopped?" field explicitly indicates that the reason for stopping included the SARS-CoV-2 pandemic.

Manually extracted data columns were single-coded by Dr Benjamin Gregory Carlisle. To ensure data quality, a random sample of 100 trials were tripled-coded by two other independent raters. A Light's kappa of 1 was calculated among the three sets of ratings, indicating perfect agreement.

The comparator dataset for stopped trials for the three years prior includes all the same columns as the c19stoppedtrials dataset, except for the manually coded fields whether the trial stopped due to the SARS-CoV-2 pandemic.

To install and use

This package is not available on CRAN, and must be installed via Github:

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

After installation, the package and data set can be loaded as follows:

library(ctcovidstop)

data(c19stoppedtrials)
data(comparator)

This package provides two data frames, c19stoppedtrials and comparator, which can be loaded via the R package with data(c19stoppedtrials) and data(comparator), respectively. The same data frames are also provided as CSV files in this repository as inst/extdata/c19stoppedtrials.csv and inst/extdata/comparator.csv.

Dataset: c19stoppedtrials, trials stopped during the SARS-Cov-2 pandemic

c19stoppedtrials contains 13,323 rows of 8 columns. See below for example rows:

nctid	stop_date	stop_status	restart_date	restart_status	why_stopped	covid19_explicit	restart_expected
NCT04007003	2019-12-02	Terminated	NA	NA	Sponsor decision	FALSE	NA
NCT03693833	2020-03-16	Suspended	2020-06-15	Recruiting	COVID-19	TRUE	FALSE
NCT04161976	2020-04-20	Suspended	2020-06-03	Recruiting	Enrollment on hold due to COVID-19 pandemic.	TRUE	TRUE

Each row in this data frame contains an NCT Number from ClinicalTrials.gov (nctid column) and a date on which the corresponding clinical trial record's overall status was first changed to "Terminated", "Suspended" or "Withdrawn" from any other overall status after 2019-12-01 but before 2022-11-30 (inclusive, stop_date column). The status that the trial was changed to on that date is indicated in the stop_status column.

A trial is only included if the study's overall status changed to "Terminated", "Suspended" or "Withdrawn" from any other overall status after 2019-12-01 but before 2022-11-30 (inclusive). If a trial's overall status was already "Terminated", "Suspended" or "Withdrawn" prior to 2019-12-01 and it never became active and then stopped after 2019-12-01, it would not be included, even if the "why stopped?" field was updated to include a reference to Covid-19 (e.g. NCT03365921).

If the trial started again (overall status changed from "Terminated", "Suspended" or "Withdrawn" to any other overall status) after being "stopped" according to the definition above by the date that this data set was last updated, the date that the trial restarted is recorded under restart_date; otherwise this column contains NA. The status that the stopped trial was changed to is indicated in the restart_status column.

The reason that the trial was stopped, as reported on the first stopped historical version of the clinical trial registry entry on ClinicalTrials.gov, is recorded in the why_stopped field. If no reason is given, this column contains NA.

If why_stopped cites Covid-19 explicitly as a reason why the trial was stopped, the covid19_explicit column is TRUE, otherwise FALSE. In the case that there is no value for why_stopped, covid19_explicit is FALSE. This data point was manually rated by BGC.

Trials that cite waning levels of Covid-19 infections, etc. as their rationale for stopping were not considered to be stopped because of Covid-19, and so covid19_explicit would be FALSE (e.g. NCT04390191).

The stop_date, stop_status and why_stopped will reflect only the first time the trial was stopped after 2019-12-01. In cases where a trial stops after 2019-12-01 without citing Covid-19 in the why_stopped field, starts again, and then stops a second time, citing Covid-19 as a reason why the study stopped (e.g. NCT03728504), the trial's covid19_explicit column is FALSE.

In cases where a trial was stopped with no rationale reported in the version of the trial history where it was stopped, and then in a later version, the why_stopped field was updated to include a rationale, the updated rationale for stopping would not be included in this data set.

If covid19_explicit is FALSE, restart_expected is NA. If covid19_explicit is TRUE, and there is also a stated expectation that the trial will start again in why_stopped, restart_expected is TRUE, otherwise FALSE. Trials that mention the study is "on hold" or "expected to resume" or that the stop was "temporary", etc. were included. This data point was manually rated by BGC.

Dataset: comparator, trials that stopped in a comparator arm taken 3 years prior

comparator contains 9665 rows of 6 columns. See below for example rows:

nctid	stop_date	stop_status	restart_date	restart_status	why_stopped
NCT02464891	2017-03-02	Terminated	NA	NA	NA
NCT02424955	2017-05-10	Suspended	2017-06-29	Recruiting	Logistics
NCT02937402	2019-09-05	Terminated	NA	NA	Slow accrual

Each row in this data frame contains an NCT Number from ClinicalTrials.gov (nctid column) and a date on which the corresponding clinical trial record's overall status was first changed to "Terminated", "Suspended" or "Withdrawn" from any other overall status after 2016-12-01 but before 2019-11-30 (inclusive, stop_date column). The status that the trial was changed to on that date is indicated in the stop_status column.

The definitions for the columns are identical to the c19stoppedtrials table, above.

The covid19_explicit and restart_expected columns are not included in the comparator dataset.

Citing ctcovidstop

These data are provided under a Creative Commons by-attribution licence.

Here is a BibTeX entry for ctcovidstop:

@Manual{ctcovidstop-carlisle,
  Title          = {ctcovidstop},
  Author         = {Carlisle, Benjamin Gregory},
  Organization   = {The Grey Literature},
  Address        = {Montreal, Canada},
  url            = {https://github.com/bgcarlisle/ctcovidstop},
  year           = 2022
}

If you use this data set and you found it useful, I would take it as a kindness if you cited it.

Best,

Benjamin Gregory Carlisle PhD