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"Withdrawn").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),
and 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