ctrdata
for clinical trial informationctrdata
on a R systemctrdata
ctrdata
on a R systemThe R Project website (https://www.r-project.org/) provides installers for the R system.
Alternatively, the R system can be used from software products such as R Studio (https://www.rstudio.com/products/RStudio/), which includes an open source integrated development environment (IDE), or Microsoft R Open (https://mran.microsoft.com/open/).
General information on the ctrdata
package is available here: https://github.com/rfhb/ctrdata.
The above should install package ctrdata
into the user’s library. If this installation does not succeed, the following sections offer potential solutions.
For using the development version of package ctrdata
, install from GitHub:
A remote or a local mongo database server can be used with the package ctrdata
. Suggested installation instructions for a local database server are here. An example of a remote mongo database server is here.
Functions in package ctrdata
that start with ctr...
require access to internet resources via https
. Package ctrdata
checks and automatically uses the proxy that is set under MS Windows in system settings.
However, proxy settings need to be set by the user for other operating systems and for authenticating proxies, such as follows:
On MS Windows, it seems recommended to not use UNC notation (such as \\server\directory
) for specifying the user’s library location:
As noted in the README for package ctrdata
, on MS Windows the cygwin environment has to be installed, into the local directory c:\cygwin
. The applications php, bash, perl, cat and sed in the cygwin environment are required for function ctrLoadQueryIntoDb()
of package ctrdata
(other functions in the package do not have this requirement). The installation of a minimal cygwin environment on MS Windows can be done from package ctrdata
as follows:
If need be, a proxy can be specified:
Users who want or need to install cygwin manually can download the setup executable from here. In MS Windows command window or Powershell window, use the following command line. The parameters are explained here.
ctrdata
These functions open the browser, where the user can start searching for trials of interest.
Refine the search until the trials of interest are listed in the browser. Currently, the total number of trials that can be retrieved with package ctrdata
is intentionally set to 5000 (CTGOV).
Using operating system functions.
The next steps are executed in the R environment:
# find names of fields of interest in database:
dbFindFields(namepart = "status",
allmatches = TRUE)
# [1] "overall_status" "b1_sponsor.b31_and_b32_status_of_the_sponsor"
# [3] "p_end_of_trial_status" "location.status"
# Get all records that have values in all specified fields.
# Note that b31_... is a field within the array b1_...
result <- dbGetFieldsIntoDf(fields = c("b1_sponsor.b31_and_b32_status_of_the_sponsor",
"p_end_of_trial_status"))
# Tabulate the status of the clinical trial on the date of information retrieval
with(result,
table("Status" = p_end_of_trial_status,
"Sponsor type" = b1_sponsor.b31_and_b32_status_of_the_sponsor))
# Sponsor type
# Status Commercial Non-Commercial
# Completed 138 30
# Not Authorised 3 0
# Ongoing 339 290
# Prematurely Ended 35 4
# Restarted 8 0
# Temporarily Halted 14 4