Description
Creates Safety Results Summary in XML to Upload to EudraCT, or ClinicalTrials.gov.
Description
The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by EudraCT and formats them into the precise requirements to directly upload an XML file into the web portal, with no further data entry by hand.
README.md
eudract
The goal of eudract is to provide tools to easily produce summaries of safety data from clinical trials that can easily be uploaded into eudraCT or ClinTrials.gov .
An additional feature produces commonly used tables and figures that feature in statistical reports and papers for clinical trials.
Installation
You can install from CRAN directly with
install.packages("eudract")
You can install the very latest version on github with:
install.packages("devtools")
devtools::install_github("shug0131/eudract_pkg")
Documentation
https://eudract-tool.medschl.cam.ac.uk provides full documentation
Go and read the help pages within R ?eudract::safety_summary
safety_statistics <- safety_summary(safety,
exposed=c("Experimental"=60,"Control"=67))
simple <- tempfile(fileext = ".xml")
eudract <- tempfile(fileext = ".xml")
ct <- tempfile(fileext = ".xml")
simple_safety_xml(safety_statistics, simple)
eudract_convert(input=simple,
output=eudract)
clintrials_gov_convert(input=simple,
original=system.file("extdata", "1234.xml", package ="eudract"),
output=ct)
\dontrun{
# This needs a real user account to work
clintrials_gov_upload(
input=simple,
orgname="CTU",
username="Student",
password="Guinness",
studyid="1234"
)
}
And for produce standard reporting outputs
library(eudract)
safety_statistics <- safety_summary(safety,
exposed=c("Control"=99, "Experimental"=101))
safety_statistics$GROUP
#> title subjectsAffectedBySeriousAdverseEvents
#> 1 Control 15
#> 2 Experimental 33
#> subjectsAffectedByNonSeriousAdverseEvents deathsResultingFromAdverseEvents
#> 1 15 9
#> 2 24 22
#> subjectsExposed deathsAllCauses
#> 1 99 9
#> 2 101 22
head( incidence_table(safety_statistics, type="serious") )
#> System Organ Class Preferred Term
#> 1 Blood and lymphatic system disorders B-cell lymphoma
#> 2 Cardiac disorders Cardiac arrest
#> 3 Cardiac failure congestive
#> 4 Gastrointestinal disorders Abdominal pain
#> 5 Gastroenteritis viral
#> 6 Gastrointestinal haemorrhage
#> Control (N = 99) Experimental (N = 101)
#> 1 1% (1, 1) 0% (0, 0)
#> 2 1% (1, 1) 0% (0, 0)
#> 3 0% (0, 0) 1% (1, 1)
#> 4 1% (1, 1) 0% (0, 0)
#> 5 0% (0, 0) 1% (1, 1)
#> 6 0% (0, 0) 1% (1, 1)
relative_risk_table(safety_statistics, type="serious")
#> System Organ Class Preferred Term Relative Risk (C.I.)
#> 1 Hepatobiliary disorders Cholecystitis acute 0.98 (0.0605, 15.9)
#> 2 Immune system disorders Vasculitis 1.96 (0.175, 22)
#> 3 Surgical and medical procedures Hip arthroplasty 1.96 (0.175, 22)
#> 4 Vascular disorders Deep vein thrombosis 2.94 (0.301, 28.8)
#> 5 Pulmonary embolism 0.98 (0.0605, 15.9)
dot_plot(safety_statistics, type="serious", base=4)
