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://shug0131.github.io/eudraCT/ 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)