clintrials_gov_convert: applies a conversion using xslt from a simple xml file to a...

In eudract: Creates Safety Results Summary in XML to Upload to EudraCT, or ClinicalTrials.gov

applies a conversion using xslt from a simple xml file to a ClinicalTrials.gov compatible file, and checks against the schema

Description

applies a conversion using xslt from a simple xml file to a ClinicalTrials.gov compatible file, and checks against the schema

Usage

clintrials_gov_convert(
  input,
  original,
  output,
  xslt = system.file("extdata", "simpleToCtGov.xslt", package = "eudract"),
  schema_input = system.file("extdata", "simple.xsd", package = "eudract"),
  schema_results = system.file("extdata", "RRSUploadSchema.xsd", package = "eudract"),
  schema_output = system.file("extdata", "ProtocolRecordSchema.xsd", package = "eudract"),
  soc = system.file("extdata", "soc.xml", package = "eudract")
)

Arguments

input	a character string giving the file path to the simple xml file
original	a character string giving the file path to the study file downloaded from ClinicalTrials.gov
output	a character string naming the output file
xslt	a character string giving the file path to the xslt script. Defaults to the script provided in this package
schema_input	a character string giving the file path to the schema for the simple xml file. Defaults to the schema provided in this package
schema_results	a character string giving the file path to the schema for the results section of the output. A copy was downloaded and is provided in this package as the default.
schema_output	a character string giving the file path to the schema for the overall output. A copy was downloaded and is provided in this package as the default.
soc	a character string giving an xml file that contains the System Organ Class look-up table going from EudraCT numbers to ClinicalTrials words.

Value

the output from the validation against the schema. A new file is created as a side-effect, which is suitable to upload into ClinicalTrials.gov. This over-writes the file given in original with the additional safety events.

See Also

safety_summary simple_safety_xml

Examples

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)
## Not run: 
  # This needs a real user account to work
  clintrials_gov_upload(
    input=simple,
    orgname="CTU",
    username="Student",
    password="Guinness",
    studyid="1234"
    )


## End(Not run)

eudract documentation built on Aug. 10, 2023, 1:10 a.m.