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What is a define.xml?
Q: I don’t quite understand what this is about. What is a define.xml? Do I need one?
A: The define.xml is a special XML file used to describe data sent to regulatory bodies for drug applications. If you don’t know what it is, then you don’t need one.
How do I generate a define.xml for ADaM?
Q: The defineR generator seems to always create a define.xml for SDTM. I want to create one for ADaM. How can I do that?
A: There is a parameter called type on
the write_define() function that you can use to specify an
SDTM or ADaM define. Here is an example:
# Get temporary directory for output
tmp <- tempdir()
# Create demo spreadsheet
pth <- write_metadata(tmp, type = "adam", demo = TRUE)
# Generate define for ADaM
res <- write_define(pth, tmp, type = "adam")
# View XML
# file.show(file.path(tmp, "define.adam.xml"))
# View check report
# file.show(file.path(tmp, "check.adam.pdf"))
# View HTML
# file.show(file.path(tmp, "define.adam.html"))
Where can I get a metadata template?
Q: I’d like to try out defineR. Where can I get a starting template?
A: You can generate a starting template. It it
recommended to start with the demo template, rather than a blank
template. To do that, set the demo option on the
write_metadata() function. Like this:
# Get temporary directory
tmp <- tempdir()
# Create metadata template
write_metadata(tmp,
type = "<sdtm or adam>",
demo = TRUE)Can I generate a define.xml for SEND?
Q: I am working on an animal study, and need to generate a define.xml for SEND. Can defineR do that?
A: Not at this time. If you desire this feature, please submit a request to the GitHub issue list.
Can I use my XPT files to generate a metadata file?
Q: I have some XPT files already. Can I use them to generate metadata?
A: Yes. Use the write_metadata()
function, and supply the src_dir parameter with the
directory that contains your XPT files. Like this:
# Get temporary directory
tmp <- tempdir()
# Create metadata template
write_metadata(tmp,
type = "<sdtm or adam>",
src_dir = "<source data path>")Can I use other files to generate a metadata file?
Q: What if I don’t have XPT files? Can I generate metadata from Excel files or SAS datasets?
A: Not in the current release. If you desire this feature, please submit a request to the GitHub issue list, and we can up the priority.
Does the package support define 2.1?
Q: Our organization is getting ready for define version 2.1. Does the defineR package support it?
A: Not yet. Define version 2.1 will be coming in a future release.
What if I want to use a different XSLT style sheet?
Q: I have a custom style sheet, and want to use it with defineR. Can I do that?
A: Yes. There is a global option to specify a custom style sheet. The option is called “defineR.xslt”, and you can set it as follows:
options("defineR.xslt" = "<path>")Can it read in an existing define.xml?
Q: I have a define.xml alread and want to create a metadata template from it. Can this package do it?
A: Not at this time. If there is sufficient interest in this feature, we can add it.
Is this the same template as the SAS® toolkit?
Q: This template looks exactly like the template in the SAS® Clinical Standards Toolkit. Are they the same?
A: Yes. The metadata template for the defineR package was taken directly from the SAS® template. This was done for ease of interchange/migration between the two systems.