Below are some frequently asked questions about the defineR package. Click on the links below to navigate to the full question and answer content.
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.
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
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"))
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)
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.
Q: I have some XPT files already. Can I use them to generate metadata?
A: Yes. Use the
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>")
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.
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.
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>")
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.
Q: This template looks similar to the template in the SAS® Clinical Standards Toolkit. Are they the same?
A: No. The metadata template for the defineR package was taken from the book “Implementing CDISC Using SAS: An End-to-End Guide” by Chris Holland and Jack Shostak. This book was published by SAS Institute®, but the metadata format is different than what was used for the SAS® Clinical Standards Toolkit.