Frequently Asked Questions

Below are some frequently asked questions about the defineR package. Click on the links below to navigate to the full question and answer content.

Index

Content

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.

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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"))

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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)

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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.

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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>")

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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.

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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.

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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>")

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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.

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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.

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