xportr-package: The 'xportr' package

In xportr: Utilities to Output CDISC SDTM/ADaM XPT Files

The xportr package

Description

xportr is designed to be a clinical workflow friendly method for outputting CDISC complaint data sets in R, to XPT version 5 files. It was designed with options in mind to allow for flexible setting of options while allowing projects and system administrators to set sensible defaults for their organizations workflows. Below are a list of options that can be set to customize how xportr works in your environment.

xportr options

• xportr.df_domain_name - The name of the domain "name" column in dataset metadata. Default: "dataset"

• xportr.df_label - The column noting the dataset label in dataset metadata. Default: "label"

• xportr.domain_name - The name of the domain "name" column in variable metadata. Default: "dataset"

• xportr.variable_name - The name of the variable "name" in variable metadata. Default: "variable"

• xportr.type_name - The name of the variable type column in variable metadata. Default: "type"

• xportr.label - The name of the variable label column in variable metadata. Default: "label"

• xportr.length - The name of the variable length column in variable metadata. Default: "length"

• xportr.order_name - The name of the variable order column in variable metadata. Default: "order"

• xportr.format_name - The name of the variable format column in variable metadata. Default: "format"

• xportr.format_verbose - The default argument for the 'verbose' argument for xportr_format. Default: "none"

• xportr.label_verbose - The default argument for the 'verbose' argument for xportr_label. Default: "none"

• xportr.length_verbose - The default argument for the 'verbose' argument for xportr_length. Default: "none"

• xportr.type_verbose - The default argument for the 'verbose' argument for xportr_type. Default: "none"

• xportr.character_types - The default character vector used to explicitly coerce R classes to character XPT types. Default: "character"

• xportr.character_metadata_types - The default character vector used to explicitly coerce R classes to character XPT types. Default: c("character", "char", "text", "date", "posixct", "posixt", "datetime", "time", "partialdate", "partialtime", "partialdatetime", "incompletedatetime", "durationdatetime", "intervaldatetime")'

• xportr.numeric_metadata_types - The default character vector used to explicitly coerce R classes to numeric XPT types. Default: c("integer", "numeric", "num", "float")

• xportr.numeric_types - The default character vector used to explicitly coerce R classes to numeric XPT types. Default: c("integer", "float", "numeric", "posixct", "posixt", "time", "date")

Updating Options

• For a single session, an option can be changed by ⁠option(<optionToChange> = <NewValue>)⁠

• To change an option for a single projects across sessions in that projects, place the options update in the .Rprofile in that project directory.

• To change an option for a user across all sessions, place the options update in the .Rprofile file in the users home directory.

• To change an option for all users in an R environment, place the options update in the .Rprofile.site file in the R home directory.

Author(s)

Maintainer: Eli Miller [e-mail] (ORCID)

Authors:

• Ben Straub

• Zelos Zhu

• Ethan Brockmann

• Vedha Viyash

• Andre Verissimo

• Sophie Shapcott

• Celine Piraux

• Kangjie Zhang

• Adrian Chan

• Sadchla Mascary

Other contributors:

• Atorus/GSK JPT [copyright holder]

See Also

Useful links:

• https://atorus-research.github.io/xportr/

• https://github.com/atorus-research/xportr

• Report bugs at https://github.com/atorus-research/xportr/issues

xportr documentation built on Oct. 8, 2024, 1:08 a.m.