xportr-package {xportr} | R Documentation |
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", "hms")
Updating Options
For a single session, an option can be changed by
options(<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 Eli.Miller@AtorusResearch.com (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:
Report bugs at https://github.com/atorus-research/xportr/issues