ox_metadata: Metadata in a list of dataframes

In acobos/ox: Reads OpenClinica xml export files

Description

Returns a list of dataframes containing metadata, from a parsed OpenClinica odm1.3 .xml export file provided as argument.

Usage

ox_metadata(parsed_xml)

Arguments

parsed_xml

An object of class XMLInternalDocument, as returned by XML::xmlParse().

Value

A list containing the following elements:

• file_info: a list with .xml file information.

• global_vars: a list with global study variables.

• event_def: a dataframe of event definitions.

• event_ref: a dataframe of event references.

• form_def: a dataframe of form definitions.

• form_ref: a dataframe of form references.

• group_def: a dataframe of (item) group definitions.

• group_ref: a dataframe of (item) group references.

• codelist: a dataframe of codelists.

• codelist_item: a dataframe of codelist items.

• codelist_ref: a dataframe of codelist references.

• units: a dataframe of unit definitions.

• sites: a dataframe of study sites.

• subjects: a dataframe of study subjects.

Examples

# The example odm1.3 xml file address
my_file <- system.file("extdata",
                       "odm1.3_full_example.xml",
                       package = "ox",
                       mustWork = TRUE)

# Parsing the xml file
library(XML)
doc <- xmlParse(my_file)

# Get metadata
md <- ox_metadata(doc)
class(md)
names(md)

# Accessing metadata elements:
# Event definitions
head(md$event_def)

# Codelist items
head(md$codelist_item)

# etc.

acobos/ox documentation built on May 13, 2019, 12:17 p.m.