dbFindFields: Find names of fields in the database collection

In ctrdata: Retrieve and Analyze Clinical Trials in Public Registers

Find names of fields in the database collection

Description

Given part of the name of a field of interest to the user, this function returns the full field names used in records that were previously loaded into a collection (using ctrLoadQueryIntoDb). Only names of fields that have a value in the collection can be returned. Set sample = FALSE to force screening all records in the collection for field names, see below.

Usage

dbFindFields(namepart = ".*", con, sample = TRUE, verbose = FALSE)

Arguments

namepart	A character string (can be a regular expression, including Perl-style) to be searched among all field names (keys) in the collection, case-insensitive. The default '".*"' lists all fields.
con	A connection object, see section 'Databases' in ctrdata.
sample	If TRUE (default), uses a sample of only 5 trial records per register to identify fields, to rapidly return a possibly incomplete set of field names. If FALSE, uses all trial records in the collection, which will take more time with more trials but ensures to returns all names of all fields in the collection.
verbose	If TRUE, prints additional information (default FALSE).

Details

The full names of child fields are returned in dot notation (e.g., clinical_results.outcome_list.outcome.measure.class_list.class.title) In addition, names of parent fields (e.g., clinical_results) are returned. Data in parent fields is typically complex (nested), see dfTrials2Long for easily handling it. For field definitions of the registers, see "Definition" in ctrdata-registers. Note: When dbFindFields is first called after ctrLoadQueryIntoDb, it will take a moment.

Value

Vector of strings with full names of field(s) found, ordered by register and alphabet, see examples. Names of the vector are the names of the register holding the respective fields. The field names can be fed into dbGetFieldsIntoDf to extract the data for the field(s) from the collection into a data frame.

Examples

dbc <- nodbi::src_sqlite(
    dbname = system.file("extdata", "demo.sqlite", package = "ctrdata"),
    collection = "my_trials"
)

dbFindFields(namepart = "date", con = dbc)[1:5]

# view all 3350+ fields from all registers:

allFields <- dbFindFields(con = dbc, sample = FALSE)

if (interactive()) View(data.frame(
  register = names(allFields),
  field = allFields))

ctrdata documentation built on Sept. 30, 2024, 9:39 a.m.