dfName2Value: Get value for variable of interest

In ctrdata: Retrieve and Analyze Clinical Trials in Public Registers

Get value for variable of interest

Description

Get information for variable of interest (e.g., clinical endpoints) from long data frame of protocol- or result-related trial information as returned by dfTrials2Long. Parameters 'valuename', 'wherename' and 'wherevalue' are matched using Perl regular expressions and ignoring case.

Usage

dfName2Value(df, valuename = "", wherename = "", wherevalue = "")

Arguments

df	A data frame (or tibble) with four columns ('_id', 'identifier', 'name', 'value') as returned by dfTrials2Long
valuename	A character string for the name of the field that holds the value of the variable of interest (e.g., a summary measure such as "endPoints.*tendencyValue.value")
wherename	(optional) A character string to identify the variable of interest among those that repeatedly occur in a trial record (e.g., "endPoints.endPoint.title")
wherevalue	(optional) A character string with the value of the variable identified by 'wherename' (e.g., "response")

Value

A data frame (or tibble, if tibble is loaded) that includes the values of interest, with columns '_id', 'identifier', 'name', 'value' (and 'where', with the contents of 'wherevalue' found at 'wherename'). Contents of 'value' are strings unless all its elements are numbers. The 'identifier' is generated by function dfTrials2Long to identify matching elements, e.g. endpoint descriptions and measurements.

Examples

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

dfwide <- dbGetFieldsIntoDf(
    fields = c(
        ## ctgov - typical results fields
        # "clinical_results.baseline.analyzed_list.analyzed.count_list.count",
        # "clinical_results.baseline.group_list.group",
        # "clinical_results.baseline.analyzed_list.analyzed.units",
        "clinical_results.outcome_list.outcome",
        "study_design_info.allocation",
        ## euctr - typical results fields
        # "trialInformation.fullTitle",
        # "baselineCharacteristics.baselineReportingGroups.baselineReportingGroup",
        # "trialChanges.hasGlobalInterruptions",
        # "subjectAnalysisSets",
        # "adverseEvents.seriousAdverseEvents.seriousAdverseEvent",
        "endPoints.endPoint",
        "subjectDisposition.recruitmentDetails"
    ), con = dbc
)

dflong <- dfTrials2Long(df = dfwide)

## get values for the endpoint 'response'
dfName2Value(
    df = dflong,
    valuename = paste0(
        "clinical_results.*measurement.value|",
        "clinical_results.*outcome.measure.units|",
        "endPoints.endPoint.*tendencyValue.value|",
        "endPoints.endPoint.unit"
    ),
    wherename = paste0(
        "clinical_results.*outcome.measure.title|",
        "endPoints.endPoint.title"
    ),
    wherevalue = "response"
)

ctrdata documentation built on Nov. 24, 2023, 5:11 p.m.