In Roche-GSK/admiral: ADaM in R Asset Library

knitr::opts_chunk$set(
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library(admiraldev)

Introduction

To support the safety analysis, it is quite common to define specific grouping of events. One of the most common ways is to group events or medications by a specific medical concept such as a Standard MedDRA Queries (SMQs) or WHO-Drug Standardized Drug Groupings (SDGs).

To help with the derivation of these variables, the {admiral} function derive_vars_query() can be used. This function takes as input the dataset (dataset) where the grouping must occur (e.g ADAE) and a dataset containing the required information to perform the derivation of the grouping variables (dataset_queries).

The dataset passed to the dataset_queries argument of the derive_vars_query() function can be created by the create_query_data() function. For SMQs and SDGs company-specific functions for accessing the SMQ and SDG database need to be passed to the create_query_data() function (see the description of the get_terms_fun argument for details).

This vignette describes the expected structure and content of the dataset passed to the dataset_queries argument in the derive_vars_query() function.

Structure of the Query Dataset

Variables

Variable | Scope | Type | Example Value ------- | ----- | ------ | ----- PREFIX | The prefix used to define the grouping variables | Character | "SMQ01" GRPNAME | The value provided to the grouping variables name| Character | "Immune-Mediated Guillain-Barre Syndrome" SRCVAR | The variable used to define the grouping. Used in conjunction with TERMCHAR | Character | "AEDECOD" TERMCHAR | A term used to define the grouping. Used in conjunction with SRCVAR | Character | "GUILLAIN-BARRE SYNDROME" TERMNUM | A code used to define the grouping. Used in conjunction with SRCVAR | Integer | 10018767 GRPID | Id number of the query. This could be a SMQ identifier | Integer | 20000131 SCOPE | Scope (Broad/Narrow) of the query | Character | BROAD, NARROW, NA SCOPEN | Scope (Broad/Narrow) of the query | Integer | 1, 2, NA VERSION | The version of the dictionary | Character | "20.1"

Bold variables are required in dataset_queries: an error is issued if any of these variables is missing. TERMCHAR is only REQUIRED if there is character variable named in SRCVAR. TERMNUM is only REQUIRED if there is numeric variable named in SRCVAR. When SRCVAR contains both character and numeric variables, then both TERMCHAR and TERMNUM are required. Other variables are optional.

The VERSION variable is not used by derive_vars_query() but can be used to check if the dictionary version of the queries dataset and the analysis dataset are in line.

Required Content

Each row must be unique within the dataset.

As described above, the variables PREFIX, GRPNAME, SRCVAR, TERMCHAR and TERMNUM are required. The combination of these variables will allow the creation of the grouping variable.

Input

• PREFIX must be a character string starting with 2 or 3 letters, followed by a 2-digits number (e.g. "CQ01").

• GRPNAME must be a non missing character string and it must be unique within PREFIX.

• SRCVAR must be a non missing character string.

  • Each value in SRCVAR represents a variable from dataset used to define the grouping variables (e.g. AEDECOD,AEBODSYS, AELLTCD).

  • The function derive_vars_query() will check that each value given in SRCVAR has a corresponding variable in the input dataset and issue an error otherwise.

  • Different SRCVAR variables may be specified within a PREFIX.

• TERMCHAR must be a character string. This must be populated if TERMNUM is missing.

• TERMNUM must be an integer. This must be populated if TERMCHAR is missing.

Output

• PREFIX will be used to create the grouping variable appending the suffix "NAM". This variable will now be referred to as ABCzzNAM: the name of the grouping variable.

  • E.g. PREFIX == "SMQ01" will create the SMQ01NAM variable.

  • For each PREFIX, a new ABCzzNAM variable is created in dataset.

• [GRPNAME]{#GRPNAME} will be used to populate the corresponding ABCzzNAM variable.

• SRCVAR will be used to identify the variables from dataset used to perform the grouping (e.g. AEDECOD,AEBODSYS, AELLTCD).

• TERMCHAR (for character variables), TERMNUM (for numeric variables) will be used to identify the records meeting the criteria in dataset based on the variable defined in SRCVAR.

• Result:

  • For each record in dataset, where the variable defined by SRCVAR match a term from the TERMCHAR (for character variables) or TERMNUM (for numeric variables) in the datasets_queries, ABCzzNAM is populated with GRPNAME.

  • Note: The type (numeric or character) of the variable defined in SRCVAR is checked in dataset. If the variable is a character variable (e.g. AEDECOD), it is expected that TERMCHAR is populated, if it is a numeric variable (e.g. AEBDSYCD), it is expected that TERMNUM is populated, otherwise an error is issued.

Example

In this example, one standard MedDRA query (PREFIX = "SMQ01") and one customized query (PREFIX = "CQ02") are defined to analyze the adverse events.

• The standard MedDRA query variable SMQ01NAM [PREFIX] will be populated with "Standard Query 1" [GRPNAME] if any preferred term (AEDECOD) [SRCVAR] in dataset is equal to "AE1" or "AE2" [TERMCHAR]

• The customized query (CQ02NAM) [PREFIX] will be populated with "Query 2" [GRPNAME] if any Low Level Term Code (AELLTCD) [SRCVAR] in dataset is equal to 10 [TERMNUM] or any preferred term (AEDECOD) [SRCVAR] in dataset is equal to "AE4" [TERMCHAR].

Query Dataset (ds_query)

PREFIX | GRPNAME | SRCVAR | TERMCHAR | TERMNUM | ------- | ----- | ------ | ----- | ----- | ----- SMQ01| Standard Query 1 | AEDECOD | AE1 | SMQ01| Standard Query 1 | AEDECOD | AE2 | CQ02| Query 2 | AELLTCD | | 10 CQ02| Query 2 | AEDECOD | AE4|

Adverse Event Dataset (ae)

USUBJID | AEDECOD | AELLTCD ------- | ----- | ------ 0001 | AE1 | 101 | 0001 | AE3 | 10| | 0001 | AE4 | 120 | 0001 | AE5 | 130 |

Output Dataset

Generated by calling derive_vars_query(dataset = ae, dataset_queries = ds_query).

USUBJID | AEDECOD | AELLTCD | SMQ01NAM |CQ02NAM ------- | ----- | ------ | ----- | ----- 0001 | AE1 | 101 | Standard Query 1 | 0001 | AE3 | 10| | Query 2 0001 | AE4 | 120 | | Query 2 0001 | AE5 | 130 | |

Subject 0001 has one event meeting the Standard Query 1 criteria (AEDECOD = "AE1") and two events meeting the customized query (AELLTCD = 10 and AEDECOD = "AE4").

Optional Content

When standardized MedDRA Queries are added to the dataset, it is expected that the name of the query (ABCzzNAM) is populated along with its number code (ABCzzCD), and its Broad or Narrow scope (ABCzzSC).

The following variables can be added to queries_datset to derive this information.

Input

• GRPID must be an integer.

• SCOPE must be a character string. Possible values are: "BROAD", "NARROW" or NA.

• SCOPEN must be an integer. Possible values are: 1, 2 or NA.

Output

• GRPID, SCOPE and SCOPEN will be used in the same way as GRPNAME (see here) and will help in the creation of the ABCzzCD, ABCzzSC and ABCzzSCN variables.

Output Variables

These variables are optional and if not populated in dataset_queries, the corresponding output variable will not be created:

PREFIX | GRPNAME | GRPID | SCOPE |SCOPEN | Variables created ------- | ----- | ------ | ----- | ----- | ----- SMQ01| Query 1 | XXXXXXXX | NARROW | 2 | SMQ01NAM, SMQ01CD, SMQ01SC, SMQ01SCN SMQ02| Query 2 | XXXXXXXX |BROAD | | SMQ02NAM, SMQ02CD, SMQ02SC SMQ03| Query 3 | XXXXXXXX | |1 | SMQ03NAM, SMQ03CD, SMQ03SCN SMQ04| Query 4 | XXXXXXXX | | | SMQ04NAM, SMQ04CD SMQ05| Query 5| | | | SMQ05NAM

Roche-GSK/admiral documentation built on April 14, 2025, 12:36 p.m.