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.
| 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.
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.
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.
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 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.
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].
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 |
ae)| USUBJID | AEDECOD | AELLTCD |
|---|---|---|
| 0001 | AE1 | 101 |
| 0001 | AE3 | 10 |
| 0001 | AE4 | 120 |
| 0001 | AE5 | 130 |
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").
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.
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.
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.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 |