Create an query object

A query object defines a query, e.g., a Standard MedDRA Query (SMQ), a Standardized Drug Grouping (SDG), or a customized query (CQ). It is used as input to create_query_data().

query(prefix, name = auto, id = NULL, add_scope_num = FALSE, definition = NULL)

Arguments

prefix

The value is used to populate PREFIX in the output dataset of create_query_data(), e.g., "SMQ03"

Default value

none

name

The value is used to populate GRPNAME in the output dataset of create_query_data(). If the auto keyword is specified, the variable is set to the name of the query in the SMQ/SDG database.

Permitted values

A character scalar or the auto keyword. The auto keyword is permitted only for queries which are defined by an basket_select() object.

Default value

auto

id

The value is used to populate GRPID in the output dataset of create_query_data(). If the auto keyword is specified, the variable is set to the id of the query in the SMQ/SDG database.

Permitted values

A integer scalar or the auto keyword. The auto keyword is permitted only for queries which are defined by an basket_select() object.

Default value

NULL

add_scope_num

Determines if SCOPEN in the output dataset of create_query_data() is populated

If the parameter is set to TRUE, the definition must be an basket_select() object.

Default: FALSE

Permitted values

TRUE, FALSE

Default value

FALSE

definition

Definition of terms belonging to the query

There are three different ways to define the terms:

• An basket_select() object is specified to select a query from the SMQ database.

• A data frame with columns SRCVAR and TERMCHAR or TERMNUM can be specified to define the terms of a customized query. The SRCVAR should be set to the name of the variable which should be used to select the terms, e.g., "AEDECOD" or "AELLTCD". SRCVAR does not need to be constant within a query. For example a query can be based on AEDECOD and AELLT.

  If SRCVAR refers to a character variable, TERMCHAR should be set to the value the variable. If it refers to a numeric variable, TERMNUM should be set to the value of the variable. If only character variables or only numeric variables are used, TERMNUM or TERMCHAR respectively can be omitted.

• A list of data frames and basket_select() objects can be specified to define a customized query based on custom terms and SMQs. The data frames must have the same structure as described for the previous item.

Permitted values

an basket_select() object, a data frame, or a list of data frames and basket_select() objects.

Default value

NULL

Value

An object of class query.

See also

create_query_data(), basket_select(), vignette("queries_dataset")

Source Objects: basket_select(), censor_source(), death_event, event(), event_joined(), event_source(), flag_event(), records_source(), tte_source()

Examples

# create a query for an SMQ
library(tibble)
library(dplyr, warn.conflicts = FALSE)

# create a query for a SMQ
query(
  prefix = "SMQ02",
  id = auto,
  definition = basket_select(
    name = "Pregnancy and neonatal topics (SMQ)",
    scope = "NARROW",
    type = "smq"
  )
)
#> <query> object
#> prefix: "SMQ02"
#> name: auto
#> id: auto
#> add_scope_num: FALSE
#> definition:
#>   <basket_select> object
#>   name: "Pregnancy and neonatal topics (SMQ)"
#>   id: NULL
#>   scope: "NARROW"
#>   type: "smq"

# create a query for an SDG
query(
  prefix = "SDG01",
  id = auto,
  definition = basket_select(
    name = "5-aminosalicylates for ulcerative colitis",
    scope = NA_character_,
    type = "sdg"
  )
)
#> <query> object
#> prefix: "SDG01"
#> name: auto
#> id: auto
#> add_scope_num: FALSE
#> definition:
#>   <basket_select> object
#>   name: "5-aminosalicylates for ulcerative colitis"
#>   id: NULL
#>   scope: "NA"
#>   type: "sdg"

# creating a query for a customized query
cqterms <- tribble(
  ~TERMCHAR, ~TERMNUM,
  "APPLICATION SITE ERYTHEMA", 10003041L,
  "APPLICATION SITE PRURITUS", 10003053L
) %>%
  mutate(SRCVAR = "AEDECOD")

query(
  prefix = "CQ01",
  name = "Application Site Issues",
  definition = cqterms
)
#> <query> object
#> prefix: "CQ01"
#> name: "Application Site Issues"
#> add_scope_num: FALSE
#> definition:
#> # A tibble: 2 × 3
#>   TERMCHAR                   TERMNUM SRCVAR 
#>   <chr>                        <int> <chr>  
#> 1 APPLICATION SITE ERYTHEMA 10003041 AEDECOD
#> 2 APPLICATION SITE PRURITUS 10003053 AEDECOD

# creating a customized query based on SMQs and additional terms
query(
  prefix = "CQ03",
  name = "Special issues of interest",
  definition = list(
    cqterms,
    basket_select(
      name = "Pregnancy and neonatal topics (SMQ)",
      scope = "NARROW",
      type = "smq"
    ),
    basket_select(
      id = 8050L,
      scope = "BROAD",
      type = "smq"
    )
  )
)
#> <query> object
#> prefix: "CQ03"
#> name: "Special issues of interest"
#> add_scope_num: FALSE
#> definition:
#>   c("APPLICATION SITE ERYTHEMA", "APPLICATION SITE PRURITUS")
#> c(10003041, 10003053)
#> c("AEDECOD", "AEDECOD")
#>   Pregnancy and neonatal topics (SMQ)
#> NULL
#> NARROW
#> smq
#>   NULL
#> 8050
#> BROAD
#> smq