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Get Query Variables

Source: R/derive_vars_query.R
get_vars_query.Rd

Create a table for the input dataset which binds the necessary rows for a derive_vars_query() call with the relevant SRCVAR, TERM_NAME_ID and a temporary index if it is necessary

Note: This function is the first step performed in derive_vars_query() requested by some users to be present independently from it.

Usage

get_vars_query(dataset, dataset_queries)

Arguments

dataset

Input dataset

dataset_queries

A dataset containing required columns PREFIX, GRPNAME, SRCVAR, TERMCHAR and/or TERMNUM, and optional columns GRPID, SCOPE, SCOPEN.

create_query_data() can be used to create the dataset.

Value

The processed query dataset with SRCVAR and TERM_NAME_ID so that that can be merged to the input dataset to execute the derivations outlined by dataset_queries.

Details

This function can be used to derive CDISC variables such as SMQzzNAM, SMQzzCD, SMQzzSC, SMQzzSCN, and CQzzNAM in ADAE and ADMH, and variables such as SDGzzNAM, SDGzzCD, and SDGzzSC in ADCM. An example usage of this function can be found in the OCCDS vignette.

A query dataset is expected as an input to this function. See the Queries Dataset Documentation vignette for descriptions, or call data("queries") for an example of a query dataset.

For each unique element in PREFIX, the corresponding "NAM" variable will be created. For each unique PREFIX, if GRPID is not "" or NA, then the corresponding "CD" variable is created; similarly, if SCOPE is not "" or NA, then the corresponding "SC" variable will be created; if SCOPEN is not "" or NA, then the corresponding "SCN" variable will be created.

For each record in dataset, the "NAM" variable takes the value of GRPNAME if the value of TERMCHAR or TERMNUM in dataset_queries matches the value of the respective SRCVAR in dataset. Note that TERMCHAR in dataset_queries dataset may be NA only when TERMNUM is non-NA and vice versa. The matching is case insensitive. The "CD", "SC", and "SCN" variables are derived accordingly based on GRPID, SCOPE, and SCOPEN respectively, whenever not missing.

See also

create_query_data()

Utilities used within Derivation functions: call_user_fun(), extract_unit(), get_flagged_records(), get_not_mapped()

Examples

library(tibble)
data("queries")
adae <- tribble(
  ~USUBJID, ~ASTDTM, ~AETERM, ~AESEQ, ~AEDECOD, ~AELLT, ~AELLTCD,
  "01", "2020-06-02 23:59:59", "ALANINE AMINOTRANSFERASE ABNORMAL",
  3, "Alanine aminotransferase abnormal", NA_character_, NA_integer_,
  "02", "2020-06-05 23:59:59", "BASEDOW'S DISEASE",
  5, "Basedow's disease", NA_character_, 1L,
  "03", "2020-06-07 23:59:59", "SOME TERM",
  2, "Some query", "Some term", NA_integer_,
  "05", "2020-06-09 23:59:59", "ALVEOLAR PROTEINOSIS",
  7, "Alveolar proteinosis", NA_character_, NA_integer_
)
get_vars_query(adae, queries)
#> # A tibble: 2 × 21
#>   USUBJID ASTDTM AETERM AESEQ SMQ02NAM SMQ02CD SMQ02SC SMQ02SCN SMQ03NAM SMQ03CD
#>   <chr>   <chr>  <chr>  <dbl> <chr>      <int> <chr>      <int> <chr>      <int>
#> 1 02      2020-… BASED…     5 NA            NA NA            NA NA            NA
#> 2 05      2020-… ALVEO…     7 NA            NA NA            NA NA            NA
#> # ℹ 11 more variables: SMQ03SC <chr>, SMQ03SCN <int>, SMQ05NAM <chr>,
#> #   SMQ05CD <int>, SMQ05SC <chr>, SMQ05SCN <int>, CQ01NAM <chr>, CQ04NAM <chr>,
#> #   CQ04CD <int>, CQ06NAM <chr>, CQ06CD <int>