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Derive ATC Class Variables

Source: R/derive_vars_transposed.R
derive_vars_atc.Rd

Add Anatomical Therapeutic Chemical class variables from FACM to ADCM.

Note: This is a wrapper function for the more generic derive_vars_transposed().

Usage

derive_vars_atc(
  dataset,
  dataset_facm,
  by_vars = exprs(USUBJID, CMREFID = FAREFID),
  id_vars = NULL,
  value_var = FASTRESC
)

Arguments

dataset

Input dataset

The variables specified by the by_vars argument are expected to be in the dataset.

dataset_facm

FACM dataset

The variables specified by the by_vars and value_var parameters, FAGRPID and FATESTCD are required

by_vars

Grouping variables

Keys used to merge dataset_facm with dataset.

id_vars

ID variables

Variables (excluding by_vars) that uniquely identify each observation in dataset_merge.

Permitted Values: list of variables created by exprs() e.g. exprs(USUBJID, VISIT)

value_var

The variable of dataset_facm containing the values of the transposed variables

Default: FASTRESC

Value

The input dataset with ATC variables added

See also

OCCDS Functions: derive_var_trtemfl(), derive_vars_query(), get_terms_from_db()

Examples

library(tibble)

cm <- tribble(
  ~USUBJID, ~CMGRPID, ~CMREFID, ~CMDECOD,
  "BP40257-1001", "14", "1192056", "PARACETAMOL",
  "BP40257-1001", "18", "2007001", "SOLUMEDROL",
  "BP40257-1002", "19", "2791596", "SPIRONOLACTONE"
)
facm <- tribble(
  ~USUBJID, ~FAGRPID, ~FAREFID, ~FATESTCD, ~FASTRESC,
  "BP40257-1001", "1", "1192056", "CMATC1CD", "N",
  "BP40257-1001", "1", "1192056", "CMATC2CD", "N02",
  "BP40257-1001", "1", "1192056", "CMATC3CD", "N02B",
  "BP40257-1001", "1", "1192056", "CMATC4CD", "N02BE",
  "BP40257-1001", "1", "2007001", "CMATC1CD", "D",
  "BP40257-1001", "1", "2007001", "CMATC2CD", "D10",
  "BP40257-1001", "1", "2007001", "CMATC3CD", "D10A",
  "BP40257-1001", "1", "2007001", "CMATC4CD", "D10AA",
  "BP40257-1001", "2", "2007001", "CMATC1CD", "D",
  "BP40257-1001", "2", "2007001", "CMATC2CD", "D07",
  "BP40257-1001", "2", "2007001", "CMATC3CD", "D07A",
  "BP40257-1001", "2", "2007001", "CMATC4CD", "D07AA",
  "BP40257-1001", "3", "2007001", "CMATC1CD", "H",
  "BP40257-1001", "3", "2007001", "CMATC2CD", "H02",
  "BP40257-1001", "3", "2007001", "CMATC3CD", "H02A",
  "BP40257-1001", "3", "2007001", "CMATC4CD", "H02AB",
  "BP40257-1002", "1", "2791596", "CMATC1CD", "C",
  "BP40257-1002", "1", "2791596", "CMATC2CD", "C03",
  "BP40257-1002", "1", "2791596", "CMATC3CD", "C03D",
  "BP40257-1002", "1", "2791596", "CMATC4CD", "C03DA"
)

derive_vars_atc(cm, facm)
#> Warning: Values from `FASTRESC` are not uniquely identified; output will contain
#> list-cols.
#> • Use `values_fn = list` to suppress this warning.
#> • Use `values_fn = {summary_fun}` to summarise duplicates.
#> • Use the following dplyr code to identify duplicates.
#>   {data} |>
#>   dplyr::summarise(n = dplyr::n(), .by = c(USUBJID, FAREFID, FATESTCD)) |>
#>   dplyr::filter(n > 1L)
#> # A tibble: 3 × 8
#>   USUBJID      CMGRPID CMREFID CMDECOD        ATC1CD    ATC2CD    ATC3CD ATC4CD
#>   <chr>        <chr>   <chr>   <chr>          <list>    <list>    <list> <list>
#> 1 BP40257-1001 14      1192056 PARACETAMOL    <chr [1]> <chr [1]> <chr>  <chr> 
#> 2 BP40257-1001 18      2007001 SOLUMEDROL     <chr [3]> <chr [3]> <chr>  <chr> 
#> 3 BP40257-1002 19      2791596 SPIRONOLACTONE <chr [1]> <chr [1]> <chr>  <chr>