derive_vars_transposed: Derive Variables by Transposing and Merging a Second Dataset

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

Derive Variables by Transposing and Merging a Second Dataset

Description

Adds variables from a vertical dataset after transposing it into a wide one.

Usage

derive_vars_transposed(
  dataset,
  dataset_merge,
  by_vars,
  id_vars = NULL,
  key_var,
  value_var,
  filter = NULL,
  relationship = NULL
)

Arguments

dataset	Input dataset The variables specified by the by_vars argument are expected to be in the dataset. Default value none
dataset_merge	Dataset to transpose and merge The variables specified by the by_vars, id_vars, key_var and value_var arguments are expected. The variables by_vars, id_vars, key_var have to be a unique key. Default value none
by_vars	Grouping variables Keys used to merge dataset_merge with dataset. Default value none
id_vars	ID variables Variables (excluding by_vars and key_var) that uniquely identify each observation in dataset_merge. Default value NULL
key_var	The variable of dataset_merge containing the names of the transposed variables Default value none
value_var	The variable of dataset_merge containing the values of the transposed variables Default value none
filter	Expression used to restrict the records of dataset_merge prior to transposing Default value NULL
relationship	Expected merge-relationship between the by_vars variable(s) in dataset and dataset_merge (after transposition) This argument is passed to the dplyr::left_join() function. See https://dplyr.tidyverse.org/reference/mutate-joins.html#arguments for more details. Permitted values "one-to-one", "one-to-many", "many-to-one", "many-to-many", NULL Default value NULL

Details

1. The records from the dataset to transpose and merge (dataset_merge) are restricted to those matching the filter condition, if provided.

2. The records from dataset_merge are checked to ensure they are uniquely identified using by_vars, id_vars and key_var.

3. dataset_merge is transposed (from "tall" to "wide"), with new variables added whose names come from key_var and values come from value_var.

4. The transposed dataset is merged with the input dataset using by_vars as keys. If a relationship has been provided, this merge must satisfy the relationship, otherwise an error is thrown.

Note that unlike other ⁠derive_vars_*()⁠ functions, the final step may cause new records to be added to the input dataset. The relationship argument can be specified to ensure this does not happen inadvertently.

Value

The input dataset with transposed variables from dataset_merge added

See Also

derive_vars_atc()

General Derivation Functions for all ADaMs that returns variable appended to dataset: derive_var_extreme_flag(), derive_var_joined_exist_flag(), derive_var_merged_ef_msrc(), derive_var_merged_exist_flag(), derive_var_merged_summary(), derive_var_obs_number(), derive_var_relative_flag(), derive_vars_cat(), derive_vars_computed(), derive_vars_joined(), derive_vars_merged(), derive_vars_merged_lookup()

Examples

library(tibble)
library(dplyr, warn.conflicts = FALSE)

# Adding ATC classes to CM using FACM
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"
)

cm %>%
  derive_vars_transposed(
    dataset_merge = facm,
    by_vars = exprs(USUBJID, CMREFID = FAREFID),
    id_vars = exprs(FAGRPID),
    key_var = FATESTCD,
    value_var = FASTRESC
  ) %>%
  select(USUBJID, CMDECOD, starts_with("CMATC"))

# Note: the `id_vars` argument here is needed to uniquely identify
# rows of dataset_merge and avoid duplicates-related errors.
# Compare the above call to when `id_vars = NULL`:

try(
  cm %>%
    derive_vars_transposed(
      dataset_merge = facm,
      by_vars = exprs(USUBJID, CMREFID = FAREFID),
      id_vars = NULL,
      key_var = FATESTCD,
      value_var = FASTRESC
    )
)

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