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Adds a Parameter Based on First or Last Record from Multiple Sources

Source: R/derive_param_extreme_record.R
derive_param_extreme_record.Rd

[Superseded] The derive_param_extreme_record() function has been superseded in favor of derive_extreme_event().

Generates parameter based on the first or last observation from multiple source datasets, based on user-defined filter, order and by group criteria. All variables of the selected observation are kept.

Usage

derive_param_extreme_record(
  dataset = NULL,
  sources,
  source_datasets,
  by_vars = NULL,
  order,
  mode,
  set_values_to
)

Arguments

dataset

Input dataset

sources

Sources

A list of records_source() objects is expected.

source_datasets

Source datasets

A named list of datasets is expected. The dataset_name field of records_source() refers to the dataset provided in the list. The variables specified by the order and the by_vars arguments are expected after applying new_vars.

by_vars

Grouping variables

If the argument is specified, for each by group the observations are selected separately.

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

order

Sort order

If the argument is set to a non-null value, for each by group the first or last observation from the source datasets is selected with respect to the specified order. Variables created via new_vars e.g., imputed date variables, can be specified as well (see examples below).

Please note that NA is considered as the last value. I.e., if a order variable is NA and mode = "last", this observation is chosen while for mode = "first" the observation is chosen only if there are no observations where the variable is not NA.

Permitted Values: list of expressions created by exprs(), e.g., exprs(ADT, desc(AVAL))

mode

Selection mode (first or last)

If "first" is specified, for each by group the first observation with respect to order is included in the output dataset. If "last" is specified, the last observation is included in the output dataset.

Permitted Values: "first", "last"

set_values_to

Variables to be set

The specified variables are set to the specified values for the new observations.

A list of variable name-value pairs is expected.

  • LHS refers to a variable.

  • RHS refers to the values to set to the variable. This can be a string, a symbol, a numeric value or NA, e.g., exprs(PARAMCD = "PD", PARAM = "First Progressive Disease").

Value

The input dataset with the first or last observation of each by group added as new observations.

Details

The following steps are performed to create the output dataset:

  1. For each source dataset the observations as specified by the filter element are selected.

  2. Variables specified by new_vars are created for each source dataset.

  3. The first or last observation (with respect to the order variable) for each by group (specified by by_vars) from multiple sources is selected and added to the input dataset.

See also

Other superseded: date_source(), derive_var_dthcaus(), derive_var_extreme_dtm(), derive_var_extreme_dt(), dthcaus_source(), get_summary_records()

Examples

aevent_samp <- tibble::tribble(
  ~USUBJID, ~PARAMCD,                       ~PARAM,     ~RSSTDTC,
  "1",          "PD",  "First Progressive Disease", "2022-04-01",
  "2",          "PD",  "First Progressive Disease", "2021-04-01",
  "3",          "PD",  "First Progressive Disease", "2023-04-01"
)

cm <- tibble::tribble(
  ~STUDYID, ~USUBJID, ~CMDECOD,     ~CMSTDTC,
  "1001",        "1",    "ACT", "2021-12-25"
)

pr <- tibble::tribble(
  ~STUDYID, ~USUBJID, ~PRDECOD,     ~PRSTDTC,
  "1001",        "1",    "ACS", "2021-12-27",
  "1001",        "2",    "ACS", "2020-12-25",
  "1001",        "3",    "ACS", "2022-12-25",
)
derive_param_extreme_record(
  dataset = aevent_samp,
  sources = list(
    records_source(
      dataset_name = "cm",
      filter = CMDECOD == "ACT",
      new_vars = exprs(
        ADT = convert_dtc_to_dt(CMSTDTC),
        AVALC = CMDECOD
      )
    ),
    records_source(
      dataset_name = "pr",
      filter = PRDECOD == "ACS",
      new_vars = exprs(
        ADT = convert_dtc_to_dt(PRSTDTC),
        AVALC = PRDECOD
      )
    )
  ),
  source_datasets = list(cm = cm, pr = pr),
  by_vars = exprs(USUBJID),
  order = exprs(ADT),
  mode = "first",
  set_values_to = exprs(
    PARAMCD = "FIRSTACT",
    PARAM = "First Anti-Cancer Therapy"
  )
)
#> # A tibble: 6 × 6
#>   USUBJID PARAMCD  PARAM                     RSSTDTC    ADT        AVALC
#>   <chr>   <chr>    <chr>                     <chr>      <date>     <chr>
#> 1 1       PD       First Progressive Disease 2022-04-01 NA         NA   
#> 2 2       PD       First Progressive Disease 2021-04-01 NA         NA   
#> 3 3       PD       First Progressive Disease 2023-04-01 NA         NA   
#> 4 1       FIRSTACT First Anti-Cancer Therapy NA         2021-12-25 ACT  
#> 5 2       FIRSTACT First Anti-Cancer Therapy NA         2020-12-25 ACS  
#> 6 3       FIRSTACT First Anti-Cancer Therapy NA         2022-12-25 ACS