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get_summary_records: Create Summary Records

get_summary_records: Create Summary Records
In admiral: ADaM in R Asset Library

View source: R/get_summary_records.R

get_summary_recordsR Documentation

Create Summary Records

Description

[Deprecated] The get_summary_records() has been deprecated in favor of derive_summary_records() (call it with the dataset_add argument and without the dataset argument).

It is not uncommon to have an analysis need whereby one needs to derive an analysis value (AVAL) from multiple records. The ADaM basic dataset structure variable DTYPE is available to indicate when a new derived records has been added to a dataset.

Usage

get_summary_records(dataset, by_vars, filter = NULL, set_values_to = NULL)

Arguments

dataset

Input dataset

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

Default value

none

by_vars

Grouping variables

Variables to consider for generation of groupwise summary records.

Default value

none

filter

Filter condition as logical expression to apply during summary calculation. By default, filtering expressions are computed within by_vars as this will help when an aggregating, lagging, or ranking function is involved.

For example,

  • filter_rows = (AVAL > mean(AVAL, na.rm = TRUE)) will filter all AVAL values greater than mean of AVAL with in by_vars.

  • filter_rows = (dplyr::n() > 2) will filter n count of by_vars greater than 2.

Default value

NULL

set_values_to

Variables to be set

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

Set a list of variables to some specified value for the new records

  • LHS refer to a variable.

  • RHS refers to the values to set to the variable. This can be a string, a symbol, a numeric value, an expression or NA. If summary functions are used, the values are summarized by the variables specified for by_vars.

For example: 

  set_values_to = exprs(
    AVAL = sum(AVAL),
    PARAMCD = "TDOSE",
    PARCAT1 = "OVERALL"
  )
Default value

NULL

Details

This function only creates derived observations and does not append them to the original dataset observations. If you would like to this instead, see the derive_summary_records() function.

Value

A data frame of derived records.

See Also

derive_summary_records(), derive_var_merged_summary()

Other deprecated: call_user_fun(), date_source(), derive_param_extreme_record(), derive_var_dthcaus(), derive_var_extreme_dt(), derive_var_extreme_dtm(), dthcaus_source()

Examples

library(tibble)

adeg <- tribble(
  ~USUBJID,   ~EGSEQ, ~PARAM,             ~AVISIT,    ~EGDTC,             ~AVAL, ~TRTA,
  "XYZ-1001", 1,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385,   NA_character_,
  "XYZ-1001", 2,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399,   NA_character_,
  "XYZ-1001", 3,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396,   NA_character_,
  "XYZ-1001", 4,      "QTcF Int. (msec)", "Visit 2",  "2016-03-08T09:45", 384,   "Placebo",
  "XYZ-1001", 5,      "QTcF Int. (msec)", "Visit 2",  "2016-03-08T09:48", 393,   "Placebo",
  "XYZ-1001", 6,      "QTcF Int. (msec)", "Visit 2",  "2016-03-08T09:51", 388,   "Placebo",
  "XYZ-1001", 7,      "QTcF Int. (msec)", "Visit 3",  "2016-03-22T10:45", 385,   "Placebo",
  "XYZ-1001", 8,      "QTcF Int. (msec)", "Visit 3",  "2016-03-22T10:48", 394,   "Placebo",
  "XYZ-1001", 9,      "QTcF Int. (msec)", "Visit 3",  "2016-03-22T10:51", 402,   "Placebo",
  "XYZ-1002", 1,      "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399,   NA_character_,
  "XYZ-1002", 2,      "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410,   NA_character_,
  "XYZ-1002", 3,      "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392,   NA_character_,
  "XYZ-1002", 4,      "QTcF Int. (msec)", "Visit 2",  "2016-03-06T09:50", 401,   "Active 20mg",
  "XYZ-1002", 5,      "QTcF Int. (msec)", "Visit 2",  "2016-03-06T09:53", 407,   "Active 20mg",
  "XYZ-1002", 6,      "QTcF Int. (msec)", "Visit 2",  "2016-03-06T09:56", 400,   "Active 20mg",
  "XYZ-1002", 7,      "QTcF Int. (msec)", "Visit 3",  "2016-03-24T10:50", 412,   "Active 20mg",
  "XYZ-1002", 8,      "QTcF Int. (msec)", "Visit 3",  "2016-03-24T10:53", 414,   "Active 20mg",
  "XYZ-1002", 9,      "QTcF Int. (msec)", "Visit 3",  "2016-03-24T10:56", 402,   "Active 20mg"
)

# Summarize the average of the triplicate ECG interval values (AVAL)
get_summary_records(
  adeg,
  by_vars = exprs(USUBJID, PARAM, AVISIT),
  set_values_to = exprs(
    AVAL = mean(AVAL, na.rm = TRUE),
    DTYPE = "AVERAGE"
  )
)

# Derive more than one summary variable
get_summary_records(
  adeg,
  by_vars = exprs(USUBJID, PARAM, AVISIT),
  set_values_to = exprs(
    AVAL = mean(AVAL),
    ASTDTM = min(convert_dtc_to_dtm(EGDTC)),
    AENDTM = max(convert_dtc_to_dtm(EGDTC)),
    DTYPE = "AVERAGE"
  )
)

# Sample ADEG dataset with triplicate record for only AVISIT = 'Baseline'
adeg <- tribble(
  ~USUBJID,   ~EGSEQ, ~PARAM,             ~AVISIT,    ~EGDTC,             ~AVAL, ~TRTA,
  "XYZ-1001", 1,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:50", 385,   NA_character_,
  "XYZ-1001", 2,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:52", 399,   NA_character_,
  "XYZ-1001", 3,      "QTcF Int. (msec)", "Baseline", "2016-02-24T07:56", 396,   NA_character_,
  "XYZ-1001", 4,      "QTcF Int. (msec)", "Visit 2",  "2016-03-08T09:48", 393,   "Placebo",
  "XYZ-1001", 5,      "QTcF Int. (msec)", "Visit 2",  "2016-03-08T09:51", 388,   "Placebo",
  "XYZ-1001", 6,      "QTcF Int. (msec)", "Visit 3",  "2016-03-22T10:48", 394,   "Placebo",
  "XYZ-1001", 7,      "QTcF Int. (msec)", "Visit 3",  "2016-03-22T10:51", 402,   "Placebo",
  "XYZ-1002", 1,      "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 399,   NA_character_,
  "XYZ-1002", 2,      "QTcF Int. (msec)", "Baseline", "2016-02-22T07:58", 410,   NA_character_,
  "XYZ-1002", 3,      "QTcF Int. (msec)", "Baseline", "2016-02-22T08:01", 392,   NA_character_,
  "XYZ-1002", 4,      "QTcF Int. (msec)", "Visit 2",  "2016-03-06T09:53", 407,   "Active 20mg",
  "XYZ-1002", 5,      "QTcF Int. (msec)", "Visit 2",  "2016-03-06T09:56", 400,   "Active 20mg",
  "XYZ-1002", 6,      "QTcF Int. (msec)", "Visit 3",  "2016-03-24T10:53", 414,   "Active 20mg",
  "XYZ-1002", 7,      "QTcF Int. (msec)", "Visit 3",  "2016-03-24T10:56", 402,   "Active 20mg"
)

# Compute the average of AVAL only if there are more than 2 records within the
# by group
get_summary_records(
  adeg,
  by_vars = exprs(USUBJID, PARAM, AVISIT),
  filter = n() > 2,
  set_values_to = exprs(
    AVAL = mean(AVAL, na.rm = TRUE),
    DTYPE = "AVERAGE"
  )
)

admiral documentation built on June 26, 2025, 1:08 a.m.

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