event_joined {admiral}R Documentation

Create a event_joined Object

Description

The event_joined object is used to define events as input for the derive_extreme_event() and derive_vars_extreme_event() functions. This object should be used if the event does not depend on a single observation of the source dataset but on multiple observations. For example, if the event needs to be confirmed by a second observation of the source dataset.

The events are selected by calling filter_joined(). See its documentation for more details.

Usage

event_joined(
  dataset_name = NULL,
  condition,
  order = NULL,
  join_vars,
  join_type,
  first_cond = NULL,
  first_cond_lower = NULL,
  first_cond_upper = NULL,
  set_values_to = NULL,
  keep_source_vars = NULL,
  description = NULL
)

Arguments

dataset_name

Dataset name of the dataset to be used as input for the event. The name refers to the dataset specified for source_datasets in derive_extreme_event(). If the argument is not specified, the input dataset (dataset) of derive_extreme_event() is used.

Permitted Values: a character scalar

condition

An unquoted condition for selecting the observations, which will contribute to the extreme event.

The condition is applied to the joined dataset for selecting the confirmed observations. The condition can include summary functions like all() or any(). The joined dataset is grouped by the original observations. I.e., the summary function are applied to all observations up to the confirmation observation. For example in the oncology setting when using this function for confirmed best overall response, condition = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) & count_vals(var = AVALC.join, val = "NE") <= 1 selects observations with response "CR" and for all observations up to the confirmation observation the response is "CR" or "NE" and there is at most one "NE".

Permitted Values: an unquoted condition

order

If specified, the specified variables or expressions are used to select the first observation.

For handling of NAs in sorting variables see Sort Order.

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

join_vars

Variables to keep from joined dataset

The variables needed from the other observations should be specified for this parameter. The specified variables are added to the joined dataset with suffix ".join". For example to select all observations with AVALC == "Y" and AVALC == "Y" for at least one subsequent visit join_vars = exprs(AVALC, AVISITN) and condition = AVALC == "Y" & AVALC.join == "Y" & AVISITN < AVISITN.join could be specified.

The ⁠*.join⁠ variables are not included in the output dataset.

Permitted Values: a named list of expressions, e.g., created by exprs()

join_type

Observations to keep after joining

The argument determines which of the joined observations are kept with respect to the original observation. For example, if join_type = "after" is specified all observations after the original observations are kept.

Permitted Values: "before", "after", "all"

first_cond

Condition for selecting range of data

[Deprecated]

This argument is deprecated, please use first_cond_upper instead.

If this argument is specified, the other observations are restricted up to the first observation where the specified condition is fulfilled. If the condition is not fulfilled for any of the subsequent observations, all observations are removed.

Permitted Values: an unquoted condition

first_cond_lower

Condition for selecting range of data (before)

If this argument is specified, the other observations are restricted from the first observation before the current observation where the specified condition is fulfilled up to the current observation. If the condition is not fulfilled for any of the other observations, no observations are considered, i.e., the observation is not flagged.

This parameter should be specified if condition contains summary functions which should not apply to all observations but only from a certain observation before the current observation up to the current observation.

Permitted Values: an unquoted condition

first_cond_upper

Condition for selecting range of data (after)

If this argument is specified, the other observations are restricted up to the first observation where the specified condition is fulfilled. If the condition is not fulfilled for any of the other observations, no observations are considered, i.e., the observation is not flagged.

This parameter should be specified if condition contains summary functions which should not apply to all observations but only up to the confirmation assessment.

Permitted Values: an unquoted condition

set_values_to

A named list returned by exprs() defining the variables to be set for the event, e.g. exprs(PARAMCD = "WSP", PARAM = "Worst Sleeping Problems"). The values can be a symbol, a character string, a numeric value, NA or an expression.

Permitted Values: a named list of expressions, e.g., created by exprs()

keep_source_vars

Variables to keep from the source dataset

The specified variables are kept for the selected observations. The variables specified for by_vars (of derive_extreme_event()) and created by set_values_to are always kept.

Permitted Values: A list of expressions where each element is a symbol or a tidyselect expression, e.g., exprs(VISIT, VISITNUM, starts_with("RS")).

description

Description of the event

The description does not affect the derivations where the event is used. It is intended for documentation only.

Permitted Values: a character scalar

Value

An object of class event_joined

See Also

derive_extreme_event(), derive_vars_extreme_event(), event()

Source Objects: basket_select(), censor_source(), death_event, event(), event_source(), flag_event(), query(), records_source(), tte_source()

Examples

library(tibble)
library(dplyr)
library(lubridate)
# Derive confirmed best overall response (using event_joined())
# CR - complete response, PR - partial response, SD - stable disease
# NE - not evaluable, PD - progressive disease
adsl <- tribble(
  ~USUBJID, ~TRTSDTC,
  "1",      "2020-01-01",
  "2",      "2019-12-12",
  "3",      "2019-11-11",
  "4",      "2019-12-30",
  "5",      "2020-01-01",
  "6",      "2020-02-02",
  "7",      "2020-02-02",
  "8",      "2020-02-01"
) %>%
  mutate(TRTSDT = ymd(TRTSDTC))

adrs <- tribble(
  ~USUBJID, ~ADTC,        ~AVALC,
  "1",      "2020-01-01", "PR",
  "1",      "2020-02-01", "CR",
  "1",      "2020-02-16", "NE",
  "1",      "2020-03-01", "CR",
  "1",      "2020-04-01", "SD",
  "2",      "2020-01-01", "SD",
  "2",      "2020-02-01", "PR",
  "2",      "2020-03-01", "SD",
  "2",      "2020-03-13", "CR",
  "4",      "2020-01-01", "PR",
  "4",      "2020-03-01", "NE",
  "4",      "2020-04-01", "NE",
  "4",      "2020-05-01", "PR",
  "5",      "2020-01-01", "PR",
  "5",      "2020-01-10", "PR",
  "5",      "2020-01-20", "PR",
  "6",      "2020-02-06", "PR",
  "6",      "2020-02-16", "CR",
  "6",      "2020-03-30", "PR",
  "7",      "2020-02-06", "PR",
  "7",      "2020-02-16", "CR",
  "7",      "2020-04-01", "NE",
  "8",      "2020-02-16", "PD"
) %>%
  mutate(
    ADT = ymd(ADTC),
    PARAMCD = "OVR",
    PARAM = "Overall Response by Investigator"
  ) %>%
  derive_vars_merged(
    dataset_add = adsl,
    by_vars = exprs(USUBJID),
    new_vars = exprs(TRTSDT)
  )

derive_extreme_event(
  adrs,
  by_vars = exprs(USUBJID),
  order = exprs(ADT),
  mode = "first",
  source_datasets = list(adsl = adsl),
  events = list(
    event_joined(
      description = paste(
        "CR needs to be confirmed by a second CR at least 28 days later",
        "at most one NE is acceptable between the two assessments"
      ),
      join_vars = exprs(AVALC, ADT),
      join_type = "after",
      first_cond_upper = AVALC.join == "CR" &
        ADT.join >= ADT + 28,
      condition = AVALC == "CR" &
        all(AVALC.join %in% c("CR", "NE")) &
        count_vals(var = AVALC.join, val = "NE") <= 1,
      set_values_to = exprs(
        AVALC = "CR"
      )
    ),
    event_joined(
      description = paste(
        "PR needs to be confirmed by a second CR or PR at least 28 days later,",
        "at most one NE is acceptable between the two assessments"
      ),
      join_vars = exprs(AVALC, ADT),
      join_type = "after",
      first_cond_upper = AVALC.join %in% c("CR", "PR") &
        ADT.join >= ADT + 28,
      condition = AVALC == "PR" &
        all(AVALC.join %in% c("CR", "PR", "NE")) &
        count_vals(var = AVALC.join, val = "NE") <= 1,
      set_values_to = exprs(
        AVALC = "PR"
      )
    ),
    event(
      description = paste(
        "CR, PR, or SD are considered as SD if occurring at least 28",
        "after treatment start"
      ),
      condition = AVALC %in% c("CR", "PR", "SD") & ADT >= TRTSDT + 28,
      set_values_to = exprs(
        AVALC = "SD"
      )
    ),
    event(
      condition = AVALC == "PD",
      set_values_to = exprs(
        AVALC = "PD"
      )
    ),
    event(
      condition = AVALC %in% c("CR", "PR", "SD", "NE"),
      set_values_to = exprs(
        AVALC = "NE"
      )
    ),
    event(
      description = "set response to MISSING for patients without records in ADRS",
      dataset_name = "adsl",
      condition = TRUE,
      set_values_to = exprs(
        AVALC = "MISSING"
      ),
      keep_source_vars = exprs(TRTSDT)
    )
  ),
  set_values_to = exprs(
    PARAMCD = "CBOR",
    PARAM = "Best Confirmed Overall Response by Investigator"
  )
) %>%
  filter(PARAMCD == "CBOR")
[Package admiral version 1.1.1 Index]