derive_vars_joined {admiral}R Documentation

Add Variables from an Additional Dataset Based on Conditions from Both Datasets

Description

The function adds variables from an additional dataset to the input dataset. The selection of the observations from the additional dataset can depend on variables from both datasets. For example, add the lowest value (nadir) before the current observation.

Usage

derive_vars_joined(
  dataset,
  dataset_add,
  by_vars = NULL,
  order = NULL,
  new_vars = NULL,
  join_vars = NULL,
  filter_add = NULL,
  filter_join = NULL,
  mode = NULL,
  missing_values = NULL,
  check_type = "warning"
)

Arguments

dataset

Input dataset

The variables specified by by_vars are expected.

dataset_add

Additional dataset

The variables specified by the by_vars, the new_vars, the join_vars, and the order argument are expected.

by_vars

Grouping variables

The two datasets are joined by the specified variables. Variables from the additional dataset can be renamed by naming the element, i.e., ⁠by_vars = exprs(<name in input dataset> = <name in additional dataset>)⁠.

Permitted Values: list of variables created by exprs()

order

Sort order

If the argument is set to a non-null value, for each observation of the input dataset the first or last observation from the joined dataset is selected with respect to the specified order. The specified variables are expected in the additional dataset (dataset_add). If a variable is available in both dataset and dataset_add, the one from dataset_add is used for the sorting.

If an expression is named, e.g., exprs(EXSTDT = convert_dtc_to_dt(EXSTDTC), EXSEQ), a corresponding variable (EXSTDT) is added to the additional dataset and can be used in the filter conditions (filter_add, filter_join) and for join_vars and new_vars. The variable is not included in the output dataset.

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

new_vars

Variables to add

The specified variables from the additional dataset are added to the output dataset. Variables can be renamed by naming the element, i.e., ⁠new_vars = exprs(<new name> = <old name>)⁠.

For example new_vars = exprs(var1, var2) adds variables var1 and var2 from dataset_add to the input dataset.

And new_vars = exprs(var1, new_var2 = old_var2) takes var1 and old_var2 from dataset_add and adds them to the input dataset renaming old_var2 to new_var2.

Values of the added variables can be modified by specifying an expression. For example, new_vars = LASTRSP = exprs(str_to_upper(AVALC)) adds the variable LASTRSP to the dataset and sets it to the upper case value of AVALC.

If the argument is not specified or set to NULL, all variables from the additional dataset (dataset_add) are added.

Permitted Values: list of variables or named expressions created by exprs()

join_vars

Variables to use from additional dataset

Any extra variables required from the additional dataset for filter_join should be specified for this argument. Variables specified for new_vars do not need to be repeated for join_vars. If a specified variable exists in both the input dataset and the additional dataset, the suffix ".join" is added to the variable from the additional dataset.

If an expression is named, e.g., exprs(EXTDT = convert_dtc_to_dt(EXSTDTC)), a corresponding variable is added to the additional dataset and can be used in the filter conditions (filter_add, filter_join) and for new_vars. The variable is not included in the output dataset.

The variables are not included in the output dataset.

Permitted Values: list of variables or named expressions created by exprs()

filter_add

Filter for additional dataset (dataset_add)

Only observations from dataset_add fulfilling the specified condition are joined to the input dataset. If the argument is not specified, all observations are joined.

Variables created by order or new_vars arguments can be used in the condition.

Permitted Values: a condition

filter_join

Filter for the joined dataset

The specified condition is applied to the joined dataset. Therefore variables from both datasets dataset and dataset_add can be used.

Variables created by order or new_vars arguments can be used in the condition.

Permitted Values: a condition

mode

Selection mode

Determines if the first or last observation is selected. If the order argument is specified, mode must be non-null.

If the order argument is not specified, the mode argument is ignored.

Permitted Values: "first", "last", NULL

missing_values

Values for non-matching observations

For observations of the input dataset (dataset) which do not have a matching observation in the additional dataset (dataset_add) the values of the specified variables are set to the specified value. Only variables specified for new_vars can be specified for missing_values.

Permitted Values: named list of expressions, e.g., exprs(BASEC = "MISSING", BASE = -1)

check_type

Check uniqueness?

If "warning" or "error" is specified, the specified message is issued if the observations of the (restricted) joined dataset are not unique with respect to the by variables and the order.

This argument is ignored if order is not specified. In this case an error is issued independent of check_type if the restricted joined dataset contains more than one observation for any of the observations of the input dataset.

Permitted Values: "none", "warning", "error"

Details

  1. The variables specified by order are added to the additional dataset (dataset_add).

  2. The variables specified by join_vars are added to the additional dataset (dataset_add).

  3. The records from the additional dataset (dataset_add) are restricted to those matching the filter_add condition.

  4. The input dataset and the (restricted) additional dataset are left joined by the grouping variables (by_vars). If no grouping variables are specified, a full join is performed.

  5. The joined dataset is restricted by the filter_join condition.

  6. If order is specified, for each observation of the input dataset the first or last observation (depending on mode) is selected.

  7. The variables specified for new_vars are created (if requested) and merged to the input dataset. I.e., the output dataset contains all observations from the input dataset. For observations without a matching observation in the joined dataset the new variables are set as specified by missing_values (or to NA for variables not in missing_values). Observations in the additional dataset which have no matching observation in the input dataset are ignored.

Value

The output dataset contains all observations and variables of the input dataset and additionally the variables specified for new_vars from the additional dataset (dataset_add).

See Also

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

Examples

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

# Add AVISIT (based on time windows), AWLO, and AWHI
adbds <- tribble(
  ~USUBJID, ~ADY,
  "1",       -33,
  "1",        -2,
  "1",         3,
  "1",        24,
  "2",        NA,
)

windows <- tribble(
  ~AVISIT,    ~AWLO, ~AWHI,
  "BASELINE",   -30,     1,
  "WEEK 1",       2,     7,
  "WEEK 2",       8,    15,
  "WEEK 3",      16,    22,
  "WEEK 4",      23,    30
)

derive_vars_joined(
  adbds,
  dataset_add = windows,
  filter_join = AWLO <= ADY & ADY <= AWHI
)

# derive the nadir after baseline and before the current observation
adbds <- tribble(
  ~USUBJID, ~ADY, ~AVAL,
  "1",        -7,    10,
  "1",         1,    12,
  "1",         8,    11,
  "1",        15,     9,
  "1",        20,    14,
  "1",        24,    12,
  "2",        13,     8
)

derive_vars_joined(
  adbds,
  dataset_add = adbds,
  by_vars = exprs(USUBJID),
  order = exprs(AVAL),
  new_vars = exprs(NADIR = AVAL),
  join_vars = exprs(ADY),
  filter_add = ADY > 0,
  filter_join = ADY.join < ADY,
  mode = "first",
  check_type = "none"
)

# add highest hemoglobin value within two weeks before AE,
# take earliest if more than one
adae <- tribble(
  ~USUBJID, ~ASTDY,
  "1",           3,
  "1",          22,
  "2",           2
)

adlb <- tribble(
  ~USUBJID, ~PARAMCD, ~ADY, ~AVAL,
  "1",      "HGB",       1,   8.5,
  "1",      "HGB",       3,   7.9,
  "1",      "HGB",       5,   8.9,
  "1",      "HGB",       8,   8.0,
  "1",      "HGB",       9,   8.0,
  "1",      "HGB",      16,   7.4,
  "1",      "HGB",      24,   8.1,
  "1",      "ALB",       1,    42,
)

derive_vars_joined(
  adae,
  dataset_add = adlb,
  by_vars = exprs(USUBJID),
  order = exprs(AVAL, desc(ADY)),
  new_vars = exprs(HGB_MAX = AVAL, HGB_DY = ADY),
  filter_add = PARAMCD == "HGB",
  filter_join = ASTDY - 14 <= ADY & ADY <= ASTDY,
  mode = "last"
)

# Add APERIOD, APERIODC based on ADSL
adsl <- tribble(
  ~USUBJID, ~AP01SDT,     ~AP01EDT,     ~AP02SDT,     ~AP02EDT,
  "1",      "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
  "2",      "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
  mutate(across(ends_with("DT"), ymd)) %>%
  mutate(STUDYID = "xyz")

period_ref <- create_period_dataset(
  adsl,
  new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT)
)

period_ref

adae <- tribble(
  ~USUBJID, ~ASTDT,
  "1",      "2021-01-01",
  "1",      "2021-01-05",
  "1",      "2021-02-05",
  "1",      "2021-03-05",
  "1",      "2021-04-05",
  "2",      "2021-02-15",
) %>%
  mutate(
    ASTDT = ymd(ASTDT),
    STUDYID = "xyz"
  )

derive_vars_joined(
  adae,
  dataset_add = period_ref,
  by_vars = exprs(STUDYID, USUBJID),
  join_vars = exprs(APERSDT, APEREDT),
  filter_join = APERSDT <= ASTDT & ASTDT <= APEREDT
)

# Add day since last dose (LDRELD)
adae <- tribble(
  ~USUBJID, ~ASTDT,       ~AESEQ,
  "1",      "2020-02-02",      1,
  "1",      "2020-02-04",      2
) %>%
  mutate(ASTDT = ymd(ASTDT))

ex <- tribble(
  ~USUBJID, ~EXSDTC,
  "1",      "2020-01-10",
  "1",      "2020-01",
  "1",      "2020-01-20",
  "1",      "2020-02-03"
)

## Please note that EXSDT is created via the order argument and then used
## for new_vars, filter_add, and filter_join
derive_vars_joined(
  adae,
  dataset_add = ex,
  by_vars = exprs(USUBJID),
  order = exprs(EXSDT = convert_dtc_to_dt(EXSDTC)),
  new_vars = exprs(LDRELD = compute_duration(
    start_date = EXSDT, end_date = ASTDT
  )),
  filter_add = !is.na(EXSDT),
  filter_join = EXSDT <= ASTDT,
  mode = "last"
)
[Package admiral version 0.12.1 Index]