admiral (version 1.3.0)

derive_param_bmi: Adds a Parameter for BMI

Description

Adds a record for BMI/Body Mass Index using Weight and Height each by group (e.g., subject and visit) where the source parameters are available.

Note: This is a wrapper function for the more generic derive_param_computed().

Usage

derive_param_bmi(
  dataset,
  by_vars,
  set_values_to = exprs(PARAMCD = "BMI"),
  weight_code = "WEIGHT",
  height_code = "HEIGHT",
  get_unit_expr,
  filter = NULL,
  constant_by_vars = NULL
)

Value

The input dataset with the new parameter added. Note, a variable will only be populated in the new parameter rows if it is specified in by_vars.

Arguments

dataset

Input dataset

The variables specified by the by_vars argument are expected to be in the dataset. PARAMCD, and AVAL are expected as well.

The variable specified by by_vars and PARAMCD must be a unique key of the input dataset after restricting it by the filter condition (filter parameter) and to the parameters specified by weight_code and height_code.

Default value

none

by_vars

Grouping variables

For each group defined by by_vars an observation is added to the output dataset. Only variables specified in by_vars will be populated in the newly created records.

Permitted values

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

Default value

none

set_values_to

Variables to be set

The specified variables are set to the specified values for the new observations. For example exprs(PARAMCD = "MAP") defines the parameter code for the new parameter.

Permitted values

List of variable-value pairs

Default value

exprs(PARAMCD = "MAP")

weight_code

WEIGHT parameter code

The observations where PARAMCD equals the specified value are considered as the WEIGHT. It is expected that WEIGHT is measured in kg

Permitted values

character value

Default value

"WEIGHT"

height_code

HEIGHT parameter code

The observations where PARAMCD equals the specified value are considered as the HEIGHT. It is expected that HEIGHT is measured in cm

Permitted values

logical scalar

Default value

"HEIGHT"

get_unit_expr

An expression providing the unit of the parameter

The result is used to check the units of the input parameters.

Permitted values

An expression which is evaluable in the input dataset and results in a character value

Default value

none

filter

Filter condition

The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account.

Permitted values

an unquoted condition, e.g., AVISIT == "BASELINE"

Default value

NULL

constant_by_vars

By variables for when HEIGHT is constant

When HEIGHT is constant, the HEIGHT parameters (measured only once) are merged to the other parameters using the specified variables.

If height is constant (e.g. only measured once at screening or baseline) then use constant_by_vars to select the subject-level variable to merge on (e.g. USUBJID). This will produce BMI at all visits where weight is measured. Otherwise it will only be calculated at visits with both height and weight collected.

Default value

NULL

Details

The analysis value of the new parameter is derived as $$BMI = \frac{WEIGHT}{HEIGHT^2}$$

See Also

compute_bmi()

BDS-Findings Functions for adding Parameters/Records: default_qtc_paramcd(), derive_expected_records(), derive_extreme_event(), derive_extreme_records(), derive_locf_records(), derive_param_bsa(), derive_param_computed(), derive_param_doseint(), derive_param_exist_flag(), derive_param_exposure(), derive_param_framingham(), derive_param_map(), derive_param_qtc(), derive_param_rr(), derive_param_wbc_abs(), derive_summary_records()

Examples

# Example 1: Derive BMI where height is measured only once using constant_by_vars
advs <- tibble::tribble(
  ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVISIT,
  "01-701-1015", "HEIGHT", "Height (cm)", 147, "SCREENING",
  "01-701-1015", "WEIGHT", "Weight (kg)", 54.0, "SCREENING",
  "01-701-1015", "WEIGHT", "Weight (kg)", 54.4, "BASELINE",
  "01-701-1015", "WEIGHT", "Weight (kg)", 53.1, "WEEK 2",
  "01-701-1028", "HEIGHT", "Height (cm)", 163, "SCREENING",
  "01-701-1028", "WEIGHT", "Weight (kg)", 78.5, "SCREENING",
  "01-701-1028", "WEIGHT", "Weight (kg)", 80.3, "BASELINE",
  "01-701-1028", "WEIGHT", "Weight (kg)", 80.7, "WEEK 2"
)

derive_param_bmi(
  advs,
  by_vars = exprs(USUBJID, AVISIT),
  weight_code = "WEIGHT",
  height_code = "HEIGHT",
  set_values_to = exprs(
    PARAMCD = "BMI",
    PARAM = "Body Mass Index (kg/m^2)"
  ),
  get_unit_expr = extract_unit(PARAM),
  constant_by_vars = exprs(USUBJID)
)

# Example 2: Derive BMI where height is measured only once and keep only one record
# where both height and weight are measured.
derive_param_bmi(
  advs,
  by_vars = exprs(USUBJID, AVISIT),
  weight_code = "WEIGHT",
  height_code = "HEIGHT",
  set_values_to = exprs(
    PARAMCD = "BMI",
    PARAM = "Body Mass Index (kg/m^2)"
  ),
  get_unit_expr = extract_unit(PARAM)
)

# Example 3: Pediatric study where height and weight are measured multiple times
advs <- tibble::tribble(
  ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT,
  "01-101-1001", "HEIGHT", "Height (cm)", 47.1, "BASELINE",
  "01-101-1001", "HEIGHT", "Height (cm)", 59.1, "WEEK 12",
  "01-101-1001", "HEIGHT", "Height (cm)", 64.7, "WEEK 24",
  "01-101-1001", "HEIGHT", "Height (cm)", 68.2, "WEEK 48",
  "01-101-1001", "WEIGHT", "Weight (kg)", 2.6, "BASELINE",
  "01-101-1001", "WEIGHT", "Weight (kg)", 5.3, "WEEK 12",
  "01-101-1001", "WEIGHT", "Weight (kg)", 6.7, "WEEK 24",
  "01-101-1001", "WEIGHT", "Weight (kg)", 7.4, "WEEK 48",
)

derive_param_bmi(
  advs,
  by_vars = exprs(USUBJID, VISIT),
  weight_code = "WEIGHT",
  height_code = "HEIGHT",
  set_values_to = exprs(
    PARAMCD = "BMI",
    PARAM = "Body Mass Index (kg/m^2)"
  ),
  get_unit_expr = extract_unit(PARAM)
)