Adds a record for BSA (Body Surface Area) using the specified derivation method for 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().
derive_param_bsa(
dataset,
by_vars,
method,
set_values_to = exprs(PARAMCD = "BSA"),
height_code = "HEIGHT",
weight_code = "WEIGHT",
get_unit_expr,
filter = NULL,
constant_by_vars = NULL
)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.
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 HEIGHT and WEIGHT.
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)
Derivation method to use. Note that HEIGHT is expected
in cm and WEIGHT is expected in kg:
Mosteller: sqrt(height * weight / 3600)
DuBois-DuBois: 0.20247 * (height/100) ^ 0.725 * weight ^ 0.425
Haycock: 0.024265 * height ^ 0.3964 * weight ^ 0.5378
Gehan-George: 0.0235 * height ^ 0.42246 * weight ^ 0.51456
Boyd: 0.0003207 * (height ^ 0.3) * (1000 * weight) ^ (0.7285 - (0.0188 * log10(1000 * weight)))
Fujimoto: 0.008883 * height ^ 0.663 * weight ^ 0.444
Takahira: 0.007241 * height ^ 0.725 * weight ^ 0.425
Permitted Values: character value
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
HEIGHT parameter code
The observations where PARAMCD equals the specified value are considered
as the HEIGHT assessments. It is expected that HEIGHT is measured in cm.
Permitted Values: character value
WEIGHT parameter code
The observations where PARAMCD equals the specified value are considered
as the WEIGHT assessments. It is expected that WEIGHT is measured in kg.
Permitted Values: character value
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
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: a condition
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 BSA at all visits where weight is measured. Otherwise
it will only be calculated at visits with both height and weight collected.
Permitted Values: list of variables created by exprs()
e.g. exprs(USUBJID, VISIT)
compute_bsa()
BDS-Findings Functions for adding Parameters/Records:
default_qtc_paramcd(),
derive_expected_records(),
derive_extreme_event(),
derive_extreme_records(),
derive_locf_records(),
derive_param_bmi(),
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()
library(tibble)
# Example 1: Derive BSA where height is measured only once using constant_by_vars
advs <- tibble::tribble(
~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT,
"01-701-1015", "HEIGHT", "Height (cm)", 170, "BASELINE",
"01-701-1015", "WEIGHT", "Weight (kg)", 75, "BASELINE",
"01-701-1015", "WEIGHT", "Weight (kg)", 78, "MONTH 1",
"01-701-1015", "WEIGHT", "Weight (kg)", 80, "MONTH 2",
"01-701-1028", "HEIGHT", "Height (cm)", 185, "BASELINE",
"01-701-1028", "WEIGHT", "Weight (kg)", 90, "BASELINE",
"01-701-1028", "WEIGHT", "Weight (kg)", 88, "MONTH 1",
"01-701-1028", "WEIGHT", "Weight (kg)", 85, "MONTH 2",
)
derive_param_bsa(
advs,
by_vars = exprs(USUBJID, VISIT),
method = "Mosteller",
set_values_to = exprs(
PARAMCD = "BSA",
PARAM = "Body Surface Area (m^2)"
),
get_unit_expr = extract_unit(PARAM),
constant_by_vars = exprs(USUBJID)
)
derive_param_bsa(
advs,
by_vars = exprs(USUBJID, VISIT),
method = "Fujimoto",
set_values_to = exprs(
PARAMCD = "BSA",
PARAM = "Body Surface Area (m^2)"
),
get_unit_expr = extract_unit(PARAM),
constant_by_vars = exprs(USUBJID)
)
# Example 2: Derive BSA where height is measured only once and keep only one record
# where both height and weight are measured.
derive_param_bsa(
advs,
by_vars = exprs(USUBJID, VISIT),
method = "Mosteller",
set_values_to = exprs(
PARAMCD = "BSA",
PARAM = "Body Surface Area (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_bsa(
advs,
by_vars = exprs(USUBJID, VISIT),
method = "Mosteller",
set_values_to = exprs(
PARAMCD = "BSA",
PARAM = "Body Surface Area (m^2)"
),
get_unit_expr = extract_unit(PARAM)
)
Run the code above in your browser using DataLab