Adds a parameter for Waist to Height Ratio using Waist Circumference and Height 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 admiral::derive_param_computed().
derive_param_waisthgt(
dataset,
by_vars,
wstcir_code = "WSTCIR",
height_code = "HEIGHT",
set_values_to = exprs(PARAMCD = "WAISTHGT"),
filter = NULL,
constant_by_vars = NULL,
get_unit_expr
)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 argument) and to the parameters
specified by wstcir_code and height_code.
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)
Waist Circumference parameter code
The observations where PARAMCD equals the specified value are considered
as the Waist Circumference.
Permitted Values: character value
Height parameter code
The observations where PARAMCD equals the specified value are considered as the Height.
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 = "RATIO") defines the parameter code
for the new parameter.
Permitted Values: List of variable-value pairs
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 Waist to Height Ratio at all visits where Waist Circumference is measured.
Otherwise it will only be calculated at visits with both Height and Waist Circumference
collected.
Permitted Values: list of variables created by exprs(), e.g. exprs(USUBJID, VISIT)
An expression providing the unit of the parameter
The result is used to check the units of the input parameters. If the units are not consistent within each parameter, an error will be thrown.
Additionally, if the input parameters are measured in different units but are mutually convertible (e.g., centimeters for one parameter and inches for another), an automatic conversion will be performed in order to uniform the values before calculating the ratio.
Note: Conversion factors come from unit definitions as per CDISC standards.
m is defined as 100 cm
mm is defined as 0.1 cm
in is defined as 2.54 cm
ft is defined as 30.48 cm
Permitted Values: A variable of the input dataset or a function call
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.
The analysis value of the new parameter is derived as $$WAISTHGT = \frac{WSTCIR}{HEIGHT}$$
admiral::derive_param_computed()
ADVS Functions for adding Parameters:
derive_param_waisthip()
library(tibble)
library(rlang)
# Example 1: Derive Waist to Height Ratio where Height is measured only once
advs <- tribble(
~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
"01-101-1001", "HEIGHT", "Height (cm)", 147, "cm", "SCREENING",
"01-101-1001", "WSTCIR", "Waist Circumference (cm)", 110, "cm", "SCREENING",
"01-101-1001", "WSTCIR", "Waist Circumference (cm)", 108, "cm", "WEEK 2",
"01-101-1001", "WSTCIR", "Waist Circumference (cm)", 107, "cm", "WEEK 3",
"01-101-1002", "HEIGHT", "Height (cm)", 163, "cm", "SCREENING",
"01-101-1002", "WSTCIR", "Waist Circumference (cm)", 120, "cm", "SCREENING",
"01-101-1002", "WSTCIR", "Waist Circumference (cm)", 118, "cm", "WEEK 2",
"01-101-1002", "WSTCIR", "Waist Circumference (cm)", 117, "cm", "WEEK 3",
)
derive_param_waisthgt(
advs,
by_vars = exprs(USUBJID, VISIT),
wstcir_code = "WSTCIR",
height_code = "HEIGHT",
set_values_to = exprs(
PARAMCD = "WAISTHGT",
PARAM = "Waist to Height Ratio"
),
constant_by_vars = exprs(USUBJID),
get_unit_expr = admiral::extract_unit(PARAM)
)
#> # A tibble: 14 × 6
#> USUBJID PARAMCD PARAM AVAL AVALU VISIT
#> <chr> <chr> <chr> <dbl> <chr> <chr>
#> 1 01-101-1001 HEIGHT Height (cm) 147 cm SCREENING
#> 2 01-101-1001 WSTCIR Waist Circumference (cm) 110 cm SCREENING
#> 3 01-101-1001 WSTCIR Waist Circumference (cm) 108 cm WEEK 2
#> 4 01-101-1001 WSTCIR Waist Circumference (cm) 107 cm WEEK 3
#> 5 01-101-1002 HEIGHT Height (cm) 163 cm SCREENING
#> 6 01-101-1002 WSTCIR Waist Circumference (cm) 120 cm SCREENING
#> 7 01-101-1002 WSTCIR Waist Circumference (cm) 118 cm WEEK 2
#> 8 01-101-1002 WSTCIR Waist Circumference (cm) 117 cm WEEK 3
#> 9 01-101-1001 WAISTHGT Waist to Height Ratio 0.748 NA SCREENING
#> 10 01-101-1001 WAISTHGT Waist to Height Ratio 0.735 NA WEEK 2
#> 11 01-101-1001 WAISTHGT Waist to Height Ratio 0.728 NA WEEK 3
#> 12 01-101-1002 WAISTHGT Waist to Height Ratio 0.736 NA SCREENING
#> 13 01-101-1002 WAISTHGT Waist to Height Ratio 0.724 NA WEEK 2
#> 14 01-101-1002 WAISTHGT Waist to Height Ratio 0.718 NA WEEK 3
# Example 2: Same as above but only adding Waist to Height Ratio
# at certain visits
derive_param_waisthgt(
advs,
by_vars = exprs(USUBJID, VISIT),
wstcir_code = "WSTCIR",
height_code = "HEIGHT",
set_values_to = exprs(
PARAMCD = "WAISTHGT",
PARAM = "Waist to Height Ratio"
),
constant_by_vars = exprs(USUBJID),
get_unit_expr = admiral::extract_unit(PARAM),
filter = VISIT %in% c("SCREENING", "WEEK 3")
)
#> # A tibble: 12 × 6
#> USUBJID PARAMCD PARAM AVAL AVALU VISIT
#> <chr> <chr> <chr> <dbl> <chr> <chr>
#> 1 01-101-1001 HEIGHT Height (cm) 147 cm SCREENING
#> 2 01-101-1001 WSTCIR Waist Circumference (cm) 110 cm SCREENING
#> 3 01-101-1001 WSTCIR Waist Circumference (cm) 108 cm WEEK 2
#> 4 01-101-1001 WSTCIR Waist Circumference (cm) 107 cm WEEK 3
#> 5 01-101-1002 HEIGHT Height (cm) 163 cm SCREENING
#> 6 01-101-1002 WSTCIR Waist Circumference (cm) 120 cm SCREENING
#> 7 01-101-1002 WSTCIR Waist Circumference (cm) 118 cm WEEK 2
#> 8 01-101-1002 WSTCIR Waist Circumference (cm) 117 cm WEEK 3
#> 9 01-101-1001 WAISTHGT Waist to Height Ratio 0.748 NA SCREENING
#> 10 01-101-1001 WAISTHGT Waist to Height Ratio 0.728 NA WEEK 3
#> 11 01-101-1002 WAISTHGT Waist to Height Ratio 0.736 NA SCREENING
#> 12 01-101-1002 WAISTHGT Waist to Height Ratio 0.718 NA WEEK 3
# Example 3: Pediatric study where Height and Waist Circumference
# are measured multiple times
advs <- tribble(
~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
"01-101-1001", "HEIGHT", "Height (cm)", 147, "cm", "SCREENING",
"01-101-1001", "HEIGHT", "Height (cm)", 148, "cm", "WEEK 2",
"01-101-1001", "HEIGHT", "Height (cm)", 149, "cm", "WEEK 3",
"01-101-1001", "WSTCIR", "Waist Circumference (cm)", 100, "cm", "SCREENING",
"01-101-1001", "WSTCIR", "Waist Circumference (cm)", 99, "cm", "WEEK 2",
"01-101-1001", "WSTCIR", "Waist Circumference (cm)", 98, "cm", "WEEK 3",
"01-101-1002", "HEIGHT", "Height (cm)", 163, "cm", "SCREENING",
"01-101-1002", "HEIGHT", "Height (cm)", 164, "cm", "WEEK 2",
"01-101-1002", "HEIGHT", "Height (cm)", 165, "cm", "WEEK 3",
"01-101-1002", "WSTCIR", "Waist Circumference (cm)", 110, "cm", "SCREENING",
"01-101-1002", "WSTCIR", "Waist Circumference (cm)", 109, "cm", "WEEK 2",
"01-101-1002", "WSTCIR", "Waist Circumference (cm)", 108, "cm", "WEEK 3"
)
derive_param_waisthgt(
advs,
by_vars = exprs(USUBJID, VISIT),
wstcir_code = "WSTCIR",
height_code = "HEIGHT",
set_values_to = exprs(
PARAMCD = "WAISTHGT",
PARAM = "Waist to Height Ratio"
),
get_unit_expr = admiral::extract_unit(PARAM)
)
#> # A tibble: 18 × 6
#> USUBJID PARAMCD PARAM AVAL AVALU VISIT
#> <chr> <chr> <chr> <dbl> <chr> <chr>
#> 1 01-101-1001 HEIGHT Height (cm) 147 cm SCREENING
#> 2 01-101-1001 HEIGHT Height (cm) 148 cm WEEK 2
#> 3 01-101-1001 HEIGHT Height (cm) 149 cm WEEK 3
#> 4 01-101-1001 WSTCIR Waist Circumference (cm) 100 cm SCREENING
#> 5 01-101-1001 WSTCIR Waist Circumference (cm) 99 cm WEEK 2
#> 6 01-101-1001 WSTCIR Waist Circumference (cm) 98 cm WEEK 3
#> 7 01-101-1002 HEIGHT Height (cm) 163 cm SCREENING
#> 8 01-101-1002 HEIGHT Height (cm) 164 cm WEEK 2
#> 9 01-101-1002 HEIGHT Height (cm) 165 cm WEEK 3
#> 10 01-101-1002 WSTCIR Waist Circumference (cm) 110 cm SCREENING
#> 11 01-101-1002 WSTCIR Waist Circumference (cm) 109 cm WEEK 2
#> 12 01-101-1002 WSTCIR Waist Circumference (cm) 108 cm WEEK 3
#> 13 01-101-1001 WAISTHGT Waist to Height Ratio 0.680 NA SCREENING
#> 14 01-101-1001 WAISTHGT Waist to Height Ratio 0.669 NA WEEK 2
#> 15 01-101-1001 WAISTHGT Waist to Height Ratio 0.658 NA WEEK 3
#> 16 01-101-1002 WAISTHGT Waist to Height Ratio 0.675 NA SCREENING
#> 17 01-101-1002 WAISTHGT Waist to Height Ratio 0.665 NA WEEK 2
#> 18 01-101-1002 WAISTHGT Waist to Height Ratio 0.655 NA WEEK 3
# Example 4: Automatic conversion is performed when deriving the ratio
# if parameters are provided in different units (e.g. centimeters and inches)
advs <- tribble(
~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
"01-101-1001", "HEIGHT", "Height (cm)", 147, "cm", "SCREENING",
"01-101-1001", "WSTCIR", "Waist Circumference (in)", 39.37, "in", "SCREENING",
"01-101-1001", "WSTCIR", "Waist Circumference (in)", 38.98, "in", "WEEK 2",
"01-101-1001", "WSTCIR", "Waist Circumference (in)", 38.58, "in", "WEEK 3",
"01-101-1002", "HEIGHT", "Height (cm)", 163, "cm", "SCREENING",
"01-101-1002", "WSTCIR", "Waist Circumference (in)", 43.31, "in", "SCREENING",
"01-101-1002", "WSTCIR", "Waist Circumference (in)", 42.91, "in", "WEEK 2",
"01-101-1002", "WSTCIR", "Waist Circumference (in)", 42.52, "in", "WEEK 3"
)
derive_param_waisthgt(
advs,
by_vars = exprs(USUBJID, VISIT),
wstcir_code = "WSTCIR",
height_code = "HEIGHT",
set_values_to = exprs(
PARAMCD = "WAISTHGT",
PARAM = "Waist to Height Ratio"
),
constant_by_vars = exprs(USUBJID),
get_unit_expr = admiral::extract_unit(PARAM)
)
#> ℹ Unit conversion performed for "HEIGHT". Values converted from "cm" to "in".
#> # A tibble: 14 × 6
#> USUBJID PARAMCD PARAM AVAL AVALU VISIT
#> <chr> <chr> <chr> <dbl> <chr> <chr>
#> 1 01-101-1001 HEIGHT Height (cm) 147 cm SCREENING
#> 2 01-101-1001 WSTCIR Waist Circumference (in) 39.4 in SCREENING
#> 3 01-101-1001 WSTCIR Waist Circumference (in) 39.0 in WEEK 2
#> 4 01-101-1001 WSTCIR Waist Circumference (in) 38.6 in WEEK 3
#> 5 01-101-1002 HEIGHT Height (cm) 163 cm SCREENING
#> 6 01-101-1002 WSTCIR Waist Circumference (in) 43.3 in SCREENING
#> 7 01-101-1002 WSTCIR Waist Circumference (in) 42.9 in WEEK 2
#> 8 01-101-1002 WSTCIR Waist Circumference (in) 42.5 in WEEK 3
#> 9 01-101-1001 WAISTHGT Waist to Height Ratio 0.680 NA SCREENING
#> 10 01-101-1001 WAISTHGT Waist to Height Ratio 0.674 NA WEEK 2
#> 11 01-101-1001 WAISTHGT Waist to Height Ratio 0.667 NA WEEK 3
#> 12 01-101-1002 WAISTHGT Waist to Height Ratio 0.675 NA SCREENING
#> 13 01-101-1002 WAISTHGT Waist to Height Ratio 0.669 NA WEEK 2
#> 14 01-101-1002 WAISTHGT Waist to Height Ratio 0.663 NA WEEK 3