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Adds a Parameter for Waist to Height Ratio

Source: R/derive_advs_params.R
derive_param_waisthgt.Rd

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().

Usage

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
)

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 argument) and to the parameters specified by wstcir_code and height_code.

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)

wstcir_code

Waist Circumference parameter code

The observations where PARAMCD equals the specified value are considered as the Waist Circumference.

Permitted Values: character value

height_code

Height parameter code

The observations where PARAMCD equals the specified value are considered as the Height.

Permitted Values: character value

set_values_to

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

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

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 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)

get_unit_expr

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

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.

Details

The analysis value of the new parameter is derived as $$WAISTHGT = \frac{WSTCIR}{HEIGHT}$$

See also

admiral::derive_param_computed()

ADVS Functions for adding Parameters: derive_param_waisthip()

Examples

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 ALERT: 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