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Adds a Parameter for Waist to Hip Ratio

Source: R/derive_advs_params.R
derive_param_waisthip.Rd

Adds a parameter for Waist to Hip Ratio using Waist Circumference and Hip Circumference 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_waisthip(
  dataset,
  by_vars,
  wstcir_code = "WSTCIR",
  hipcir_code = "HIPCIR",
  set_values_to = exprs(PARAMCD = "WAISTHIP"),
  filter = 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 hipcir_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

hipcir_code

Hip Circumference parameter code

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

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

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 $$WAISTHIP = \frac{WSTCIR}{HIPCIR}$$

See also

admiral::derive_param_computed()

ADVS Functions for adding Parameters: derive_param_waisthgt()

Examples

library(tibble)
library(rlang)

advs <- tribble(
  ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
  "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",
  "01-101-1001", "HIPCIR", "Hip Circumference (cm)", 125, "cm", "SCREENING",
  "01-101-1001", "HIPCIR", "Hip Circumference (cm)", 124, "cm", "WEEK 2",
  "01-101-1001", "HIPCIR", "Hip Circumference (cm)", 123, "cm", "WEEK 3",
  "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",
  "01-101-1002", "HIPCIR", "Hip Circumference (cm)", 135, "cm", "SCREENING",
  "01-101-1002", "HIPCIR", "Hip Circumference (cm)", 133, "cm", "WEEK 2",
  "01-101-1002", "HIPCIR", "Hip Circumference (cm)", 132, "cm", "WEEK 3"
)

derive_param_waisthip(
  advs,
  by_vars = exprs(USUBJID, VISIT),
  wstcir_code = "WSTCIR",
  hipcir_code = "HIPCIR",
  set_values_to = exprs(
    PARAMCD = "WAISTHIP",
    PARAM = "Waist to Hip 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 WSTCIR   Waist Circumference (cm) 110     cm    SCREENING
#>  2 01-101-1001 WSTCIR   Waist Circumference (cm) 108     cm    WEEK 2   
#>  3 01-101-1001 WSTCIR   Waist Circumference (cm) 107     cm    WEEK 3   
#>  4 01-101-1001 HIPCIR   Hip Circumference (cm)   125     cm    SCREENING
#>  5 01-101-1001 HIPCIR   Hip Circumference (cm)   124     cm    WEEK 2   
#>  6 01-101-1001 HIPCIR   Hip Circumference (cm)   123     cm    WEEK 3   
#>  7 01-101-1002 WSTCIR   Waist Circumference (cm) 120     cm    SCREENING
#>  8 01-101-1002 WSTCIR   Waist Circumference (cm) 118     cm    WEEK 2   
#>  9 01-101-1002 WSTCIR   Waist Circumference (cm) 117     cm    WEEK 3   
#> 10 01-101-1002 HIPCIR   Hip Circumference (cm)   135     cm    SCREENING
#> 11 01-101-1002 HIPCIR   Hip Circumference (cm)   133     cm    WEEK 2   
#> 12 01-101-1002 HIPCIR   Hip Circumference (cm)   132     cm    WEEK 3   
#> 13 01-101-1001 WAISTHIP Waist to Hip Ratio         0.88  NA    SCREENING
#> 14 01-101-1001 WAISTHIP Waist to Hip Ratio         0.871 NA    WEEK 2   
#> 15 01-101-1001 WAISTHIP Waist to Hip Ratio         0.870 NA    WEEK 3   
#> 16 01-101-1002 WAISTHIP Waist to Hip Ratio         0.889 NA    SCREENING
#> 17 01-101-1002 WAISTHIP Waist to Hip Ratio         0.887 NA    WEEK 2   
#> 18 01-101-1002 WAISTHIP Waist to Hip Ratio         0.886 NA    WEEK 3   

# Only adding Waist to Hip Ratio at certain visits

derive_param_waisthip(
  advs,
  by_vars = exprs(USUBJID, VISIT),
  wstcir_code = "WSTCIR",
  hipcir_code = "HIPCIR",
  set_values_to = exprs(
    PARAMCD = "WAISTHIP",
    PARAM = "Waist to Hip Ratio"
  ),
  get_unit_expr = admiral::extract_unit(PARAM),
  filter = VISIT %in% c("SCREENING", "WEEK 3")
)
#> # A tibble: 16 × 6
#>    USUBJID     PARAMCD  PARAM                       AVAL AVALU VISIT    
#>    <chr>       <chr>    <chr>                      <dbl> <chr> <chr>    
#>  1 01-101-1001 WSTCIR   Waist Circumference (cm) 110     cm    SCREENING
#>  2 01-101-1001 WSTCIR   Waist Circumference (cm) 108     cm    WEEK 2   
#>  3 01-101-1001 WSTCIR   Waist Circumference (cm) 107     cm    WEEK 3   
#>  4 01-101-1001 HIPCIR   Hip Circumference (cm)   125     cm    SCREENING
#>  5 01-101-1001 HIPCIR   Hip Circumference (cm)   124     cm    WEEK 2   
#>  6 01-101-1001 HIPCIR   Hip Circumference (cm)   123     cm    WEEK 3   
#>  7 01-101-1002 WSTCIR   Waist Circumference (cm) 120     cm    SCREENING
#>  8 01-101-1002 WSTCIR   Waist Circumference (cm) 118     cm    WEEK 2   
#>  9 01-101-1002 WSTCIR   Waist Circumference (cm) 117     cm    WEEK 3   
#> 10 01-101-1002 HIPCIR   Hip Circumference (cm)   135     cm    SCREENING
#> 11 01-101-1002 HIPCIR   Hip Circumference (cm)   133     cm    WEEK 2   
#> 12 01-101-1002 HIPCIR   Hip Circumference (cm)   132     cm    WEEK 3   
#> 13 01-101-1001 WAISTHIP Waist to Hip Ratio         0.88  NA    SCREENING
#> 14 01-101-1001 WAISTHIP Waist to Hip Ratio         0.870 NA    WEEK 3   
#> 15 01-101-1002 WAISTHIP Waist to Hip Ratio         0.889 NA    SCREENING
#> 16 01-101-1002 WAISTHIP Waist to Hip Ratio         0.886 NA    WEEK 3   

# Automatic conversion is performed when deriving the ratio
# if parameters are provided in different units

advs <- tribble(
  ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
  "01-101-1001", "HIPCIR", "Hip Circumference (cm)", 125, "cm", "SCREENING",
  "01-101-1001", "HIPCIR", "Hip Circumference (cm)", 124, "cm", "WEEK 2",
  "01-101-1001", "HIPCIR", "Hip Circumference (cm)", 123, "cm", "WEEK 3",
  "01-101-1001", "WSTCIR", "Waist Circumference (in)", 43.31, "in", "SCREENING",
  "01-101-1001", "WSTCIR", "Waist Circumference (in)", 42.52, "in", "WEEK 2",
  "01-101-1001", "WSTCIR", "Waist Circumference (in)", 42.13, "in", "WEEK 3",
  "01-101-1002", "HIPCIR", "Hip Circumference (cm)", 135, "cm", "SCREENING",
  "01-101-1002", "HIPCIR", "Hip Circumference (cm)", 133, "cm", "WEEK 2",
  "01-101-1002", "HIPCIR", "Hip Circumference (cm)", 132, "cm", "WEEK 3",
  "01-101-1002", "WSTCIR", "Waist Circumference (in)", 47.24, "in", "SCREENING",
  "01-101-1002", "WSTCIR", "Waist Circumference (in)", 46.46, "in", "WEEK 2",
  "01-101-1002", "WSTCIR", "Waist Circumference (in)", 46.06, "in", "WEEK 3"
)

derive_param_waisthip(
  advs,
  by_vars = exprs(USUBJID, VISIT),
  wstcir_code = "WSTCIR",
  hipcir_code = "HIPCIR",
  set_values_to = exprs(
    PARAMCD = "WAISTHIP",
    PARAM = "Waist to Hip Ratio"
  ),
  get_unit_expr = admiral::extract_unit(PARAM)
)
#> ℹ ALERT: Unit conversion performed for "HIPCIR". Values converted from "cm" to
#> "in".
#> # A tibble: 18 × 6
#>    USUBJID     PARAMCD  PARAM                       AVAL AVALU VISIT    
#>    <chr>       <chr>    <chr>                      <dbl> <chr> <chr>    
#>  1 01-101-1001 HIPCIR   Hip Circumference (cm)   125     cm    SCREENING
#>  2 01-101-1001 HIPCIR   Hip Circumference (cm)   124     cm    WEEK 2   
#>  3 01-101-1001 HIPCIR   Hip Circumference (cm)   123     cm    WEEK 3   
#>  4 01-101-1001 WSTCIR   Waist Circumference (in)  43.3   in    SCREENING
#>  5 01-101-1001 WSTCIR   Waist Circumference (in)  42.5   in    WEEK 2   
#>  6 01-101-1001 WSTCIR   Waist Circumference (in)  42.1   in    WEEK 3   
#>  7 01-101-1002 HIPCIR   Hip Circumference (cm)   135     cm    SCREENING
#>  8 01-101-1002 HIPCIR   Hip Circumference (cm)   133     cm    WEEK 2   
#>  9 01-101-1002 HIPCIR   Hip Circumference (cm)   132     cm    WEEK 3   
#> 10 01-101-1002 WSTCIR   Waist Circumference (in)  47.2   in    SCREENING
#> 11 01-101-1002 WSTCIR   Waist Circumference (in)  46.5   in    WEEK 2   
#> 12 01-101-1002 WSTCIR   Waist Circumference (in)  46.1   in    WEEK 3   
#> 13 01-101-1001 WAISTHIP Waist to Hip Ratio         0.880 NA    SCREENING
#> 14 01-101-1001 WAISTHIP Waist to Hip Ratio         0.871 NA    WEEK 2   
#> 15 01-101-1001 WAISTHIP Waist to Hip Ratio         0.870 NA    WEEK 3   
#> 16 01-101-1002 WAISTHIP Waist to Hip Ratio         0.889 NA    SCREENING
#> 17 01-101-1002 WAISTHIP Waist to Hip Ratio         0.887 NA    WEEK 2   
#> 18 01-101-1002 WAISTHIP Waist to Hip Ratio         0.886 NA    WEEK 3