Help for package admiralmetabolic

Type:

Package

Title:

Metabolism Extension Package for ADaM in 'R' Asset Library

Version:

0.2.0

Description:

A toolbox for programming Clinical Data Standards Interchange Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, https://www.cdisc.org/standards/foundational/adam). The package is an extension package of the 'admiral' package focusing on the metabolism therapeutic area.

License:

Apache License (≥ 2)

URL:

https://pharmaverse.github.io/admiralmetabolic/, https://github.com/pharmaverse/admiralmetabolic

BugReports:

https://github.com/pharmaverse/admiralmetabolic/issues

Depends:

R (≥ 4.1)

Imports:

admiral (≥ 1.1.1), admiraldev (≥ 1.2.0), cli (≥ 3.6.2), dplyr (≥ 0.8.4), lifecycle (≥ 0.1.0), lubridate (≥ 1.7.4), magrittr (≥ 1.5), purrr (≥ 0.3.3), rlang (≥ 0.4.4), stringr (≥ 1.4.0), tidyselect (≥ 1.0.0)

Suggests:

diffdf, DT, htmltools, knitr, methods, pharmaversesdtm (≥ 1.3.0), rmarkdown, testthat (≥ 3.0.0), tibble, usethis (≥ 2.2.3)

VignetteBuilder:

knitr

Config/testthat/edition:

Encoding:

UTF-8

Language:

en-US

LazyData:

true

RoxygenNote:

7.3.2

NeedsCompilation:

Packaged:

2025-07-16 10:52:41 UTC; iakd

Author:

Anders Askeland

[aut, cre], Andrii Yurovskyi

[aut], Kathrin Flunkert [aut], Edoardo Mancini

[aut], Shunsuke Goto [aut], Siddhesh Pujari

[aut], Sonali Das [aut], Olga Starostecka [aut], Vang Le-Quy

[aut], Keita Takahashi

[aut]

Maintainer:

Anders Askeland <iakd@novonordisk.com>

Repository:

CRAN

Date/Publication:

2025-07-16 11:10:02 UTC

admiralmetabolic: Metabolism Extension Package for ADaM in 'R' Asset Library

Description

Author(s)

Maintainer: Anders Askeland iakd@novonordisk.com (ORCID)

Authors:

Andrii Yurovskyi andrii.yurovskyi@intego-group.com (ORCID)
Kathrin Flunkert kathrin.flunkert@roche.com
Edoardo Mancini edoardo.mancini@roche.com (ORCID)
Shunsuke Goto shunsuke.goto@novartis.com
Siddhesh Pujari spuj@novonordisk.com (ORCID)
Sonali Das sxd@novonordisk.com
Olga Starostecka olga.starostecka@boehringer-ingelheim.com
Vang Le-Quy vqul@novonordisk.com (ORCID)
Keita Takahashi keita.takahashi.4.biz@gmail.com (ORCID)

Subject Level Analysis Dataset

Description

An example subject level analysis dataset

Usage

admiralmetabolic_adsl

Format

An object of class tbl_df (inherits from tbl, data.frame) with 306 rows and 54 columns.

Source

Derived from the ad_adsl_metabolic template

Vital sings Dataset

Description

An example vital sings analysis dataset

Usage

admiralmetabolic_advs

Format

An object of class tbl_df (inherits from tbl, data.frame) with 760 rows and 101 columns.

Source

Derived from the ad_advs template

Adds a Ratio Parameter Computed from the Analysis Value of Other Parameters

Description

Adds a record for a generic Ratio parameter using two existing parameter (numerator and denominator) 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_ratio(
  dataset,
  by_vars,
  numerator_code,
  denominator_code,
  set_values_to,
  constant_numerator = FALSE,
  constant_denominator = FALSE,
  filter = NULL,
  constant_by_vars = NULL,
  get_unit_expr = NULL,
  unit_conversion = FALSE
)

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 numerator_code and denominator_code.

by_vars

Grouping variables

Grouping variables uniquely identifying a set of records for which new_vars are to be calculated.

Permitted Values: list of variables created by exprs()

numerator_code

Numerator parameter code

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

Permitted Values: character value

denominator_code

Denominator parameter code

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

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

constant_numerator

Is numerator parameter constant?

It is expected that the parameter code (PARAMCD) specified in numerator_code which is required to derive the new parameter is measured only once. For example, if Height to Weight Ratio should be derived and height is measured only once while Weight is measured at each visit. Height could be specified in the numerator_code argument and constant_numerator is to be set to TRUE.

Permitted Values: logical scalar

constant_denominator

Is denominator parameter constant?

It is expected that the parameter code (PARAMCD) specified in numerator_code which is required to derive the new parameter is measured only once. For example, if Waist to Height Ratio should be derived and height is measured only once while Waist Circumference is measured at each visit. Height could be specified in the denominator_code argument and constant_denominator is to be set to TRUE.

Permitted Values: logical scalar

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 numerator and/or denominator is constant

When numerator and/or denominator is constant, the parameters (measured only once) are merged to the other parameters using the specified variables.

If numerator and/or denominator 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 a generic Ratio parameter at all visits where numerator and/or denominator is measured. Otherwise it will only be calculated at visits with both numerator and denominator parameters 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

unit_conversion

Enable/Disable unit conversion

Unit conversion is disabled by default. Ignored if get_unit_expr is NULL.

Permitted Values: logical scalar

Details

The analysis value of the new parameter is derived as

RATIO = \frac{NUMERATOR}{DENOMINATOR}

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.

Adds a Parameter for Waist to Height Ratio

Description

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.

by_vars

Grouping variables

Grouping variables uniquely identifying a set of records for which new_vars are to be calculated.

Permitted Values: list of variables created by exprs()

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.

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

Details

The analysis value of the new parameter is derived as

WAISTHGT = \frac{WSTCIR}{HEIGHT}

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.

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)
)

# 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")
)

# 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)
)

# 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)
)

Adds a Parameter for Waist to Hip Ratio

Description

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.

by_vars

Grouping variables

Grouping variables uniquely identifying a set of records for which new_vars are to be calculated.

Permitted Values: list of variables created by exprs()

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.

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

Details

The analysis value of the new parameter is derived as

WAISTHIP = \frac{WSTCIR}{HIPCIR}

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.

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)
)

# 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")
)

# 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)
)

Unit conversion

Description

get_conv_factor() extracts a conversion factor for a pair of units. Fails with error if units are not supported/convertible.

get_conv_factors_all() returns all conversion factors supported.

Note: Conversion factors come from unit definitions as per CDISC standards.

Usage

get_conv_factor(from_unit, to_unit)

get_conv_factors_all()

admiralmetabolic: Metabolism Extension Package for ADaM in 'R' Asset Library

Description

Author(s)

See Also

Subject Level Analysis Dataset

Description

Usage

Format

Source

See Also

Vital sings Dataset

Description

Usage

Format

Source

See Also

Adds a Ratio Parameter Computed from the Analysis Value of Other Parameters

Description

Usage

Arguments

Details

Value

See Also

Adds a Parameter for Waist to Height Ratio

Description

Usage

Arguments

Details

Value

See Also

Examples

Adds a Parameter for Waist to Hip Ratio

Description

Usage

Arguments

Details

Value

See Also

Examples

Unit conversion

Description

Usage