Type: Package
Title: Neuroscience Extension Package for ADaM in 'R' Asset Library
Version: 0.1.0
Description: Programming neuroscience Clinical Data Standards Interchange Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets. 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). This package extends the 'admiral' package.
License: Apache License (≥ 2)
URL: https://pharmaverse.github.io/admiralneuro/, https://github.com/pharmaverse/admiralneuro
Depends: R (≥ 4.1)
Imports: admiral (≥ 1.2.0), admiraldev (≥ 1.2.0), cli (≥ 3.6.2), dplyr (≥ 1.0.5), hms (≥ 0.5.3), lifecycle (≥ 0.1.0), lubridate (≥ 1.7.4), magrittr (≥ 1.5), purrr (≥ 0.3.3), rlang (≥ 0.4.4), stringr (≥ 1.4.0), tibble (≥ 3.2.1), tidyr (≥ 1.0.2), tidyselect (≥ 1.1.0)
Suggests: diffdf, DT, htmltools, knitr, metatools, methods, pharmaversesdtm (≥ 1.0.0), reactable, readxl, rmarkdown, testthat (≥ 3.0.0),
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-09-09 16:42:48 UTC; c085541
Author: Jian Wang ORCID iD [aut, cre], Miles Almond ORCID iD [aut], Xiao Chen ORCID iD [aut], Fanny Gautier ORCID iD [aut], Gayatri G. [aut], Meilin Jiang ORCID iD [aut], Leena Khatri ORCID iD [aut], Edoardo Mancini ORCID iD [aut], Eric Nantz [aut], Lina Patil [aut], Chris Pelentrides [aut], Eli Lilly and Company [cph, fnd], Cytel Inc. [cph, fnd], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Jian Wang <wang_jian_wj@lilly.com>
Repository: CRAN
Date/Publication: 2025-09-14 16:20:08 UTC

admiralneuro: Neuroscience Extension Package for ADaM in 'R' Asset Library

Description

logo

Programming neuroscience Clinical Data Standards Interchange Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets. 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). This package extends the 'admiral' package.

Author(s)

Maintainer: Jian Wang wang_jian_wj@lilly.com (ORCID)

Authors:

Other contributors:

See Also

Useful links:

Amyloid PET Scan Analysis Dataset - Neuro

Description

An updated ADaM ADAPET dataset using NV, AG, SUPPNV, ADSL

Usage

admiralneuro_adapet

Format

An object of class tbl_df (inherits from tbl, data.frame) with 83 rows and 50 columns.

See Also

Other datasets: admiralneuro_adtpet, adsl_neuro, ag_neuro, dm_neuro, nv_neuro, suppnv_neuro

Tau PET Scan Analysis Dataset - Neuro

Description

An updated ADaM ADTPET dataset using NV, AG, SUPPNV, ADSL

Usage

admiralneuro_adtpet

Format

An object of class tbl_df (inherits from tbl, data.frame) with 34 rows and 47 columns.

See Also

Other datasets: admiralneuro_adapet, adsl_neuro, ag_neuro, dm_neuro, nv_neuro, suppnv_neuro

Subject Level Analysis Dataset-updated

Description

An updated ADaM ADSL dataset with Alzheimer's Disease patients

Usage

adsl_neuro

Format

An object of class tbl_df (inherits from tbl, data.frame) with 15 rows and 36 columns.

See Also

Other datasets: admiralneuro_adapet, admiralneuro_adtpet, ag_neuro, dm_neuro, nv_neuro, suppnv_neuro

Procedure Agents for Nervous System Dataset

Description

A SDTM AG domain dataset containing procedure agents for nervous system

Usage

ag_neuro

Format

A data frame with 12 columns:

STUDYID

Study Identifier

DOMAIN

Domain Abbreviation

USUBJID

Unique Subject Identifier

AGSEQ

Sequence Number

AGTRT

Reported Agent Name

AGCAT

Category for Category

AGDOSE

Dose per Administration

AGDOSEU

Dose Units

AGROUTE

Route of Administration

AGLNKID

Link ID

VISITNUM

Visit Number

VISIT

Visit Name

AGSTDTC

Start Date/Time of Agent

Details

Procedure Agents for Nervous System Dataset

A SDTM AG domain dataset

Source

Constructed using nv_neuro from {admiralneuro} package

See Also

Other datasets: admiralneuro_adapet, admiralneuro_adtpet, adsl_neuro, dm_neuro, nv_neuro, suppnv_neuro

Compute Centiloid Value

Description

Computes the Centiloid value based on an amyloid Positron Emission Tomography (PET) scan radioactive tracer, Standardized Uptake Value Ratio (SUVR) value, pipeline, and reference region. Also allows for custom formula parameters.

Usage

compute_centiloid(
  tracer,
  pipeline,
  ref_region,
  suvr,
  custom_slope = NULL,
  custom_intercept = NULL
)

Arguments

tracer

Amyloid PET tracer

A character string is expected. If custom_slope and custom_intercept are specified, this parameter is ignored. See Details section for accepted values in combination with pipeline and ref_region.

pipeline

SUVR pipeline

A character string is expected. If custom_slope and custom_intercept are specified, this parameter is ignored. See Details section for accepted values in combination with tracer and ref_region.

ref_region

Reference region

A character string is expected. If custom_slope and custom_intercept are specified, this parameter is ignored. See Details section for accepted values in combination with tracer and ref_region.

suvr

SUVR value

A numeric value is expected.

custom_slope

Optional slope parameter for custom Centiloid calculation formula

A numeric value is expected when provided. When custom_slope is specified (along with custom_intercept), this overrides the standard formula parameters tracer, pipeline, and ref_region. Default is NULL.

custom_intercept

Optional intercept parameter for custom centiloid calculation formula

A numeric value is expected when provided. When custom_intercept is specified (along with custom_slope), this overrides the standard formula parameters tracer, pipeline, and ref_region. Default is NULL.

Details

The Centiloid scale is a standardized quantitative measure for amyloid PET imaging that allows comparison between different tracers and analysis methods. This function converts SUVR values to the Centiloid scale based on published conversion equations for specific tracer, pipeline, and reference region combinations.

Centiloid is calculated as:

Centiloid = slope \times SUVR + intercept

where slope and intercept are formula parameters. If custom_slope and custom_intercept are not specified, this function uses pre-defined slope and intercept based on the user's selections of tracer, pipeline, and reference region.

The combinations of tracer, pipeline and reference region in the table below are supported. The columns "slope" and "intercept" then show the values of the slope and intercept that compute_centiloid() will use to calculate the centiloid value in each case.

tracer pipeline ref_region slope intercept
18F-Florbetapir AVID FBP SUVR PIPELINE¹ Whole Cerebellum 183.07 -177.26
18F-Florbetaben AVID FBB SUVR PIPELINE² Whole Cerebellum 156.06 -148.13
18F-Florbetapir BERKELEY FBP SUVR PIPELINE³ Whole Cerebellum 188.22 -189.16
18F-Florbetaben BERKELEY FBB SUVR PIPELINE³ Whole Cerebellum 157.15 -151.87

The equations used for the conversions are based on the following references:

¹ Navitsky, et al. (2018). doi:10.1016/j.jalz.2018.06.1353 ² Sims, et al. (2024). doi:10.1001/jama.2023.13239 ³ Royse, et al. (2021). doi:10.1186/s13195-021-00836-1

Alternatively, the user can override the pre-selection by specifying both custom_slope and custom_intercept instead. When custom_slope and custom_intercept are specified, the function ignores tracer, pipeline and ref_region for calculation purposes. However, this function always requires specification of tracer, pipeline, and ref_region parameters, even when using custom slope and intercept values. This design choice ensures that users remain cognizant of the imaging context and analysis methodology when computing Centiloid values.

For additional Centiloid transformation formulas, see: Iaccarino, L. et al. (2025). doi:10.1016/j.nicl.2025.103765

If a matching combination of tracer, pipeline, and reference region is not specified and both custom_slope and custom_intercept are not specified, the function aborts with an error.

Value

A numeric Centiloid value.

Examples

# Using standard parameters
compute_centiloid(
  tracer = "18F-Florbetapir",
  pipeline = "AVID FBP SUVR PIPELINE",
  ref_region = "Whole Cerebellum",
  suvr = 1.25
)

# Using custom parameters
compute_centiloid(
  tracer = "MyTracer",
  pipeline = "MyPipeline",
  ref_region = "MyRegion",
  suvr = 1.25,
  custom_slope = 193,
  custom_intercept = -187
)

Demographic Dataset - Neuro

Description

An updated SDTM DM dataset subset with age appropriate Alzheimer's Disease patients

Usage

dm_neuro

Format

An object of class tbl_df (inherits from tbl, data.frame) with 15 rows and 26 columns.

See Also

Other datasets: admiralneuro_adapet, admiralneuro_adtpet, adsl_neuro, ag_neuro, nv_neuro, suppnv_neuro

Nervous System Findings Dataset

Description

A SDTM NV domain dataset containing nervous system findings and measurements

Usage

nv_neuro

Format

A data frame with 20 columns:

STUDYID

Study Identifier

DOMAIN

Domain Abbreviation

USUBJID

Unique Subject Identifier

NVSEQ

Sequence Number

NVLNKID

Link ID

NVTESTCD

Short Name of Nervous System Test

NVTEST

Name of Nervous System Test

NVCAT

Category for Nervous System Test

NVLOC

Location Used for the Measurement

NVMETHOD

Method of Test or Examination

NVNAM

Vendor Name

NVORRES

Result or Finding in Original Units

NVORRESU

Original Units

NVSTRESC

Character Result/Finding in Std Format

NVSTRESN

Numeric Result/Finding in Standard Units

NVSTRESU

Standard Units

VISITNUM

Visit Number

VISIT

Visit Name

NVDTC

Date/Time of Collection

NVDY

Study Day of Collection

NVLOBXFL

Last Observation Before Exposure Flag

Details

Nervous System Findings Dataset

A SDTM NV domain dataset for Alzheimer's disease observational and interventional studies, including amyloid and tau PET data at baseline and two follow-up visits reflect levels of pathology appropriate for disease or treatment course

Source

Constructed using dm_neuro from {admiralneuro} package for USUBJID and cohort information, vs from {pharmaversesdtm} for visit schedule such as VISIT, NVDTC, NVDY

See Also

Other datasets: admiralneuro_adapet, admiralneuro_adtpet, adsl_neuro, ag_neuro, dm_neuro, suppnv_neuro

Supplemental Nervous System Findings Dataset

Description

A SDTM SUPPNV domain dataset containing reference regions used for SUVR calculation

Usage

suppnv_neuro

Format

A data frame with 8 columns:

STUDYID

Study Identifier

RDOMAIN

Related Domain Abbreviation

USUBJID

Unique Subject Identifier

IDVAR

Identifying Variable

IDVARVAL

Identifying Variable Value

QNAM

Qualifier Variable Name

QLABEL

Qualifier Variable Label

QVAL

Data Value

QORIG

Origin

QEVAL

Evaluator

Details

Supplemental Nervous System Findings Dataset

A SDTM SUPPNV domain dataset

Source

Constructed using nv_neuro from {admiralneuro} package

See Also

Other datasets: admiralneuro_adapet, admiralneuro_adtpet, adsl_neuro, ag_neuro, dm_neuro, nv_neuro

mirror server hosted at Truenetwork, Russian Federation.