| Type: | Package |
| Title: | Reference Values for CT-Assessed Body Composition |
| Version: | 2.0.1 |
| Maintainer: | J. Peter Marquardt <peter@kmarquardt.de> |
| Description: | Get z-scores, percentiles, absolute values, and percent of predicted of a reference cohort. Functionality requires installing the data packages 'adiposerefdata' and 'musclerefdata'. For more information on the underlying research, please visit our website which also includes a graphical interface. The models and underlying data are described in Marquardt JP et al.(planned publication 2025; reserved doi 10.1097/RLI.0000000000001104), "Subcutaneous and Visceral adipose tissue Reference Values from Framingham Heart Study Thoracic and Abdominal CT", *Investigative Radiology* and Tonnesen PE et al. (2023), "Muscle Reference Values from Thoracic and Abdominal CT for Sarcopenia Assessment [column] The Framingham Heart Study", *Investigative Radiology*, <doi:10.1097/RLI.0000000000001012>. |
| URL: | https://bodycomp-metrics.mgh.harvard.edu, https://github.com/p-mq/bodycompref |
| Depends: | R (≥ 4.0.0) |
| Imports: | assertthat, gamlss, stats, sae |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.1 |
| Suggests: | testthat (≥ 3.0.0), usethis, adiposerefdata, musclerefdata, knitr, rmarkdown |
| Config/testthat/edition: | 3 |
| Additional_repositories: | https://p-mq.github.io/drat |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2024-07-18 18:20:28 UTC; petem |
| Author: | J. Peter Marquardt
 [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2024-07-21 10:20:01 UTC |
Get the lambda used to build a model
Description
For each reference LMSP model, get the lambdas used before fitting
Usage
.Get_lambda(metric, sex, level = NA)
Arguments
metric |
character, body composition metric |
sex |
character, "Female" or "Male" |
level |
character, used vertebral level |
Value
lambda (numeric, range [-2, 2], increments of 0.1)
Author(s)
J Peter Marquardt
Get % of expected value
Description
For a given constellation of metric, sex, vertebral level, and age returns the ratio of actual and expected value (percentile 50) in percent
Usage
.Get_percent_predicted(
metric,
sex,
level,
age,
measurement,
verbose = FALSE,
digits = 0
)
Arguments
metric |
character, body composition metric |
sex |
character, "Female" or "Male" |
level |
character, used vertebral level |
age |
integer, age |
measurement |
numeric, raw value of measurement |
verbose |
logical, should messages be discplayed |
digits |
integer, digits to round return value |
Value
numeric, corresponding percentile
Author(s)
J. Peter Marquardt
Get reference models
Description
For a given combination of metric, sex, and level return the appropriate LMSP model. Imports the non-CRAN packages musclerefdata and adiposerefdata
Usage
.Get_reference_model(fitted_metric, sex, level)
Arguments
fitted_metric |
string, name of fitted metric (abbreviation, includes a lowercase b prefix for metrics with box-cox-transformation) |
sex |
character, "Male" or "Female" |
level |
string, vertebral level, T5, T8, T10, or L3 |
Value
LMSP model
Author(s)
J.Peter Marquardt
Get percentile for a given combination of model and measurement
Description
For a given constellation of metric, sex, vertebral level, and age returns the corresponding percentile for a given measurement
Usage
.Get_reference_percentile(
metric,
sex,
level,
age,
measurement,
verbose = FALSE,
digits = 0
)
Arguments
metric |
character, body composition metric |
sex |
character, "Female" or "Male" |
level |
character, used vertebral level |
age |
integer, age |
measurement |
numeric, raw value of measurement |
verbose |
logical, should messages be displayed |
digits |
integer, digits to round percentile to |
Value
numeric, corresponding percentile
Author(s)
J. Peter Marquardt
Get reference for a given combination of model and percentile/z-score
Description
For a given constellation of metric, sex, vertebral level, and age returns the corresponding measurement for a given percentile/z-score
Usage
.Get_reference_value(
metric,
sex,
level,
age,
percentile = NULL,
z_score = NULL,
verbose = FALSE,
digits = 0
)
Arguments
metric |
character, body composition metric |
sex |
character, "Female" or "Male" |
level |
character, used vertebral level |
age |
integer, age |
percentile |
numeric, percentile to return value for. If both percentile and z_score are given, only percentile is evaluated |
z_score |
numeric, z score to return value for. If both percentile and z_score are given, only percentile is evaluated |
verbose |
logical, should messages be discplayed |
digits |
integer, digits to round reference value |
Value
numeric, corresponding percentile
Author(s)
J. Peter Marquardt
Get z-score for a given combination of model and measurement
Description
For a given constellation of metric, sex, vertebral level, and age returns the corresponding z-score for a given measurement
Usage
.Get_reference_z_score(
metric,
sex,
level,
age,
measurement,
verbose = FALSE,
digits = 2
)
Arguments
metric |
character, body composition metric |
sex |
character, "Female" or "Male" |
level |
character, used vertebral level |
age |
integer, age |
measurement |
numeric, raw value of measurement |
verbose |
logical, should messages be displayed |
digits |
integer, digits to round percentile to |
Value
numeric, corresponding z-score
Author(s)
J. Peter Marquardt
Get body composition reference values
Description
For a given constellation of metric, sex, vertebral level, and age returns either - the reference percentile - the reference z-score - the reference value - the percent of predicted value
Usage
bodycomp_reference(
metric,
sex,
level,
age,
type,
measurement = NULL,
percentile = NULL,
z_score = NULL,
verbose = FALSE,
digits = 2
)
Arguments
metric |
character (vector), body composition metric. |
sex |
character (vector), ""Female" or "Male" |
level |
character (vector), used vertebral level |
age |
integer (vector), age |
type |
character, type of value to return, either of "percentile", "z_score", "reference_value", "percent_predicted" |
measurement |
numeric (vector), raw value of measurement |
percentile |
numeric (vector), percentile to return value for. If both percentile and z_score are given, only percentile is evaluated |
z_score |
numeric (vector), z score to return value for. If both percentile and z_score are given, only percentile is evaluated |
verbose |
logical, should messages be displayed |
digits |
integer, digits to round return value to |
Details
Reference models are available for the following metrics: - CSMA: Cross-sectional muscle area [cm²] - SMI: Skeletal Muscle Index [cm²/m²] - SMRA: Skeletal Muscle Radioattenuation [Hounsfield Units (HU)] - SMG: Skeletal Muscle Gauge [cm² * HU/ m²] - CSFA: Cross-sectional (subcutaneous) fat area [cm²] - SATI: Subcutaneous Adipose Tissue Index [cm²/m²] - SATRA: Subcutaneous Adipose Tissue Radioattenuation [HU] - SATG: Subcutaneous Adipose Tissue Gauge [cm² * HU/ m²] - CSVFA: Cross-sectional Visceral Fat Area [cm²] - VATI: Visceral Adipose Tissue Index [cm²/m²] - VATRA: Visceral Adipose Tissue Radioattenuation [HU] - VATG: Visceral Adipose Tissue Gauge [cm² * HU/ m²] - TAT: Cross-sectional Total Adipose Tissue Area [cm²] (SATA + VATA) - TATI: Total Adipose Tissue Index [cm²/m²] (SATI + VATI) - VAT_SAT_ratio: VAT/SAT ratio []
Measurement values must be >= -124 for SATRA and VATRA, <= -1 for SATG and VATG, and >= 1 for all other metrics.
The reference values are based on LMSP models constructed from the Framingham Heart Study published in the following publications: - Marquardt JP, Tonnesen PE, Mercaldo ND, Graur A, Allaire B, Bouxsein ML, Samelson EJ, Kiel DP, Fintelmann FJ. Subcutaneous and Visceral adipose tissue Reference Values from Framingham Heart Study Thoracic and Abdominal CT. Investigative Radiology, 2024. - Tonnesen PE, Mercaldo ND, Tahir I, Dietrich ASW, Amari W, Graur A, Allaire B, Bouxsein ML, Samelson EJ, Kiel DP, Fintelmann FJ. Muscle Reference Values from Thoracic and Abdominal CT for Sarcopenia Assessment: The Framingham Heart Study. Investigative Radiology, 2023.
Value
numeric, corresponding percentile
Author(s)
J. Peter Marquardt
Examples
bodycomp_reference(metric=c("CSFA", "CSFA"), sex=c("Female","Male"),
level=c("T5","L3"), age=c(42,68), measurement=c(100,200),
type = "percentile")
Get % of expected value
Description
For a given constellation of metric, sex, vertebral level, and age returns the ratio of actual and expected value (percentile 50) in percent
Usage
percent_predicted(
metric,
sex,
level,
age,
measurement,
verbose = FALSE,
digits = 0
)
Arguments
metric |
character (vector), body composition metric |
sex |
character (vector), ""Female" or "Male" |
level |
character (vector), used vertebral level |
age |
integer (vector), age |
measurement |
numeric (vector), raw value of measurement |
verbose |
logical, should messages be displayed |
digits |
integer, digits to round return value to |
Value
numeric, corresponding percentile
Author(s)
J. Peter Marquardt
See Also
[bodycomp_reference()]
Examples
percent_predicted(metric=c("CSFA", "CSFA"), sex=c("Female","Male"),
level=c("T5","L3"), age=c(42,68), measurement=c(100,200))
Get percentile(s) for a given combination of model and measurement
Description
For a given constellation of metric, sex, vertebral level, and age returns the corresponding percentiles for a given measurement
Usage
reference_percentiles(
metric,
sex,
level,
age,
measurement,
verbose = FALSE,
digits = 0
)
Arguments
metric |
character (vector), body composition metric |
sex |
character (vector), "Female" or "Male" |
level |
character (vector), used vertebral level |
age |
integer (vector), age |
measurement |
numeric (vector), raw value of measurement |
verbose |
logical, should messages be discplayed |
digits |
integer, digits to round percentile to |
Value
numeric, corresponding percentile
Author(s)
J. Peter Marquardt
See Also
[bodycomp_reference()]
Examples
reference_percentiles(metric=c("CSFA", "CSFA"), sex=c("Female","Male"),
level=c("T5","L3"), age=c(42,68), measurement=c(50,50))
Get reference values for a given combination of model and percentile/z-score
Description
For a given constellation of metric, sex, vertebral level, and age returns the corresponding measurements to a given percentile/z-score
Usage
reference_values(
metric,
sex,
level,
age,
percentile = NULL,
z_score = NULL,
verbose = FALSE,
digits = 0
)
Arguments
metric |
character (vector), body composition metric |
sex |
character (vector), ""Female" or "Male" |
level |
character (vector), used vertebral level |
age |
integer (vector), age |
percentile |
numeric (vector), percentile to return value for. If both percentile and z_score are given, only percentile is evaluated |
z_score |
numeric (vector), z score to return value for. If both percentile and z_score are given, only percentile is evaluated |
verbose |
logical, should messages be displayed |
digits |
integer, digits to round return value to |
Value
numeric, corresponding percentile
Author(s)
J. Peter Marquardt
See Also
[bodycomp_reference()]
Examples
reference_values(metric=c("CSFA", "CSFA"), sex=c("Female","Male"),
level=c("T5","L3"), age=c(42,68), percentile=c(50,50))
Get z-scores for a given combination of model and measurement
Description
For a given constellation of metric, sex, vertebral level, and age returns the corresponding z-scores for a given set of measurements
Usage
reference_z_scores(
metric,
sex,
level,
age,
measurement,
verbose = FALSE,
digits = 2
)
Arguments
metric |
character (vector), body composition metric |
sex |
character (vector), "Female" or "Male" |
level |
character (vector), used vertebral level |
age |
integer (vector), age |
measurement |
numeric (vector), raw value of measurement |
verbose |
logical, should messages be displayed |
digits |
integer, digits to round percentile to |
Value
numeric, corresponding z-score
Author(s)
J. Peter Marquardt
See Also
[bodycomp_reference()]
Examples
reference_z_scores(metric=c("CSFA", "CSFA"), sex=c("Female","Male"),
level=c("T5","L3"), age=c(42,68), measurement=c(50,50))