| Title: | Reference Values for CT-Assessed Body Composition |
|---|---|
| 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>. |
| Authors: | J. Peter Marquardt [aut, cre] |
| Maintainer: | J. Peter Marquardt <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 2.0.1 |
| Built: | 2024-11-01 11:31:47 UTC |
| Source: | https://github.com/p-mq/bodycompref |
For each reference LMSP model, get the lambdas used before fitting
.Get_lambda(metric, sex, level = NA).Get_lambda(metric, sex, level = NA)
metric |
character, body composition metric |
sex |
character, "Female" or "Male" |
level |
character, used vertebral level |
lambda (numeric, range [-2, 2], increments of 0.1)
J Peter Marquardt
For a given constellation of metric, sex, vertebral level, and age returns the ratio of actual and expected value (percentile 50) in percent
.Get_percent_predicted( metric, sex, level, age, measurement, verbose = FALSE, digits = 0 ).Get_percent_predicted( metric, sex, level, age, measurement, verbose = FALSE, digits = 0 )
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 |
numeric, corresponding percentile
J. Peter Marquardt
For a given combination of metric, sex, and level return the appropriate LMSP model. Imports the non-CRAN packages musclerefdata and adiposerefdata
.Get_reference_model(fitted_metric, sex, level).Get_reference_model(fitted_metric, sex, level)
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 |
LMSP model
J.Peter Marquardt
For a given constellation of metric, sex, vertebral level, and age returns the corresponding percentile for a given measurement
.Get_reference_percentile( metric, sex, level, age, measurement, verbose = FALSE, digits = 0 ).Get_reference_percentile( metric, sex, level, age, measurement, verbose = FALSE, digits = 0 )
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 |
numeric, corresponding percentile
J. Peter Marquardt
For a given constellation of metric, sex, vertebral level, and age returns the corresponding measurement for a given percentile/z-score
.Get_reference_value( metric, sex, level, age, percentile = NULL, z_score = NULL, verbose = FALSE, digits = 0 ).Get_reference_value( metric, sex, level, age, percentile = NULL, z_score = NULL, verbose = FALSE, digits = 0 )
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 |
numeric, corresponding percentile
J. Peter Marquardt
For a given constellation of metric, sex, vertebral level, and age returns the corresponding z-score for a given measurement
.Get_reference_z_score( metric, sex, level, age, measurement, verbose = FALSE, digits = 2 ).Get_reference_z_score( metric, sex, level, age, measurement, verbose = FALSE, digits = 2 )
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 |
numeric, corresponding z-score
J. Peter Marquardt
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
bodycomp_reference( metric, sex, level, age, type, measurement = NULL, percentile = NULL, z_score = NULL, verbose = FALSE, digits = 2 )bodycomp_reference( metric, sex, level, age, type, measurement = NULL, percentile = NULL, z_score = NULL, verbose = FALSE, digits = 2 )
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 |
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.
numeric, corresponding percentile
J. Peter Marquardt
bodycomp_reference(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), measurement=c(100,200), type = "percentile")bodycomp_reference(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), measurement=c(100,200), type = "percentile")
For a given constellation of metric, sex, vertebral level, and age returns the ratio of actual and expected value (percentile 50) in percent
percent_predicted( metric, sex, level, age, measurement, verbose = FALSE, digits = 0 )percent_predicted( metric, sex, level, age, measurement, verbose = FALSE, digits = 0 )
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 |
numeric, corresponding percentile
J. Peter Marquardt
[bodycomp_reference()]
percent_predicted(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), measurement=c(100,200))percent_predicted(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), measurement=c(100,200))
For a given constellation of metric, sex, vertebral level, and age returns the corresponding percentiles for a given measurement
reference_percentiles( metric, sex, level, age, measurement, verbose = FALSE, digits = 0 )reference_percentiles( metric, sex, level, age, measurement, verbose = FALSE, digits = 0 )
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 |
numeric, corresponding percentile
J. Peter Marquardt
[bodycomp_reference()]
reference_percentiles(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), measurement=c(50,50))reference_percentiles(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), measurement=c(50,50))
For a given constellation of metric, sex, vertebral level, and age returns the corresponding measurements to a given percentile/z-score
reference_values( metric, sex, level, age, percentile = NULL, z_score = NULL, verbose = FALSE, digits = 0 )reference_values( metric, sex, level, age, percentile = NULL, z_score = NULL, verbose = FALSE, digits = 0 )
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 |
numeric, corresponding percentile
J. Peter Marquardt
[bodycomp_reference()]
reference_values(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), percentile=c(50,50))reference_values(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), percentile=c(50,50))
For a given constellation of metric, sex, vertebral level, and age returns the corresponding z-scores for a given set of measurements
reference_z_scores( metric, sex, level, age, measurement, verbose = FALSE, digits = 2 )reference_z_scores( metric, sex, level, age, measurement, verbose = FALSE, digits = 2 )
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 |
numeric, corresponding z-score
J. Peter Marquardt
[bodycomp_reference()]
reference_z_scores(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), measurement=c(50,50))reference_z_scores(metric=c("CSFA", "CSFA"), sex=c("Female","Male"), level=c("T5","L3"), age=c(42,68), measurement=c(50,50))