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Compute Bone Health & Body-Composition Markers (HM-CS v3)

Source: R/bone_markers.R
bone_markers.Rd

Given DXA, anthropometry, and optional bone-turnover markers, computes:

  • OSTA: (weight - age) x 0.2

  • ALMI: Appendicular Lean Mass Index = ALM / height^2

  • FMI: Fat Mass Index = FM / height^2

  • BMD_Tscore: (BMD - ref_mean) / ref_sd and (if in col_map + data) passes through: TBS, HSA, PINP, CTX, BSAP, Osteocalcin.

Usage

bone_markers(
  data,
  col_map,
  na_action = c("keep", "omit", "error"),
  check_extreme = FALSE,
  sds_limit = 6,
  extreme_action = c("cap", "NA", "error"),
  verbose = FALSE
)

Arguments

data

A data.frame or tibble with subject-level DXA/anthropometry data.

col_map

Named list mapping keys to column names. Required keys:

  • age, weight, height, ALM, FM, BMD, BMD_ref_mean, BMD_ref_sd Optional (passed-through if present and found in data): TBS, HSA, PINP, CTX, BSAP, Osteocalcin.

na_action

One of "keep", "omit", or "error" controlling how missing/non-finite input values are treated.

check_extreme

Logical; if TRUE, scan mapped columns whose key names contain "sds" (case-insensitive) for absolute values > sds_limit.

sds_limit

Positive numeric; SDS magnitude limit used when check_extreme is TRUE.

extreme_action

One of "cap", "NA", or "error" for handling extreme SDS-like values.

verbose

Logical; if TRUE, emits progress messages via hm_inform().

Value

A tibble with columns: OSTA, ALMI, FMI, BMD_Tscore, and optionally TBS, HSA, PINP, CTX, BSAP, Osteocalcin (in that order).

Details

Notes:

  • Units: height in meters; ALM, FM, weight in kilograms; BMD in g/cm^2; ALMI/FMI in kg/m^2.

  • Non-finite values are treated as NA; division by zero is prevented by input checks.

References

Koh LK, Ben Sedrine W, Torralba TP, Kung A, others (2001). “A Simple Tool to Identify Asian Women at Increased Risk of Osteoporosis.” Osteoporosis International, 12(8), 699–705. doi:10.1007/s001980170070 . ; Kelly TL, Wilson KE, Heymsfield SB (2009). “Dual Energy X-Ray Absorptiometry Body Composition Reference Values from NHANES.” PLoS ONE, 33(6), 783–789. doi:10.1371/journal.pone.0007038 . ; World Health Organization (1994). Assessment of Fracture Risk and Its Application to Screening for Postmenopausal Osteoporosis, volume 843 of Technical Report Series. World Health Organization. No DOI for this WHO report; see URL, https://iris.who.int/handle/10665/39142.

Examples

library(tibble)
df <- tibble(
  age = c(60, 72), weight = c(65, 50), height = c(1.65, 1.58),
  ALM = c(18.2, 14.7), FM = c(22.0, 20.5),
  BMD = c(0.95, 0.80), BMD_ref_mean = c(1.00, 1.00), BMD_ref_sd = c(0.12, 0.12)
)
col_map <- list(
  age = "age", weight = "weight", height = "height",
  ALM = "ALM", FM = "FM", BMD = "BMD",
  BMD_ref_mean = "BMD_ref_mean", BMD_ref_sd = "BMD_ref_sd"
)
bone_markers(df, col_map)
#> # A tibble: 2 × 10
#>    OSTA  ALMI   FMI BMD_Tscore   TBS   HSA  PINP   CTX  BSAP Osteocalcin
#>   <dbl> <dbl> <dbl>      <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>       <dbl>
#> 1   1    6.69  8.08     -0.417    NA    NA    NA    NA    NA          NA
#> 2  -4.4  5.89  8.21     -1.67     NA    NA    NA    NA    NA          NA