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Compute liver-related indices (FLI, NFS, APRI, FIB-4, BARD, ALBI, MELD-XI) with validation and diagnostics

Source: R/liver_markers.R
liver_markers.Rd

Given routine labs and anthropometry, computes:

  • FLI - Fatty Liver Index (Bedogni et al. 2006)

  • NFS - NAFLD Fibrosis Score (Angulo et al. 2007)

  • APRI - AST-to-Platelet Ratio Index

  • FIB4 - Fibrosis-4 Index

  • BARD - BMI-AST/ALT-Diabetes score

  • ALBI - Albumin-Bilirubin score

  • MELD_XI - MELD excluding INR

Usage

liver_markers(
  data,
  col_map = list(BMI = "BMI", waist = "waist", TG = "TG", GGT = "GGT", age = "age", AST =
    "AST", ALT = "ALT", platelets = "platelets", albumin = "albumin", diabetes =
    "diabetes", bilirubin = "bilirubin", creatinine = "creatinine"),
  verbose = FALSE,
  na_action = c("keep", "omit", "error", "ignore", "warn"),
  na_warn_prop = 0.2,
  check_extreme = FALSE,
  extreme_action = c("warn", "cap", "error", "ignore", "NA"),
  extreme_rules = NULL
)

Arguments

data

A data.frame or tibble containing your liver and anthropometry data.

col_map

Named list mapping these keys -> column names in data:

  • BMI (kg/m^2), waist (cm), TG (mg/dL), GGT (U/L),

  • age (years), AST (U/L), ALT (U/L), platelets (10^9/L),

  • albumin (g/L), diabetes (0/1 or logical),

  • bilirubin (mg/dL), creatinine (mg/dL).

verbose

Logical; if TRUE, prints stepwise messages and a final summary. Default FALSE.

na_action

One of c("keep","omit","error") controlling missing-data policy. Default "keep" (preserves prior behavior).

  • "keep": leave NAs; they propagate to outputs.

  • "omit": drop rows with NA in any required input.

  • "error": abort if any required input contains NA.

na_warn_prop

Numeric in \([0,1]\); per-variable threshold for high-missingness warnings. Default 0.2.

check_extreme

Logical; if TRUE, scan inputs for out-of-range values (see extreme_rules). Default FALSE.

extreme_action

One of c("warn","cap","error","ignore") when extremes are detected (only used if check_extreme = TRUE).

  • "warn": only warn (default), "cap": truncate to allowed range, "error": abort, "ignore": do nothing.

extreme_rules

Optional named list of c(min,max) ranges for keys in col_map. If NULL, broad defaults are used.

Value

A tibble with one column per marker: FLI, NFS, APRI, FIB4, BARD, ALBI, MELD_XI.

Details

Enhancements:

  • Robust input validation (columns present, types) with informative errors.

  • Configurable NA policy and optional extreme-value scanning/capping.

  • Data-quality warnings (high missingness, non-positive logs, zero denominators).

  • Verbose stepwise progress and completion summary.

Units (no automatic conversion):

  • BMI: kg/m^2; Waist: cm; TG: mg/dL; GGT/AST/ALT: U/L; Platelets: 10^9/L; Albumin: g/L; Bilirubin: mg/dL; Creatinine: mg/dL.

  • ALBI uses bilirubin in mumol/L internally (converted as bilirubin (mg/dL) * 17.1).

Formulas

  • FLI = logistic(0.953ln(TG) + 0.139BMI + 0.718ln(GGT) + 0.053waist - 15.745) * 100

  • NFS = -1.675 + 0.037age + 0.094BMI + 1.13diabetes + 0.99(AST/ALT) - 0.013platelets - 0.66albumin

  • APRI = (AST / 40) / platelets * 100; assumes AST upper limit of normal = 40 U/L

  • FIB-4 = (age * AST) / (platelets * sqrt(ALT))

  • BARD = 1 if BMI>=28, +1 if AST/ALT>=0.8, +1 if diabetes present; sum in 0,1,2,3

  • ALBI = 0.66log10(bilirubin (mumol/L)) - 0.0852albumin (g/L)

  • MELD-XI = 5.11ln(bilirubin (mg/dL)) + 11.76ln(creatinine (mg/dL)) + 9.44

References

Bedogni G, Bellentani S, Miglioli L, others (2006). “The Fatty Liver Index: a simple and accurate predictor of hepatic steatosis in the general population.” BMC Gastroenterology, 6, 33. doi:10.1186/1471-230X-6-33 . Angulo P, Hui JM, Marchesini G, others (2007). “The NAFLD fibrosis score: a noninvasive system that identifies liver fibrosis in patients with NAFLD.” Hepatology, 45(4), 846–854. doi:10.1002/hep.21496 . Wai CT, Greenson JK, Fontana RJ, others (2003). “A simple noninvasive index can predict both significant fibrosis and cirrhosis in patients with chronic hepatitis C.” Hepatology, 38(2), 518–526. doi:10.1053/jhep.2003.50346 . Sterling RK, Lissen E, Clumeck N, others (2006). “Development of a simple noninvasive index to predict significant fibrosis in patients with HIV/HCV coinfection (FIB-4).” Hepatology, 43(6), 1317–1325. doi:10.1002/hep.21178 . Harrison SA, Oliver D, Arnold HL, others (2008). “Development and validation of a simple NAFLD clinical scoring system for identifying patients without advanced disease.” Gut, 57(10), 1441–1447. doi:10.1136/gut.2007.146019 . Johnson PJ, Berhane S, Kagebayashi C, others (2015). “Assessment of liver function in patients with hepatocellular carcinoma: the ALBI grade.” Journal of Clinical Oncology, 33(6), 550–558. doi:10.1200/JCO.2014.57.9151 . Heuman DM, Abou-Assi SG, Habib A, others (2006). “MELD-XI: A rational approach to "sickest first" liver transplantation in cirrhotic patients requiring anticoagulant therapy.” Liver Transplantation, 13(1), 30–37. doi:10.1002/lt.20906 .

See also

inflammatory_markers(), kidney_failure_risk(), iAge()

Examples

library(tibble)
df <- tibble(
  BMI           = 24,
  waist         = 80,
  TG = 150, # mg/dL
  GGT           = 30,
  age           = 45,
  AST           = 25,
  ALT           = 20,
  platelets     = 250, # 10^9/L
  albumin       = 42,  # g/L
  diabetes      = FALSE,
  bilirubin     = 1.0, # mg/dL
  creatinine    = 0.9  # mg/dL
)
liver_markers(df, verbose = TRUE)
#> liver_markers(): preparing inputs
#> liver_markers(): column map: BMI -> 'BMI', waist -> 'waist', TG -> 'TG', GGT -> 'GGT', age -> 'age', AST -> 'AST', ALT -> 'ALT', platelets -> 'platelets', albumin -> 'albumin', diabetes -> 'diabetes', bilirubin -> 'bilirubin', creatinine -> 'creatinine'
#> liver_markers(): results: FLI 1/1, NFS 1/1, APRI 1/1, FIB4 1/1, BARD 1/1, ALBI 1/1, MELD_XI 1/1
#> # A tibble: 1 × 7
#>     FLI   NFS  APRI  FIB4  BARD  ALBI MELD_XI
#>   <dbl> <dbl> <dbl> <dbl> <int> <dbl>   <dbl>
#> 1  27.9 -27.5  0.25  1.01     1 -2.76    8.20

# \donttest{
# With extreme-value capping and diagnostics
liver_markers(
  df,
  check_extreme = TRUE,
  extreme_action = "cap",
  verbose = TRUE
)
#> liver_markers(): preparing inputs
#> liver_markers(): column map: BMI -> 'BMI', waist -> 'waist', TG -> 'TG', GGT -> 'GGT', age -> 'age', AST -> 'AST', ALT -> 'ALT', platelets -> 'platelets', albumin -> 'albumin', diabetes -> 'diabetes', bilirubin -> 'bilirubin', creatinine -> 'creatinine'
#> liver_markers(): results: FLI 1/1, NFS 1/1, APRI 1/1, FIB4 1/1, BARD 1/1, ALBI 1/1, MELD_XI 1/1
#> # A tibble: 1 × 7
#>     FLI   NFS  APRI  FIB4  BARD  ALBI MELD_XI
#>   <dbl> <dbl> <dbl> <dbl> <int> <dbl>   <dbl>
#> 1  27.9 -27.5  0.25  1.01     1 -2.76    8.20
# }