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Kidney Failure Risk Equation (KFRE, 2- and 5-year risk)

Source: R/kidney_kfre.R
kidney_failure_risk.Rd

Compute 2- and 5-year risk of end-stage kidney disease using the original 4-variable KFRE (Tangri et al., 2011) with optional data-quality diagnostics, extreme-value handling, and verbose progress reporting.

Usage

kidney_failure_risk(
  data,
  col_map = list(age = "age", sex = "sex", eGFR = "eGFR", UACR = "UACR"),
  na_action = c("keep", "error", "omit", "warn"),
  na_warn_prop = 0.2,
  check_extreme = FALSE,
  extreme_action = c("warn", "cap", "error", "ignore", "NA"),
  extreme_rules = NULL,
  verbose = FALSE
)

Arguments

data

A data.frame or tibble containing at least the columns mapped in col_map.

col_map

Named list mapping:

  • age -> age in years

  • sex -> sex code (1 = male, 2 = female)

  • eGFR -> estimated GFR (mL/min/1.73 m^2)

  • UACR -> urine albumin-to-creatinine ratio (mg/g)

na_action

One of c("keep","error","omit","warn"). Default "keep" to preserve previous behavior:

  • "keep": propagate NA/NaN through logs and outputs.

  • "error": abort if any required input contains missing values.

  • "omit": drop rows with NA in required inputs before computation.

  • "warn": like "keep" but emits high-missingness warnings.

na_warn_prop

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

check_extreme

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

extreme_action

One of c("warn","cap","error","ignore","NA") used when check_extreme = TRUE.

  • "warn": only warn about out-of-range values (default).

  • "cap": truncate to range and warn.

  • "error": abort if any out-of-range is detected.

  • "ignore": do nothing.

  • "NA": set out-of-range input values to NA before computation.

extreme_rules

Optional named list of numeric c(min,max) ranges for c(age, eGFR, UACR). If NULL, broad defaults are used: age (18, 120), eGFR (1, 200), UACR (0.1, 10000) (mg/g).

verbose

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

Value

A tibble with:

  • KFRE_2yr risk (0-1) at 2 years

  • KFRE_5yr risk (0-1) at 5 years

Details

This function preserves prior behavior by default:

  • Inputs are taken as-is; NA values propagate to outputs (na_action = "keep").

  • No capping or out-of-range checks are applied unless requested.

Units (no automatic conversion):

  • age: years; sex: 1 = male, 2 = female

  • eGFR: mL/min/1.73 m^2

  • UACR: mg/g (albumin-to-creatinine ratio)

Details

  • Prognostic index: PI = 0.220 x log(age) + (-0.556) x log(eGFR) + 0.451 x log(UACR) + 0.391 x (male) where male = 1 if sex == 1, else 0.

  • Baseline survival: S0(2y) = 0.934, S0(5y) = 0.881 (Tangri 2011).

  • Risks: KFRE_t = 1 - (S0_t ^ exp(PI)).

  • The 2016 JAMA study provides a large, multinational validation of the KFRE in humans.

References

Tangri N, Stevens LA, Griffith J, others (2011). “A predictive model for progression of chronic kidney disease to kidney failure.” JAMA, 305(15), 1553–1559. doi:10.1001/jama.2011.451 . ; Tangri N, Grams ME, Levey AS, others (2016). “Multinational assessment of accuracy of equations for predicting risk of kidney failure: a meta-analysis.” JAMA, 315(2), 164–174. doi:10.1001/jama.2015.18202 . ; Gansevoort RT, Matsushita K, van der Velde M, Astor BC, others (2011). “Lower estimated GFR and higher albuminuria are associated with adverse kidney outcomes. A collaborative meta-analysis of general and high-risk population cohorts.” Kidney International, 80(1), 93–104. doi:10.1038/ki.2010.531 . ; Hundemer GL, Tangri N, Sood MM, Ramsay T, Bugeja A, Brown PA, Clark EG, Biyani M, White CA, Akbari A (2020). “Performance of the Kidney Failure Risk Equation by Disease Etiology in Advanced CKD.” Clinical Journal of the American Society of Nephrology, 15(10), 1424–1432. doi:10.2215/CJN.03940320 .

See also

inflammatory_markers(), iAge(), impute_missing()

Examples

library(tibble)
df <- tibble(
  age  = c(65, 72),
  sex  = c(1, 2),          # 1 = male, 2 = female
  eGFR = c(45, 22),        # mL/min/1.73 m^2
  UACR = c(300, 1200)      # mg/g
)
# Default behavior (NA propagate, no extreme checks)
kidney_failure_risk(
  data = df,
  col_map = list(age = "age", sex = "sex", eGFR = "eGFR", UACR = "UACR")
)
#> # A tibble: 2 × 2
#>   KFRE_2yr KFRE_5yr
#>      <dbl>    <dbl>
#> 1    0.329    0.523
#> 2    0.536    0.759

# With diagnostics and capping
# \donttest{
kidney_failure_risk(
  data = df,
  col_map = list(age = "age", sex = "sex", eGFR = "eGFR", UACR = "UACR"),
  check_extreme = TRUE, extreme_action = "cap", verbose = TRUE
)
#> kidney_failure_risk(): preparing inputs
#> kidney_failure_risk(): column map: age -> 'age', sex -> 'sex', eGFR -> 'eGFR', UACR -> 'UACR'
#> kidney_failure_risk(): results: KFRE_2yr 2/2, KFRE_5yr 2/2
#> # A tibble: 2 × 2
#>   KFRE_2yr KFRE_5yr
#>      <dbl>    <dbl>
#> 1    0.329    0.523
#> 2    0.536    0.759
# }