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Calculate pulmonary function markers (FEV1/FVC, z-scores, percent predicted, LLN, etc.)

Source: R/pulmo_markers.R
pulmo_markers.Rd

Uses the rspiro reference equations to compute predicted normals, z-scores, percent predicted and lower limits of normal (LLN) for FEV1, FVC, and the FEV1/FVC ratio.

Usage

pulmo_markers(
  data,
  equation = c("GLI", "GLIgl", "NHANES3"),
  na_action = c("keep", "omit", "error"),
  na_warn_prop = 0.2,
  verbose = FALSE
)

Arguments

data

A data.frame or tibble with columns:

  • age (numeric): years

  • sex (character or numeric): "male"/"female" (case-insensitive) or codes 1/2 or 0/1

  • height (numeric): cm or m (auto-detected)

  • ethnicity (character): e.g. "Caucasian", "African-American", "NE Asian", "SE Asian", "Other/Mixed"

  • fev1 (numeric): observed FEV1 in L

  • fvc (numeric): observed FVC in L

equation

One of c("GLI","GLIgl","NHANES3") (see rspiro for details). GLIgl ignores ethnicity.

na_action

One of c("keep","omit","error") for handling missing values in required inputs. Default "keep".

na_warn_prop

Proportion \([0,1]\) to trigger high-missingness warnings on required inputs. Default 0.2.

verbose

Logical; if TRUE prints progress messages and a completion summary.

Value

A tibble with columns:

  • fev1_pred, fev1_z, fev1_pctpred, fev1_LLN

  • fvc_pred, fvc_z, fvc_pctpred, fvc_LLN

  • fev1_fvc_ratio, fev1_fvc_pred, fev1_fvc_z, fev1_fvc_pctpred, fev1_fvc_LLN

Details

Inputs are validated, missingness is handled via na_action, and heights are auto-detected as cm when any height > 3; otherwise interpreted as metres (no automatic unit conversion beyond that heuristic, preserving prior behavior).

References

Quanjer PH, Stanojevic S, Cole TJ, Baur X, Hall GL, Culver BH, et al. (2012). “Multi-ethnic reference values for spirometry for the 3–95-yr age range: the global lung function 2012 equations.” European Respiratory Journal, 40, 1324–1343. doi:10.1183/09031936.00080312 . Hankinson JL, Odencrantz JR, Fedan KB (1999). “Spirometric reference values from a sample of the general U.S. population.” American Journal of Respiratory and Critical Care Medicine, 159, 179–187. doi:10.1164/ajrccm.159.1.9712108 . Bowerman SD, Quanjer PH, others (2023). “GLI-Global update.” European Respiratory Journal, 61, 2201632. DOI not resolvable in Crossref as of 2026-03-16.

See also

rspiro

Examples

if (requireNamespace("rspiro", quietly = TRUE)) {
  df <- data.frame(
    age = c(40, 55), sex = c("male", "female"),
    height = c(175, 162), ethnicity = c("Caucasian", "Caucasian"),
    fev1 = c(3.5, 2.4), fvc = c(4.4, 3.1)
  )
  pulmo_markers(df)
}
#> # A tibble: 2 × 13
#>   fev1_pred fev1_z fev1_pctpred fev1_LLN fvc_pred  fvc_z fvc_pctpred fvc_LLN
#>       <dbl>  <dbl>        <dbl>    <dbl>    <dbl>  <dbl>       <dbl>   <dbl>
#> 1      4.08 -1.13          85.8     3.23     5.05 -1.04         87.0    4.02
#> 2      2.62 -0.595         91.7     2.01     3.29 -0.410        94.2    2.54
#> # ℹ 5 more variables: fev1_fvc_ratio <dbl>, fev1_fvc_pred <dbl>,
#> #   fev1_fvc_z <dbl>, fev1_fvc_pctpred <dbl>, fev1_fvc_LLN <dbl>