set_missing_limits {zlog}

Set Missing Limits in Reference Tables

Description

Sometimes reference limits are not specified. That is often the case for biomarkers that are related to infection or cancer. Using zero as lower boundary results in skewed distributions (Hoffmann et al. 2017; fig. 7). Haeckel et al. 2015 suggested to set the lower reference limit to 0.15 of the upper one.

Usage

set_missing_limits(x, fraction = c(0.15, 20/3))

Arguments

x

data.frame, reference table, has to have the columns: "lower" and "upper", numeric for the lower and upper reference limits. Additional columns are allowed (and ignored).

fraction

numeric(2), targeted fraction of the lower to the upper and the upper to the lower limit. Haeckel et al. 2015 suggested to set the lower limit to 0.15 of the upper one. We choose 20/3 (the reciprocal of 0.15) for the upper to the lower one.

Value

data.frame, the same as x but the "lower" and "upper" columns are modified if there were NA before.

Author(s)

Sebastian Gibb

References

Georg Hoffmann, Frank Klawonn, Ralf Lichtinghagen, and Matthias Orth. 2017. "The Zlog-Value as Basis for the Standardization of Laboratory Results." LaboratoriumsMedizin 41 (1): 23–32. doi:10.1515/labmed-2016-0087.

Rainer Haeckel, Werner Wosniok, Ebrhard Gurr and Burkhard Peil. 2015. "Permissible limits for uncertainty of measurement in laboratory medicine" Clinical Chemistry and Laboratory Medicine 53 (8): 1161-1171. doi:10.1515/cclm-2014-0874.

Examples

reference <- data.frame(
    param = c("albumin", rep("bilirubin", 4)),
    age = c(0, 1, 2, 3, 7),             # ignored
    sex = "both",                       # ignored
    units = c("g/l", rep("µmol/l", 4)), # ignored
    lower = c(35, rep(NA, 4)),  # no real reference values
    upper = c(52, 5, 8, 13, 18) # no real reference values
)
set_missing_limits(reference)
set_missing_limits(reference, fraction = c(0.2, 5))