ecoffinder_nls: Find Cutoff Value by Nonlinear Regression to Truncated Data

In tpetzoldt/antibioticR: Analysis of Antibiotic Resistance Data

Description

Identifies the wild-type sub-population by fitting a cumulative normal distribution to subsets of MIC or ID data.

Usage

ecoffinder_nls(
  conc,
  count,
  startpar = "mode",
  concentrations = NA,
  log2 = TRUE,
  plot = TRUE
)

Arguments

conc	concentration of the antibiotic
count	raw frequency
startpar	start parameters for the nonlinear search, or "mode" resp. "mean" for an automatic determination
concentrations	which concentrations are tested
log2	logical determining if conc are log-transformed or not
plot	logical, switch visualization on or off

Details

Start values for the nonlinear regression can be automatically determined with function ecoffinder_startpar.

The default search interval starts one concentration level above the mode resp. mean.

Value

an object of class abr_ecoffinder-class containing the fitted parameters and statistics of the final and intermediate fits.

References

Turnidge, J., Kahlmeter, G., Kronvall, G. (2006) Statistical characterization of bacterial wild-type MIC value distributions and the determination of epidemiological cut-off values. Clin Microbial Infect 12: 418-425 doi: 10.1111/j.1469-0691.2006.01377.x

See Also

ecoffinder_startpar for heuristic methods to guess start parameters
ECOFFinder for an interactice shiny app

Examples

## raw data contain NA values
data(micdata)
plot(freq ~ log2(conc), data=micdata, type="h")

## discard NA values
measured <- na.omit(micdata)

## cumulative plot
plot(cumsum(freq) ~ log2(conc), data=measured, type="l")

x <- log2(measured$conc)
y <- measured$freq

## heuristic start values
pstart <- ecoffinder_startpar(x, y)
pstart

## nonlinear regression
p <- ecoffinder_nls(x, y, pstart)
summary(p)

tpetzoldt/antibioticR documentation built on Sept. 25, 2021, 1:17 p.m.