Find Cutoff Value by Nonlinear Regression to Truncated Data

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

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

Value

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

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.

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

#>       mean         sd          K 
#>  -1.002944   1.150871 338.000000 

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

#> Search concentration:  0 1 2 3 4 5 
summary(p)

#> 
#> Formula: cumCount ~ fnorm(conc, mean, sd, K)
#> 
#> Parameters:
#>       Estimate Std. Error t value Pr(>|t|)    
#> mean  -1.54565    0.04257  -36.31 2.91e-08 ***
#> sd     0.91042    0.05768   15.78 4.10e-06 ***
#> K    339.02677    4.00460   84.66 1.83e-10 ***
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#> 
#> Residual standard error: 7.179 on 6 degrees of freedom
#> 
#> Number of iterations to convergence: 8 
#> Achieved convergence tolerance: 8.809e-06
#> 
#> ---
#> ECOFF quantiles:
#>  Q_0.95 Q_0.975  Q_0.99 Q_0.999 
#>       1       2       2       4