[R] Failure in predicting parameters

[Bill Dunlap]

> rutledge_param <- function(p, x, y) ((p$M / (1 + exp(-1*(p$x-p$m)/p$s))) + p$B) - y

Did you mean that p$x to be just x?  As is, this returns numeric(0)
for the p that nls.lm gives it because p$x is NULL and NULL-aNumber is
numeric().

-Bill

On Sun, Mar 14, 2021 at 9:46 AM Luigi Marongiu <marongiu.luigi using gmail.com> wrote:
>
> Hello,
> I would like to use the Rutledge equation
> (https://pubmed.ncbi.nlm.nih.gov/15601990/) to model PCR data. The
> equation is:
> Fc = Fmax / (1+exp(-(C-Chalf)/k)) + Fb
> I defined the equation and another that subtracts the values from the
> expectations. I used minpack.lm to get the parameters, but I got an
> error:
> ```
>
> > library("minpack.lm")
> > h <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39,
> +        -14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 15.01,
> +        75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 5059.94,
> +        6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19,
> +        10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 11684.96,
> +        11781.77, 11863.35, 11927.44, 11980.81, 12021.88, 12058.35, 12100.63,
> +        12133.57, 12148.89, 12137.09)
> > high <- h[1:45]
> > MaxFluo <- max(high)
> > halfFluo <- MaxFluo/2
> > halfCycle = 27
> > find_slope <- function(X, Y) {
> +   Slope <- c(0)
> +   for (i in 2:length(X)) {
> +     delta_x <- X[i] - X[i-1]
> +     delta_y <- Y[i] - Y[i-1]
> +     Slope[i] <- delta_y/delta_x
> +   }
> +   return(Slope)
> + }
> > slopes <- find_slope(1:45, high)
> >
> > rutledge <- function(m, s, M, B, x) {
> +   divisor = 1 + exp(-1* ((x-m)/s) )
> +   y = (M/divisor) + B
> +   return(y)
> + }
> > rutledge_param <- function(p, x, y) ((p$M / (1 + exp(-1*(p$x-p$m)/p$s))) + p$B) - y
> >
> >
> > init = rutledge(halfFluo, slopes, MaxFluo, 0, high)
> > points(1:45, init, type="l", col="red")
> > estim <- nls.lm(par = list(m = halfFluo, s = slopes, M = MaxFluo, B = high[1]),
> +                 fn = rutledge_param, x = 1:45, y = high)
> Error in nls.lm(par = list(m = halfFluo, s = slopes, M = MaxFluo, B =
> high[1]),  :
>   evaluation of fn function returns non-sensible value!
> ```
>
> Where could the error be?
>
>
> --
> Best regards,
> Luigi
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.