> 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$x is NULL and NULL-aNumber is numeric(). -Bill On Sun, Mar 14, 2021 at 9:46 AM Luigi Marongiu <marongiu.lu...@gmail.com> wrote: > > Hello, > I would like to use the Rutledge equation > (https://pubmed.ncbi.nlm.nih.gov/15601990/) to model PCR data. The > equation is: > Fc = Fmax / (1+exp(-(C-Chalf)/k)) + Fb > I defined the equation and another that subtracts the values from the > expectations. I used minpack.lm to get the parameters, but I got an > error: > ``` > > > library("minpack.lm") > > h <- c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8, 4.52, -7.16, -17.39, > + -14.29, -20.26, -14.99, -21.05, -20.64, -8.03, -21.56, -1.28, 15.01, > + 75.26, 191.76, 455.09, 985.96, 1825.59, 2908.08, 3993.18, 5059.94, > + 6071.93, 6986.32, 7796.01, 8502.25, 9111.46, 9638.01, 10077.19, > + 10452.02, 10751.81, 11017.49, 11240.37, 11427.47, 11570.07, 11684.96, > + 11781.77, 11863.35, 11927.44, 11980.81, 12021.88, 12058.35, 12100.63, > + 12133.57, 12148.89, 12137.09) > > high <- h[1:45] > > MaxFluo <- max(high) > > halfFluo <- MaxFluo/2 > > halfCycle = 27 > > find_slope <- function(X, Y) { > + Slope <- c(0) > + for (i in 2:length(X)) { > + delta_x <- X[i] - X[i-1] > + delta_y <- Y[i] - Y[i-1] > + Slope[i] <- delta_y/delta_x > + } > + return(Slope) > + } > > slopes <- find_slope(1:45, high) > > > > rutledge <- function(m, s, M, B, x) { > + divisor = 1 + exp(-1* ((x-m)/s) ) > + y = (M/divisor) + B > + return(y) > + } > > rutledge_param <- function(p, x, y) ((p$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@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. ______________________________________________ R-help@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.
