No, I got the same. I reckon the problem is with X: this was I scalar, I was providing a vector with the actual values. Ho can mle2 optimize without knowing what are the actual data? and what values should I give for X? Thank you
On Tue, Jun 30, 2020 at 2:06 PM Eric Berger <ericjber...@gmail.com> wrote: > > I have no problem with the following code: > > library(bbmle) > holling <- function( a, b, x ) { > a*x^2 / (b^2 + x^2) > } > A=3261 > B=10 > X=30 > foo <- mle2( minuslogl=holling, start=list(a=A,b=B,x=X) ) > > foo > > # Call: > # mle2(minuslogl = holling, start = list(a = A, b = B, x = X)) > > # Coefficients: > # a b x > # 3.260044e+03 7.315124e+01 -2.332448e-14 > > # Log-likelihood: 0 > > > Does this code create a problem for you? > > On Tue, Jun 30, 2020 at 3:00 PM Luigi Marongiu <marongiu.lu...@gmail.com> > wrote: > > > > Sorry for the typo, but I have the same error if using b instead of h: > > ``` > > > O = mle2(minuslogl = holling, start = list(a = A, b = B)) > > > Error in minuslogl(a = 3261, b = 10) : > > argument "x" is missing, with no default > > # let's add x > > X = c(8, 24, 39, 63, 89, 115, 153, 196, 242, 287, 344, 408, > > 473, > > 546, 619, 705, 794, 891, 999, 1096, 1242, 1363, 1506, 1648, 1753, > > 1851, 1987, 2101, 2219, 2328, 2425, 2575, 2646, 2698, 2727, 2771, > > 2818, > > 2853, 2895, 2926, 2964, 2995, 3025, 3053, 3080, 3102, 3119, 3141, > > 3152, > > 3159, 3172, 3182, 3196, 3209, 3220, 3231, 3239, 3246, 3252, 3261) > > O = mle2(minuslogl = holling, start = list(a = A, b = B, x = X)) > > Error in mle2(minuslogl = holling, start = list(a = A, b = B, x = X)) : > > some named arguments in 'start' are not arguments to the specified > > log-likelihood function > > ``` > > And even if I use the log-likelihood function: > > ``` > > O = mle2(minuslogl = nll, start = list(p = c(A, B), n = 57200000, x = X)) > > > Error in mle2(minuslogl = nll, start = list(p = c(A, B), n = 57200000, : > > some named arguments in 'start' are not arguments to the specified > > log-likelihood function > > ``` > > > > On Tue, Jun 30, 2020 at 12:03 PM Eric Berger <ericjber...@gmail.com> wrote: > > > > > > Hi Luigi, > > > I took a quick look. > > > > > > First error: > > > You wrote > > > O = mle2(minuslogl = holling, start = list(a = A, h = B, x = X)) > > > > > > it should be b=B (h is not an argument of holling()) > > > The error message gave very precise information! > > > > > > Second error: > > > You wrote > > > O = mle2(minuslogl = nll, start = list(a = A, h = B), data = list(n > > > = 57200000, k = A)) > > > but the arguments to nll() are p,n,k. Setting start to values for a > > > and h causes the function to complain. > > > > > > HTH, > > > Eric > > > > > > On Tue, Jun 30, 2020 at 12:45 PM Luigi Marongiu > > > <marongiu.lu...@gmail.com> wrote: > > > > > > > > Hello, > > > > I would like to optimize the function: > > > > ``` > > > > holling = function(a, b, x) { > > > > y = (a * x^2) / (b^2 + x^2) > > > > return(y) > > > > } > > > > ``` > > > > I am trying to use the function mle2 from bbmle, but how do I need to > > > > feed the data? > > > > If I give `holling` as function to be optimized, passing the starting > > > > values for `a`, `b`, and `x`, I get: > > > > ``` > > > > X = 1:60 > > > > A = 3261 > > > > B = 10 > > > > O = mle2(minuslogl = holling, start = list(a = A, h = B, x = X)) > > > > > Error in mle2(minuslogl = holling, start = list(a = A, b = B, x = X)) > > > > > : > > > > some named arguments in 'start' are not arguments to the specified > > > > log-likelihood function > > > > ``` > > > > If I pass the negative log-function (assuming a binomial distribution > > > > of the data, which I am not sure about) > > > > ``` > > > > nll = function(p, n, k) { > > > > # extract parms > > > > a = p[1] > > > > h = p[2] > > > > # calculate probability of attack > > > > pred = a/(1+a*h*n) > > > > # calc NLL > > > > -sum(dbinom(k, prob = pred, size = n, log = TRUE)) > > > > } > > > > ``` > > > > then I get the same error: > > > > ``` > > > > > O = mle2(minuslogl = nll, start = list(a = A, h = B), > > > > + data = list(n = 57200000, k = A)) > > > > Error in mle2(minuslogl = nll, start = list(a = A, h = B), data = > > > > list(n = 57200000, : > > > > some named arguments in 'start' are not arguments to the specified > > > > log-likelihood function > > > > ``` > > > > but with the disadvantage of working on an assumed function (nll). > > > > How can I optimize the function `holling` properly? > > > > Thank you > > > > > > > > > > > > > > > > > > > > -- > > > > 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. > > > > > > > > -- > > Best regards, > > Luigi -- 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.