[R] Change how minpack.lm:::summary.nls.lm calculates degrees of freedom

[Valerio Leone Sciabolazza]

Eric,
you are right! If I run the code on a different instance, it works.
There must be something in my old R environment that messed this up.
Thank you very much for checking this out.
Best,
Valerio

On Wed, Aug 19, 2020 at 11:36 AM Eric Berger <ericjberger using gmail.com> wrote:
>
> Hi Valerio,
> I did a copy-paste on your reproducible example and I had no problem with chol(nls.out$hessian).
> In addition to summary() you can look at str() to display the structure of any R object.
>
> > str(nls.out)
>
> List of 9
>  $ par     :List of 3
>   ..$ a: num 8.99
>   ..$ b: num -1.01
>   ..$ c: num 6.02
>  $ hessian : num [1:3, 1:3] 10.3 43.2 19.9 43.2 382.2 ...
>   ..- attr(*, "dimnames")=List of 2
>   .. ..$ : chr [1:3] "a" "b" "c"
>   .. ..$ : chr [1:3] "a" "b" "c"
>  $ fvec    : num [1:100] 0.0232 -0.105 -0.1332 0.0388 0.1482 ...
>  $ info    : int 1
>  $ message : chr "Relative error in the sum of squares is at most `ftol'."
>  $ diag    :List of 3
>   ..$ a: num 9.98
>   ..$ b: num 88.6
>   ..$ c: num 10
>  $ niter   : int 8
>  $ rsstrace: num [1:9] 1966.2 327.2 104.8 53.9 33.2 ...
>  $ deviance: num 1.06
>  - attr(*, "class")= chr "nls.lm"
>
> Also
> > nls.out$hessian
>          a         b         c
> a 10.26361  43.17086  19.89616
> b 43.17086 382.17773 166.43747
> c 19.89616 166.43747 100.00000
>
> HTH,
> Eric
>
>
>
> On Wed, Aug 19, 2020 at 12:17 PM Valerio Leone Sciabolazza <sciabolazza using gmail.com> wrote:
>>
>> Dear R users,
>> I want to modify how the degrees of freedom are calculated from the
>> summary function of the package minpack.lm
>>
>> My first thought was to replicate how minpack.lm:::summary.nls.lm
>> works, and modify the line of the code that is relevant for my task.
>> However, for some reason I am not able to use the code contained in
>> this function to perform this operation.
>>
>> Here is a reproducible example.
>>
>> First, I run a NLLS regression using minpack.lm::nls.lm
>>
>> # From example 1 of the help page of ?minpack.lm::nls.lm
>> library(minpack.lm)
>> x <- seq(0,5,length=100)
>> getPred <- function(parS, xx) parS$a * exp(xx * parS$b) + parS$c
>> pp <- list(a=9,b=-1, c=6)
>> simDNoisy <- getPred(pp,x) + rnorm(length(x),sd=.1)
>> residFun <- function(p, observed, xx) observed - getPred(p,xx)
>> parStart <- list(a=3,b=-.001, c=1)
>> nls.out <- nls.lm(par=parStart, fn = residFun, observed = simDNoisy,
>> xx = x, control = nls.lm.control(nprint=1))
>> summary(nls.out)
>>
>> Now, by running minpack.lm:::summary.nls.lm in the console, I get the following
>> > minpack.lm:::summary.nls.lm
>> function (object, ...)
>> {
>>     param <- coef(object)
>>     pnames <- names(param)
>>     ibb <- chol(object$hessian)
>>     ih <- chol2inv(ibb)
>>     p <- length(param)
>>     rdf <- length(object$fvec) - p
>>     resvar <- deviance(object)/rdf
>>     se <- sqrt(diag(ih) * resvar)
>>     names(se) <- pnames
>>     tval <- param/se
>>     param <- cbind(param, se, tval, 2 * pt(abs(tval), rdf, lower.tail = FALSE))
>>     dimnames(param) <- list(pnames, c("Estimate", "Std. Error",
>>         "t value", "Pr(>|t|)"))
>>     ans <- list(residuals = object$fvec, sigma = sqrt(object$deviance/rdf),
>>         df = c(p, rdf), cov.unscaled = ih, info = object$info,
>>         niter = object$niter, stopmess = object$message, coefficients = param)
>>     class(ans) <- "summary.nls.lm"
>>     ans
>> }
>>
>> Specifically, my task requires to modify the object p of this
>> function, say I want to set p <- 2.
>>
>> To this purpose, I replicate what the summary function does using my
>> object (nls.out), however an error is returned at line three:
>> > param <- coef(nls.out)
>> > pnames <- names(param)
>> > ibb <- chol(nls.out$hessian)
>> Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x),  :
>>   'data' must be of a vector type, was 'NULL'
>>
>> The reason of the error is that there is no nls.out$hessian in nls.out.
>>
>> I guess that I am missing something about how summary functions work,
>> and this is the reason why I cannot use the code from
>> minpack.lm:::summary.nls.lm outside the minpack.lm environment.
>>
>> Does anyone have any hints on how to proceed? Any other way of dealing
>> with this issue will be equally appreciated.
>>
>> Thank you,
>> Valerio
>>
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