[R] outer-question

[Thomas Lumley]

You want FAQ 7.17 Why does outer() behave strangely with my function?

 	-thomas

On Thu, 27 Oct 2005, Rau, Roland wrote:

> Dear all,
>
> This is a rather lengthy message, but I don't know what I made wrong in
> my real example since the simple code works.
> I have two variables a, b and a function f for which I would like to
> calculate all possible combinations of the values of a and b.
> If f is multiplication, I would simply do:
>
> a <- 1:5
> b <- 1:5
> outer(a,b)
>
> ## A bit more complicated is this:
> f <- function(a,b,d) {
> 	return(a*b+(sum(d)))
> }
> additional <- runif(100)
> outer(X=a, Y=b, FUN=f, d=additional)
>
> ## So far so good. But now my real example. I would like to plot the
> ## log-likelihood surface for two parameters alpha and beta of
> ## a Gompertz distribution with given data
>
> ### I have a function to generate random-numbers from a
> Gompertz-Distribution
> ### (using the 'inversion method')
>
> random.gomp <- function(n, alpha, beta) {
>            return( (log(1-(beta/alpha*log(1-runif(n)))))/beta)
> }
>
> ## Now I generate some 'lifetimes'
> no.people <- 1000
> al <- 0.1
> bet <- 0.1
> lifetimes <- random.gomp(n=no.people, alpha=al, beta=bet)
>
> ### Since I neither have censoring nor truncation in this simple case,
> ### the log-likelihood should be simply the sum of the log of the
> ### the densities (following the parametrization of Klein/Moeschberger
> ### Survival Analysis, p. 38)
>
> loggomp <- function(alphas, betas, timep) {
>  return(sum(log(alphas) + betas*timep + (alphas/betas *
> (1-exp(betas*timep)))))
> }
>
> ### Now I thought I could obtain a matrix of the log-likelihood surface
> ### by specifying possible values for alpha and beta with the given
> data.
> ### I was able to produce this matrix with two for-loops. But I thought
> ### I could use also 'outer' in this case.
> ### This is what I tried:
>
> possible.alphas <- seq(from=0.05, to=0.15, length=30)
> possible.betas <- seq(from=0.05, to=0.15, length=30)
>
> outer(X=possible.alphas, Y=possible.betas, FUN=loggomp, timep=lifetimes)
>
> ### But the result is:
>> outer(X=possible.alphas, Y=possible.betas, FUN=loggomp,
> timep=lifetimes)
> Error in outer(X = possible.alphas, Y = possible.betas, FUN = loggomp,
> :
>        dim<- : dims [product 900] do not match the length of object [1]
> In addition: Warning messages:
> ...
>
> ### Can somebody give me some hint where the problem is?
> ### I checked my definition of 'loggomp' but I thought this looks fine:
> loggomp(alphas=possible.alphas[1], betas=possible.betas[1],
> timep=lifetimes)
> loggomp(alphas=possible.alphas[4], betas=possible.betas[10],
> timep=lifetimes)
> loggomp(alphas=possible.alphas[3], betas=possible.betas[11],
> timep=lifetimes)
>
>
> ### I'd appreciate any kind of advice.
> ### Thanks a lot in advance.
> ### Roland
>
>
> +++++
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Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle