R help - Jan 2006 - apply

Hello,
I have a dataset d which is
 >d
         pop     catch 
1   66462.01 10807.757 
2   87486.73 46257.885 
3   57211.64  9345.058 
4   71321.62  4892.868 
5  100024.89 27334.248 
6  104504.91 48535.092 
7   95295.51 39348.195 
8   93737.35 34343.489 
9   89375.05 28750.743 
10  95312.65 30755.064 
11 100888.17 55404.370 
12  84790.23 37751.074 
13  81129.82 29277.443 
14  69797.09 21500.398 
15  61690.34 18199.664 
16  60671.08 19349.051 
17  62852.57 16300.982 
18  90646.32 34793.148 

And a function opt1:

opt1 <- function (x) {
  Z <- x + M
  c.hat <- (x/Z)*pop*(1-exp(-Z))
  y <- (catch - c.hat)^2
  return(y)
  }

And define M = 0.25 
For each row I want to return a value F that is a minimization of the
opt1 function

I have tried many variations of:
d$F<-apply(d,2,optim(0.3,opt1,method="BFGS")
and even:
For (I in 1:length(pop))apply(d,2,optim(0.3,opt1,method="BFGS"))

Every time I get the same error message

Error in optim(0.3, opt1, method = "BFGS") : 
        objective function in optim evaluates to length 18 not 1

So the apply function is returning 18 values of F which I want but the
function only wants to return 1 value.

Any Suggestions.
Thanks,
Cam

You are not calling apply() properly. Please read relevant reference
material carefully. You might also wish to pick up one of the several good
books on R (check CRAN website) -- I like V&R's S PROGRAMMING.

I did not go through your example in detail, but your apply() call should be
of the form

apply(d,2,function(x)optim(x,...))

You may or may not get into scoping problems with the opt1 argument and have
to pass it in explicitly -- I can't remember how things work with optim. 

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
 
"The business of the statistician is to catalyze the scientific learning
process."  - George E. P. Box
 
 
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of 
> Guenther, Cameron
> Sent: Friday, January 13, 2006 11:03 AM
> To: R-help at r-project.org
> Subject: [R] apply
> 
> Hello,
> I have a dataset d which is
>  >d
>          pop     catch 
> 1   66462.01 10807.757 
> 2   87486.73 46257.885 
> 3   57211.64  9345.058 
> 4   71321.62  4892.868 
> 5  100024.89 27334.248 
> 6  104504.91 48535.092 
> 7   95295.51 39348.195 
> 8   93737.35 34343.489 
> 9   89375.05 28750.743 
> 10  95312.65 30755.064 
> 11 100888.17 55404.370 
> 12  84790.23 37751.074 
> 13  81129.82 29277.443 
> 14  69797.09 21500.398 
> 15  61690.34 18199.664 
> 16  60671.08 19349.051 
> 17  62852.57 16300.982 
> 18  90646.32 34793.148 
> 
> And a function opt1:
> 
> opt1 <- function (x) {
>   Z <- x + M
>   c.hat <- (x/Z)*pop*(1-exp(-Z))
>   y <- (catch - c.hat)^2
>   return(y)
>   }
> 
> And define M = 0.25 
> For each row I want to return a value F that is a minimization of the
> opt1 function
> 
> I have tried many variations of:
> d$F<-apply(d,2,optim(0.3,opt1,method="BFGS")
> and even:
> For (I in 1:length(pop))apply(d,2,optim(0.3,opt1,method="BFGS"))
> 
> Every time I get the same error message
> 
> Error in optim(0.3, opt1, method = "BFGS") : 
>         objective function in optim evaluates to length 18 not 1
> 
> So the apply function is returning 18 values of F which I want but the
> function only wants to return 1 value.
> 
> Any Suggestions.
> Thanks,
> Cam
> 
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