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Scott Norton

2003-Oct-28 03:34 UTC

[R] outer function problems

I'm pulling my hair (and there's not much left!) on this one. Basically
I'm
not getting the same result t when I "step" through the program and
evaluate
each element separately than when I use the outer() function in the
FindLikelihood() function below.

 

Here's the functions:

 

Dk<- function(xk,A,B) 

{

n0 *(A*exp(-0.5*(xk/w)^2) + B)

}

 

FindLikelihood <- function(Nk)

{

A <- seq(0.2,3,by=0.2)

B <- seq(0.2,3,by=0.2)

k <-7

L <- outer(A, B, function(A,B) sum( (Nk*log(Dk(seq(-k,k),A,B))) -
Dk(seq(-k,k),A,B) ))

return(L)

}

 

 

where Nk <- c(70 , 67 , 75 , 77 , 74 ,102,  75, 104 , 94 , 74 , 78 , 79 , 83
, 73 , 76)

 

 

Here's an excerpt from my debug session..

 
> Nk
 [1]  70  67  75  77  74 102  75 104  94  74  78  79  83  73  76
> debug(FindLikelihood)
> L<-FindLikelihood(Nk)
debugging in: FindLikelihood(Nk)

debug: {

    A <- seq(0.2, 3, by = 0.2)

    B <- seq(0.2, 3, by = 0.2)

    k <- 7

    L <- outer(A, B, function(A, B) sum((Nk * log(Dk(seq(-k, 

        k), A, B))) - Dk(seq(-k, k), A, B)))

    return(L)

}

Browse[1]> n

debug: A <- seq(0.2, 3, by = 0.2)

Browse[1]> n

debug: B <- seq(0.2, 3, by = 0.2)

Browse[1]> n

debug: k <- 7

Browse[1]> n

debug: L <- outer(A, B, function(A, B) sum((Nk * log(Dk(seq(-k, k), 

    A, B))) - Dk(seq(-k, k), A, B)))

Browse[1]> sum((Nk * log(Dk(seq(-k, k),0.2,0.2))) - Dk(seq(-k, k), 0.2,
0.2))      # WHY DOES THIS LINE GIVE ME THE CORRECT RESULT WHEN I SUBSTITUTE
0.2, 0.2 FOR A AND B

[1] 2495.242

Browse[1]> outer(A, B, function(A, B) sum((Nk * log(Dk(seq(-k, k), 

+     A, B))) - Dk(seq(-k, k), A, B)))

          [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]
[,8]

 [1,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48    # BUT ELEMENT (1,1) WHICH SHOULD ALSO BE (A,B) = (0.2, 0.2),
GIVES THE INCORRECT RESULT????

 [2,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

 [3,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

 [4,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

 [5,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

 [6,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

 [7,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

 [8,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

 [9,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

[10,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

[11,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

[12,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

[13,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

[14,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

[15,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
58389.48

          [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]

 [1,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

 [2,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

 [3,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

 [4,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

 [5,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

 [6,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

 [7,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

 [8,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

 [9,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

[10,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

[11,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

[12,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

[13,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

[14,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

[15,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48

Browse[1]>

 

As "commented" above, when I evaluate a single A,B element (i.e.
A=0.2,
B=0.2) I get a different result than when I use OUTER() which should also be
evaluating at A=0.2, B=0.2??

 

Any help appreciated.  I know I'm probably doing something overlooking
something simple, but can anyone point it out???

 

Thanks!

-Scott

 

Scott Norton, Ph.D.

Engineering Manager

Nanoplex Technologies, Inc.

2375 Garcia Ave.

Mountain View, CA 94043

www.nanoplextech.com

 


	[[alternative HTML version deleted]]

Spencer Graves

2003-Oct-28 13:12 UTC

head link

[R] outer function problems

I don't know that this is your problem, but I see a potential 
scoping issue:  It is not obvious to me where Dk is getting n0 and w.  
I've solved this kind of problem in the past by declaring n0 and w as 
explicit arguments to Dk and then passing them explicitly via "..." in
"outer".  In general, I prefer to avoid accessing globals from within 
functions.  This may not help you here, but it might help in the future. 

      hope this helps.  spencer graves

Scott Norton wrote:
>I'm pulling my hair (and there's not much left!) on this one.
Basically I'm
>not getting the same result t when I "step" through the program
and evaluate
>each element separately than when I use the outer() function in the
>FindLikelihood() function below.
>
> 
>
>Here's the functions:
>
> 
>
>Dk<- function(xk,A,B) 
>
>{
>
>n0 *(A*exp(-0.5*(xk/w)^2) + B)
>
>}
>
> 
>
>FindLikelihood <- function(Nk)
>
>{
>
>A <- seq(0.2,3,by=0.2)
>
>B <- seq(0.2,3,by=0.2)
>
>k <-7
>
>L <- outer(A, B, function(A,B) sum( (Nk*log(Dk(seq(-k,k),A,B))) -
>Dk(seq(-k,k),A,B) ))
>
>return(L)
>
>}
>
> 
>
> 
>
>where Nk <- c(70 , 67 , 75 , 77 , 74 ,102,  75, 104 , 94 , 74 , 78 , 79 ,
83
>, 73 , 76)
>
> 
>
> 
>
>Here's an excerpt from my debug session..
>
> 
>
>  
>
>>Nk
>>    
>>
>
> [1]  70  67  75  77  74 102  75 104  94  74  78  79  83  73  76
>
>  
>
>>debug(FindLikelihood)
>>    
>>
>
>  
>
>>L<-FindLikelihood(Nk)
>>    
>>
>
>debugging in: FindLikelihood(Nk)
>
>debug: {
>
>    A <- seq(0.2, 3, by = 0.2)
>
>    B <- seq(0.2, 3, by = 0.2)
>
>    k <- 7
>
>    L <- outer(A, B, function(A, B) sum((Nk * log(Dk(seq(-k, 
>
>        k), A, B))) - Dk(seq(-k, k), A, B)))
>
>    return(L)
>
>}
>
>Browse[1]> n
>
>debug: A <- seq(0.2, 3, by = 0.2)
>
>Browse[1]> n
>
>debug: B <- seq(0.2, 3, by = 0.2)
>
>Browse[1]> n
>
>debug: k <- 7
>
>Browse[1]> n
>
>debug: L <- outer(A, B, function(A, B) sum((Nk * log(Dk(seq(-k, k), 
>
>    A, B))) - Dk(seq(-k, k), A, B)))
>
>Browse[1]> sum((Nk * log(Dk(seq(-k, k),0.2,0.2))) - Dk(seq(-k, k), 0.2,
>0.2))      # WHY DOES THIS LINE GIVE ME THE CORRECT RESULT WHEN I SUBSTITUTE
>0.2, 0.2 FOR A AND B
>
>[1] 2495.242
>
>Browse[1]> outer(A, B, function(A, B) sum((Nk * log(Dk(seq(-k, k), 
>
>+     A, B))) - Dk(seq(-k, k), A, B)))
>
>          [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]
>[,8]
>
> [1,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48    # BUT ELEMENT (1,1) WHICH SHOULD ALSO BE (A,B) = (0.2, 0.2),
>GIVES THE INCORRECT RESULT????
>
> [2,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
> [3,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
> [4,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
> [5,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
> [6,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
> [7,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
> [8,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
> [9,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
>[10,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
>[11,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
>[12,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
>[13,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
>[14,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
>[15,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>58389.48
>
>          [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]
>
> [1,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [2,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [3,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [4,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [5,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [6,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [7,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [8,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [9,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>[10,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>[11,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>[12,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>[13,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>[14,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>[15,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>Browse[1]>
>
> 
>
>As "commented" above, when I evaluate a single A,B element (i.e.
A=0.2,
>B=0.2) I get a different result than when I use OUTER() which should also be
>evaluating at A=0.2, B=0.2??
>
> 
>
>Any help appreciated.  I know I'm probably doing something overlooking
>something simple, but can anyone point it out???
>
> 
>
>Thanks!
>
>-Scott
>
> 
>
>Scott Norton, Ph.D.
>
>Engineering Manager
>
>Nanoplex Technologies, Inc.
>
>2375 Garcia Ave.
>
>Mountain View, CA 94043
>
>www.nanoplextech.com
>
> 
>
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>  
>

Thomas W Blackwell

2003-Oct-28 14:52 UTC

head link

[R] outer function problems

Scott  -

I agree with Spencer Graves that there's a scoping issue here:
Where does function  Dk()  pick up the values for  n0  and  w,
and does it get them from the SAME place when it's called from
inside  FindLikelihood()  as from outside ?

But more important is this one:  All arithmetic on vectors or
matrices is done element by element;  every matrix or array is
treated as a vector (no 'dim' attribute) during this process,
and "the elements of shorter vectors are recycled as necessary"
(quoting from  help("Arithmetic")).  Therefore,

	Dk(seq(-k,k), 0.2, 0.2)

should return a vector of length (2 * k + 1),  and

	Nk * log(Dk())
 	#  (I omit the arguments to Dk() here.)

should produce a vector of length  max(length(Nk), 2 * k + 1)
in which element 1 of Nk is paired with  xk = -k,  element 2
of Nk is paired with  xk = (-k + 1), et cetera.  This product
then has a vector of length  (2 * k + 1)  subtracted from it
and the resulting vector is summed.

Now, maybe you have promised to only call  FindLikelihood()
with an argument  Nk  of length 15 = (2 * k + 1), in which
case all the lengths match and element i from Nk is always
paired with the value (i - 8) in the first argument of Dk(),
but there's certainly a lack of defensive programming here.

An alternate way to calculate the grid of likelihood values
which seems to be your intention is to explicitly build four
four-dimensional arrays named  A, B, xk and Nk, all with the
same dimensions, and with the values changing along only one
dimension in each array.  Then do whatever arithmetic you
want with these four arrays (such as the expressions inside
Dk() and  FindLikelihood()  and collapse the result by summing
over rows or slices or whatever at the end.  The functions
array(), aperm(), matrix() and '%*%' are useful in this process.
This business of four or five-dimensional arrays is one I use
routinely.  The result is equivalent to as.vector(outer( ...)),
but it forces you to think carefully about the various dimensions.

HTH  -  tom blackwell  -  u michigan medical school  -  ann arbor  -

On Mon, 27 Oct 2003, Scott Norton wrote:
> I'm pulling my hair (and there's not much left!) on this one.
Basically I'm
> not getting the same result t when I "step" through the program
and evaluate
> each element separately than when I use the outer() function in the
> FindLikelihood() function below.
>
>
>
> Here's the functions:
>
>
>
> Dk<- function(xk,A,B)
>
> {
>
> n0 *(A*exp(-0.5*(xk/w)^2) + B)
>
> }
>
>
>
> FindLikelihood <- function(Nk)
>
> {
>
> A <- seq(0.2,3,by=0.2)
>
> B <- seq(0.2,3,by=0.2)
>
> k <-7
>
> L <- outer(A, B, function(A,B) sum( (Nk*log(Dk(seq(-k,k),A,B))) -
> Dk(seq(-k,k),A,B) ))
>
> return(L)
>
> }
>
>
>
>
>
> where Nk <- c(70 , 67 , 75 , 77 , 74 ,102,  75, 104 , 94 , 74 , 78 , 79
, 83
> , 73 , 76)
>
>
>
>
>
> Here's an excerpt from my debug session..
>
>
>
> > Nk
>
>  [1]  70  67  75  77  74 102  75 104  94  74  78  79  83  73  76
>
> > debug(FindLikelihood)
>
> > L<-FindLikelihood(Nk)
>
> debugging in: FindLikelihood(Nk)
>
> debug: {
>
>     A <- seq(0.2, 3, by = 0.2)
>
>     B <- seq(0.2, 3, by = 0.2)
>
>     k <- 7
>
>     L <- outer(A, B, function(A, B) sum((Nk * log(Dk(seq(-k,
>
>         k), A, B))) - Dk(seq(-k, k), A, B)))
>
>     return(L)
>
> }
>
> Browse[1]> n
>
> debug: A <- seq(0.2, 3, by = 0.2)
>
> Browse[1]> n
>
> debug: B <- seq(0.2, 3, by = 0.2)
>
> Browse[1]> n
>
> debug: k <- 7
>
> Browse[1]> n
>
> debug: L <- outer(A, B, function(A, B) sum((Nk * log(Dk(seq(-k, k),
>
>     A, B))) - Dk(seq(-k, k), A, B)))
>
> Browse[1]> sum((Nk * log(Dk(seq(-k, k),0.2,0.2))) - Dk(seq(-k, k), 0.2,
> 0.2))      # WHY DOES THIS LINE GIVE ME THE CORRECT RESULT WHEN I
SUBSTITUTE
> 0.2, 0.2 FOR A AND B
>
> [1] 2495.242
>
> Browse[1]> outer(A, B, function(A, B) sum((Nk * log(Dk(seq(-k, k),
>
> +     A, B))) - Dk(seq(-k, k), A, B)))
>
>           [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]
> [,8]
>
>  [1,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48    # BUT ELEMENT (1,1) WHICH SHOULD ALSO BE (A,B) = (0.2, 0.2),
> GIVES THE INCORRECT RESULT????
>
>  [2,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
>  [3,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
>  [4,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
>  [5,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
>  [6,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
>  [7,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
>  [8,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
>  [9,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
> [10,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
> [11,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
> [12,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
> [13,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
> [14,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
> [15,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
> 58389.48
>
>           [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]
>
>  [1,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>  [2,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>  [3,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>  [4,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>  [5,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>  [6,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>  [7,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>  [8,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
>  [9,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [10,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [11,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [12,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [13,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [14,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> [15,] 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48 58389.48
>
> Browse[1]>
>
>
>
> As "commented" above, when I evaluate a single A,B element (i.e.
A=0.2,
> B=0.2) I get a different result than when I use OUTER() which should also
be
> evaluating at A=0.2, B=0.2??
>
>
>
> Any help appreciated.  I know I'm probably doing something overlooking
> something simple, but can anyone point it out???
>
>
>
> Thanks!
>
> -Scott
>
>
>
> Scott Norton, Ph.D.
>
> Engineering Manager
>
> Nanoplex Technologies, Inc.
>
> 2375 Garcia Ave.
>
> Mountain View, CA 94043
>
> www.nanoplextech.com
>
>
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>

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