[R] Help in error removal

[David Winsemius]

On Jul 13, 2011, at 6:09 AM, Mitra, Sumona wrote:

> Dear all,
>
> Thank you so much for your help. I was able to get a script that ran  
> and did what i wanted  it to do. It was as follows:-
>
>
>> correlation <- function(a)
> + {
> +   r <- matrix(nrow = dim(a)[1], ncol=dim(a)[1])
> +   for(x in c(2:dim(a)[1]))
> +   {
> +     for(y in c(x:dim(a)[1]))
> +     {
> +       r[x,y] <- (cor.test(as.vector(as.matrix(a)[x,],  
> mode="double"), as.vector(as.matrix(a)[y,], mode="double"))$p.value)
> +       r[y,x] <- r[x,y]
> +     }
> +   }
> +   return(r)
> + }
>
> Now I want to extend this to include all the possible correlations  
> that cor.test can do.

You are constructing a technique that in the wrong hands will do very  
bad statistics.

> One of the possible arguments of cor.test is method="method", where  
> method can be pearson, spearman or kendall. To include this I  
> modified my code in the following way:-
>
>> correlation <- function(a, b)
> + {
> +   r <- matrix(nrow = dim(a)[1], ncol=dim(a)[1])
> +   for(x in c(2:dim(a)[1]))
> +   {
> +     for(y in c(x:dim(a)[1]))
> +     {
> +       r[x,y] <- (cor.test(as.vector(as.matrix(a)[x,],  
> mode="double"), as.vector(as.matrix(a)[y,], mode="double"),  
> method="b")$p.value)

If you quote "b", then the interpreter will not substitute the value  
of `b`.

> +       r[y,x] <- r[x,y]
> +     }
> +   }
> +   return(r)
> + }
>
> This when executed though, gives the following error:-
>
>> correlation(a, spearman)
> Error in match.arg(method) :
>  'arg' should be one of “pearson”, “kendall”, “spearman”
>
> Please help!
>
> Sumona

-- 

David Winsemius, MD
West Hartford, CT