[R] quantiles on rows of a matrix

[David Winsemius]

On Jul 7, 2010, at 6:52 PM, Jim Bouldin wrote:

>
> I'm trying to obtain the mean of the middle 95% of the values from  
> each row
> of a matrix  (that is, the highest and lowest 2.5% of values in each  
> row
> are removed before calculating the mean).

A winsorized.mean?


>  I am having all sorts of
> problems with this; for example the command:
>
> apply(matrix1,1,function(x) quantile(c(.05,.90),na.rm=T))
>
> returns the exact same quantile values for each row, which is clearly
> wrong.

You gave quantile the same argument each time. Try:
apply(matrix1,1,function(x)  quantile( x, probs= c(.05,.90),na.rm=T) )

Or:

apply(matrix1, 1,  quantile, probs= c(.05,.90), na.rm=T )

> But even if the values were right, I'm not sure how I would then
> translate those quantile values into another apply function to get the
> mean, since they differ from row to row.

That would be a problem. There is a path to success but it would so  
much easier if someone already developed a function, wouldn't it?

RSiteSearch("winsorized")

>
> I also tried:
> apply(matrix,1,mean,na.rm=T,trim=.05))
> and the trim argument was simply ignored
>
>
> Stumped. Any help appreciated. Thanks.
>
>
> Jim Bouldin, PhD
> Research Ecologist
> Department of Plant Sciences, UC Davis
> Davis CA, 95616
> 530-554-1740
>
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David Winsemius, MD
West Hartford, CT