R help - Nov 2009 - All possible combinations of functions within a function

Dear All,

I wrote a function for cluster analysis to compute cophenetic correlations
between dissimilarity matrices (using the VEGAN library) and cluster
analyses of every possible clustering algorithm (SEE ATTACHED)
http://old.nabble.com/file/p26288610/cor.coef.R cor.coef.R .  As it is now,
it is extremely long, and for the future I was hoping to find a more
efficient way of doing this sort of thing.  

To give you an outline of the function, first I create the  dissimiarity
matrices using all possible methods in the VEGAN command "vegdist",
then
create the clusters using all possible algorithms in "hclust" and the
dissimilarity matrices I crated, then create a table, and in one column,
list all combinations, and in the other, compute and put the cophenetic
correlation.

Any help would be appreciated!  I'm pretty new to writing my own functions
but I see great time-saving potential.

Thanks!
Mike
-- 
View this message in context:
http://old.nabble.com/All-possible-combinations-of-functions-within-a-function-tp26288610p26288610.html
Sent from the R help mailing list archive at Nabble.com.

Here is a hint of how you might want to do the first part.  You might
want to study the 'lappy' function

vegList <- lapply(c('bray', ..., 'binomial'),
function(.method){
    vegdist(x, method=.method)
})

clustList <- lapply(vegList, function(.dist){
    lapply(c('average', ..., 'centroid'), function(.dist){
        hclust(.veg, .dist)
    })
})

rest left as exercise for the reader.

On Tue, Nov 10, 2009 at 2:05 PM, bikemike42 <mlt35 at tamu.edu>
wrote:
>
> Dear All,
>
> I wrote a function for cluster analysis to compute cophenetic correlations
> between dissimilarity matrices (using the VEGAN library) and cluster
> analyses of every possible clustering algorithm (SEE ATTACHED)
> http://old.nabble.com/file/p26288610/cor.coef.R cor.coef.R . ?As it is now,
> it is extremely long, and for the future I was hoping to find a more
> efficient way of doing this sort of thing.
>
> To give you an outline of the function, first I create the ?dissimiarity
> matrices using all possible methods in the VEGAN command
"vegdist", then
> create the clusters using all possible algorithms in "hclust" and
the
> dissimilarity matrices I crated, then create a table, and in one column,
> list all combinations, and in the other, compute and put the cophenetic
> correlation.
>
> Any help would be appreciated! ?I'm pretty new to writing my own
functions
> but I see great time-saving potential.
>
> Thanks!
> Mike
> --
> View this message in context:
http://old.nabble.com/All-possible-combinations-of-functions-within-a-function-tp26288610p26288610.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

Hi,
>From what I understand of your code, you might find the following
construct useful,

funs <- c("mean", "sum", "sd",
"diff")
x <- 1:10
lapply(funs, do.call, args=list(x))

and then working with lists rather than naming every object
individually. You might find mapply useful too when you have to pass
several parameters.

HTH,

baptiste

2009/11/10 bikemike42 <mlt35 at tamu.edu>:
>
> Dear All,
>
> I wrote a function for cluster analysis to compute cophenetic correlations
> between dissimilarity matrices (using the VEGAN library) and cluster
> analyses of every possible clustering algorithm (SEE ATTACHED)
> http://old.nabble.com/file/p26288610/cor.coef.R cor.coef.R . ?As it is now,
> it is extremely long, and for the future I was hoping to find a more
> efficient way of doing this sort of thing.
>
> To give you an outline of the function, first I create the ?dissimiarity
> matrices using all possible methods in the VEGAN command
"vegdist", then
> create the clusters using all possible algorithms in "hclust" and
the
> dissimilarity matrices I crated, then create a table, and in one column,
> list all combinations, and in the other, compute and put the cophenetic
> correlation.
>
> Any help would be appreciated! ?I'm pretty new to writing my own
functions
> but I see great time-saving potential.
>
> Thanks!
> Mike
> --
> View this message in context:
http://old.nabble.com/All-possible-combinations-of-functions-within-a-function-tp26288610p26288610.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>