R help - Jan 2006 - Number of replications of a term

Hello,

Is there a simple and fast function that returns a vector of the number 
of replications for each object of a vector ?
For example :
I have a vector of IDs :
ids <- c( "ID1", "ID2", "ID2", "ID3",
"ID3","ID3", "ID5")

 I want the function returns the following vector where each term is the 
number of replicates for the given id :
c( 1, 2, 2, 3,3,3,1 )

Of course I have a vector of more than 40 000 ID and the function I 
wrote (it orders my data and checks on ID:Name of the data if the next 
term is the same as the previous one (see below) ) is really slow 
(30minutes for 44290 terms). But I don't have time by now to write a C 
function.
Thanks a lot for your help,

Laetitia.



Here is the function I have written maybe I have done something not 
optimized :

repVector <- function(obj){

    # order IDName 
    ord <- gif.indexByIDName(obj)
    ordobj <- obj[ord,]

    nspots <- nrow(obj)
    # vector of spot replicates number           
    spotrep <- rep(NA, nspots )
   
    # function to get ID:Name for a given spot       
    spotidname <- function(ind){
            paste(ordobj$genes[ind, c("ID","Name") ],
collapse=":")
    }

    spot <- 1   

    while( spot < nspots ){
        i<-1
        while( spotidname(spot) == spotidname(spot + i) ){            
       
            i <- i + 1
        }
       
        spotrep[spot : (spot + i-1)] <- i
        spot <- spot + i
        #cat("spot : ",spot,"\n")   
    }       
   
    obj$genes$spotrep <- spotrep[order(ord)]

    obj
               
}

Laetitia Marisa wrote:
> Hello,
> 
> Is there a simple and fast function that returns a vector of the number 
> of replications for each object of a vector ?
> For example :
> I have a vector of IDs :
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
> 
>  I want the function returns the following vector where each term is the 
> number of replicates for the given id :
> c( 1, 2, 2, 3,3,3,1 )
One-liner:

 > table(ids)[ids]
ids
ID1 ID2 ID2 ID3 ID3 ID3 ID5
   1   2   2   3   3   3   1

  'table(ids)' computes the counts, then the subscripting [ids] looks it
all up.

  Now try it on your 40,000-long vector!

Barry

Laetitia Marisa <Laetitia.Marisa at cgm.cnrs-gif.fr> writes:
> Hello,
> 
> Is there a simple and fast function that returns a vector of the number 
> of replications for each object of a vector ?
> For example :
> I have a vector of IDs :
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
> 
>  I want the function returns the following vector where each term is the 
> number of replicates for the given id :
> c( 1, 2, 2, 3,3,3,1 )
> 
> Of course I have a vector of more than 40 000 ID and the function I 
> wrote (it orders my data and checks on ID:Name of the data if the next 
> term is the same as the previous one (see below) ) is really slow 
> (30minutes for 44290 terms). But I don't have time by now to write a C 
> function.
> Thanks a lot for your help,
Will this do it?
> table(ids)[ids]
ids
ID1 ID2 ID2 ID3 ID3 ID3 ID5
  1   2   2   3   3   3   1

Or (could be faster):
> f <- factor(ids,levels=unique(ids))
> as.vector(table(f))[f]
[1] 1 2 2 3 3 3 1


-- 
   O__  ---- Peter Dalgaard             ??ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

Laetitia Marisa wrote:
> Hello,
> 
> Is there a simple and fast function that returns a vector of the number 
> of replications for each object of a vector ?
> For example :
> I have a vector of IDs :
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
> 
>  I want the function returns the following vector where each term is the 
> number of replicates for the given id :
> c( 1, 2, 2, 3,3,3,1 )
 > rep(as.vector(table(ids)), as.vector(table(ids)))
[1] 1 2 2 3 3 3 1
> Of course I have a vector of more than 40 000 ID and the function I 
> wrote (it orders my data and checks on ID:Name of the data if the next 
> term is the same as the previous one (see below) ) is really slow 
> (30minutes for 44290 terms). But I don't have time by now to write a C 
> function.
> Thanks a lot for your help,
> 
> Laetitia.
> 
> 
> 
> Here is the function I have written maybe I have done something not 
> optimized :
> 
> repVector <- function(obj){
> 
>     # order IDName 
>     ord <- gif.indexByIDName(obj)
>     ordobj <- obj[ord,]
> 
>     nspots <- nrow(obj)
>     # vector of spot replicates number           
>     spotrep <- rep(NA, nspots )
>    
>     # function to get ID:Name for a given spot       
>     spotidname <- function(ind){
>             paste(ordobj$genes[ind, c("ID","Name") ],
collapse=":")
>     }
> 
>     spot <- 1   
> 
>     while( spot < nspots ){
>         i<-1
>         while( spotidname(spot) == spotidname(spot + i) ){            
>        
>             i <- i + 1
>         }
>        
>         spotrep[spot : (spot + i-1)] <- i
>         spot <- spot + i
>         #cat("spot : ",spot,"\n")   
>     }       
>    
>     obj$genes$spotrep <- spotrep[order(ord)]
> 
>     obj
>                
> }
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
> 
-- 
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 452-1424 (M, W, F)
fax: (917) 438-0894

This should work:
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
> table(ids)[ids]
ids
ID1 ID2 ID2 ID3 ID3 ID3 ID5 
  1   2   2   3   3   3   1 

Andy

From: Laetitia Marisa
> 
> Hello,
> 
> Is there a simple and fast function that returns a vector of 
> the number 
> of replications for each object of a vector ?
> For example :
> I have a vector of IDs :
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
> 
>  I want the function returns the following vector where each 
> term is the 
> number of replicates for the given id :
> c( 1, 2, 2, 3,3,3,1 )
> 
> Of course I have a vector of more than 40 000 ID and the function I 
> wrote (it orders my data and checks on ID:Name of the data if 
> the next 
> term is the same as the previous one (see below) ) is really slow 
> (30minutes for 44290 terms). But I don't have time by now to 
> write a C 
> function.
> Thanks a lot for your help,
> 
> Laetitia.
> 
> 
> 
> Here is the function I have written maybe I have done something not 
> optimized :
> 
> repVector <- function(obj){
> 
>     # order IDName 
>     ord <- gif.indexByIDName(obj)
>     ordobj <- obj[ord,]
> 
>     nspots <- nrow(obj)
>     # vector of spot replicates number           
>     spotrep <- rep(NA, nspots )
>    
>     # function to get ID:Name for a given spot       
>     spotidname <- function(ind){
>             paste(ordobj$genes[ind, c("ID","Name") ],
collapse=":")
>     }
> 
>     spot <- 1   
> 
>     while( spot < nspots ){
>         i<-1
>         while( spotidname(spot) == spotidname(spot + i) ){            
>        
>             i <- i + 1
>         }
>        
>         spotrep[spot : (spot + i-1)] <- i
>         spot <- spot + i
>         #cat("spot : ",spot,"\n")   
>     }       
>    
>     obj$genes$spotrep <- spotrep[order(ord)]
> 
>     obj
>                
> }
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 
>

Try this:

ave(as.numeric(factor(ds)), ds, FUN = length)

See ?ave for more info.

On 1/24/06, Laetitia Marisa <Laetitia.Marisa at cgm.cnrs-gif.fr>
wrote:
> Hello,
>
> Is there a simple and fast function that returns a vector of the number
> of replications for each object of a vector ?
> For example :
> I have a vector of IDs :
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
>
>  I want the function returns the following vector where each term is the
> number of replicates for the given id :
> c( 1, 2, 2, 3,3,3,1 )
>
> Of course I have a vector of more than 40 000 ID and the function I
> wrote (it orders my data and checks on ID:Name of the data if the next
> term is the same as the previous one (see below) ) is really slow
> (30minutes for 44290 terms). But I don't have time by now to write a C
> function.
> Thanks a lot for your help,
>
> Laetitia.
>
>
>
> Here is the function I have written maybe I have done something not
> optimized :
>
> repVector <- function(obj){
>
>    # order IDName
>    ord <- gif.indexByIDName(obj)
>    ordobj <- obj[ord,]
>
>    nspots <- nrow(obj)
>    # vector of spot replicates number
>    spotrep <- rep(NA, nspots )
>
>    # function to get ID:Name for a given spot
>    spotidname <- function(ind){
>            paste(ordobj$genes[ind, c("ID","Name") ],
collapse=":")
>    }
>
>    spot <- 1
>
>    while( spot < nspots ){
>        i<-1
>        while( spotidname(spot) == spotidname(spot + i) ){
>
>            i <- i + 1
>        }
>
>        spotrep[spot : (spot + i-1)] <- i
>        spot <- spot + i
>        #cat("spot : ",spot,"\n")
>    }
>
>    obj$genes$spotrep <- spotrep[order(ord)]
>
>    obj
>
> }
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>

table()

 	-thomas

On Tue, 24 Jan 2006, Laetitia Marisa wrote:
> Hello,
>
> Is there a simple and fast function that returns a vector of the number
> of replications for each object of a vector ?
> For example :
> I have a vector of IDs :
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
>
> I want the function returns the following vector where each term is the
> number of replicates for the given id :
> c( 1, 2, 2, 3,3,3,1 )
>
> Of course I have a vector of more than 40 000 ID and the function I
> wrote (it orders my data and checks on ID:Name of the data if the next
> term is the same as the previous one (see below) ) is really slow
> (30minutes for 44290 terms). But I don't have time by now to write a C
> function.
> Thanks a lot for your help,
>
> Laetitia.
>
>
>
> Here is the function I have written maybe I have done something not
> optimized :
>
> repVector <- function(obj){
>
>    # order IDName
>    ord <- gif.indexByIDName(obj)
>    ordobj <- obj[ord,]
>
>    nspots <- nrow(obj)
>    # vector of spot replicates number
>    spotrep <- rep(NA, nspots )
>
>    # function to get ID:Name for a given spot
>    spotidname <- function(ind){
>            paste(ordobj$genes[ind, c("ID","Name") ],
collapse=":")
>    }
>
>    spot <- 1
>
>    while( spot < nspots ){
>        i<-1
>        while( spotidname(spot) == spotidname(spot + i) ){
>
>            i <- i + 1
>        }
>
>        spotrep[spot : (spot + i-1)] <- i
>        spot <- spot + i
>        #cat("spot : ",spot,"\n")
>    }
>
>    obj$genes$spotrep <- spotrep[order(ord)]
>
>    obj
>
> }
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

?table
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
>
> x <- table(ids)
> x
ids
ID1 ID2 ID3 ID5
  1   2   3   1
> count <- x[ids] # index using the names in the string
> count
ids
ID1 ID2 ID2 ID3 ID3 ID3 ID5
  1   2   2   3   3   3   1
>


On 1/24/06, Laetitia Marisa <Laetitia.Marisa@cgm.cnrs-gif.fr>
wrote:
>
> Hello,
>
> Is there a simple and fast function that returns a vector of the number
> of replications for each object of a vector ?
> For example :
> I have a vector of IDs :
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
>
> I want the function returns the following vector where each term is the
> number of replicates for the given id :
> c( 1, 2, 2, 3,3,3,1 )
>
> Of course I have a vector of more than 40 000 ID and the function I
> wrote (it orders my data and checks on ID:Name of the data if the next
> term is the same as the previous one (see below) ) is really slow
> (30minutes for 44290 terms). But I don't have time by now to write a C
> function.
> Thanks a lot for your help,
>
> Laetitia.
>
>
>
> Here is the function I have written maybe I have done something not
> optimized :
>
> repVector <- function(obj){
>
>    # order IDName
>    ord <- gif.indexByIDName(obj)
>    ordobj <- obj[ord,]
>
>    nspots <- nrow(obj)
>    # vector of spot replicates number
>    spotrep <- rep(NA, nspots )
>
>    # function to get ID:Name for a given spot
>    spotidname <- function(ind){
>            paste(ordobj$genes[ind, c("ID","Name") ],
collapse=":")
>    }
>
>    spot <- 1
>
>    while( spot < nspots ){
>        i<-1
>        while( spotidname(spot) == spotidname(spot + i) ){
>
>            i <- i + 1
>        }
>
>        spotrep[spot : (spot + i-1)] <- i
>        spot <- spot + i
>        #cat("spot : ",spot,"\n")
>    }
>
>    obj$genes$spotrep <- spotrep[order(ord)]
>
>    obj
>
> }
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>


--
Jim Holtman
Cincinnati, OH
+1 513 247 0281

What the problem you are trying to solve?

	[[alternative HTML version deleted]]

Ah. It's a bit more complicated than just table(), because you want the 
result to be the same length.

tt <- table(id)
tt[match(id,names(tt))]


 	-thomas

On Tue, 24 Jan 2006, Laetitia Marisa wrote:
> Hello,
>
> Is there a simple and fast function that returns a vector of the number
> of replications for each object of a vector ?
> For example :
> I have a vector of IDs :
> ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
>
> I want the function returns the following vector where each term is the
> number of replicates for the given id :
> c( 1, 2, 2, 3,3,3,1 )
>
> Of course I have a vector of more than 40 000 ID and the function I
> wrote (it orders my data and checks on ID:Name of the data if the next
> term is the same as the previous one (see below) ) is really slow
> (30minutes for 44290 terms). But I don't have time by now to write a C
> function.
> Thanks a lot for your help,
>
> Laetitia.
>
>
>
> Here is the function I have written maybe I have done something not
> optimized :
>
> repVector <- function(obj){
>
>    # order IDName
>    ord <- gif.indexByIDName(obj)
>    ordobj <- obj[ord,]
>
>    nspots <- nrow(obj)
>    # vector of spot replicates number
>    spotrep <- rep(NA, nspots )
>
>    # function to get ID:Name for a given spot
>    spotidname <- function(ind){
>            paste(ordobj$genes[ind, c("ID","Name") ],
collapse=":")
>    }
>
>    spot <- 1
>
>    while( spot < nspots ){
>        i<-1
>        while( spotidname(spot) == spotidname(spot + i) ){
>
>            i <- i + 1
>        }
>
>        spotrep[spot : (spot + i-1)] <- i
>        spot <- spot + i
>        #cat("spot : ",spot,"\n")
>    }
>
>    obj$genes$spotrep <- spotrep[order(ord)]
>
>    obj
>
> }
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

There's an even faster one, which nobody seems to have mentioned yet:

rep(l <- rle(ids)$lengths, l)

Timing on my 2.8GHz NetBSD system shows:
> length(ids)
[1] 45150
> # Gabor:
> system.time(for (i in 1:100) ave(as.numeric(factor(ids)), ids, FUN length))
[1] 3.45 0.06 3.54 0.00 0.00
> # Barry (and others I think):
> system.time(for (i in 1:100) table(ids)[ids])
[1] 2.13 0.05 2.20 0.00 0.00
> Me:
> system.time(for (i in 1:100) rep(l <- rle(ids)$lengths, l))
[1] 1.60 0.00 1.62 0.00 0.00

Of course the difference between 21 milliseconds and 16 milliseconds is
not great, unless you are doing this a lot.

Ray Brownrigg
> From: Gabor Grothendieck <ggrothendieck at gmail.com>
> 
> Nice.  I timed it and its much faster than mine too.
> 
> On 1/24/06, Barry Rowlingson <B.Rowlingson at lancaster.ac.uk> wrote:
> > Laetitia Marisa wrote:
> > > Hello,
> > >
> > > Is there a simple and fast function that returns a vector of the
number
> > > of replications for each object of a vector ?
> > > For example :
> > > I have a vector of IDs :
> > > ids <- c( "ID1", "ID2", "ID2",
"ID3", "ID3","ID3", "ID5")
> > >
> > >  I want the function returns the following vector where each term
is the
> > > number of replicates for the given id :
> > > c( 1, 2, 2, 3,3,3,1 )
> >
> > One-liner:
> >
> >  > table(ids)[ids]
> > ids
> > ID1 ID2 ID2 ID3 ID3 ID3 ID5
> >   1   2   2   3   3   3   1
> >
> >  'table(ids)' computes the counts, then the subscripting [ids]
looks it
> > all up.
> >
> >  Now try it on your 40,000-long vector!
> >
> > Barry