[R] 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
}
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Re: [R] Number of replications of a term
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 __ 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
Re: [R] Number of replications of a term
Laetitia Marisa [EMAIL PROTECTED] 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 Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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
Re: [R] Number of replications of a term
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$spotrep - spotrep[order(ord)]
obj
}
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Re: [R] Number of replications of a term
This should work:
ids - c( ID1, ID2, ID2, ID3, ID3,ID3, ID5)
table(ids)[ids]
ids
ID1 ID2 ID2 ID3 ID3 ID3 ID5
1 2 2 3 3 3 1
Andy
From: Laetitia Marisa
Hello,
Is there a simple and fast function that returns a vector of
the number
of replications for each object of a vector ?
For example :
I have a vector of IDs :
ids - c( ID1, ID2, ID2, ID3, ID3,ID3, ID5)
I want the function returns the following vector where each
term is the
number of replicates for the given id :
c( 1, 2, 2, 3,3,3,1 )
Of course I have a vector of more than 40 000 ID and the function I
wrote (it orders my data and checks on ID:Name of the data if
the next
term is the same as the previous one (see below) ) is really slow
(30minutes for 44290 terms). But I don't have time by now to
write a C
function.
Thanks a lot for your help,
Laetitia.
Here is the function I have written maybe I have done something not
optimized :
repVector - function(obj){
# order IDName
ord - gif.indexByIDName(obj)
ordobj - obj[ord,]
nspots - nrow(obj)
# vector of spot replicates number
spotrep - rep(NA, nspots )
# function to get ID:Name for a given spot
spotidname - function(ind){
paste(ordobj$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
}
__
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Re: [R] Number of replications of a term
Try this:
ave(as.numeric(factor(ds)), ds, FUN = length)
See ?ave for more info.
On 1/24/06, Laetitia Marisa [EMAIL PROTECTED] 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$spotrep - spotrep[order(ord)]
obj
}
__
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Re: [R] Number of replications of a term
table()
-thomas
On Tue, 24 Jan 2006, Laetitia Marisa wrote:
Hello,
Is there a simple and fast function that returns a vector of the number
of replications for each object of a vector ?
For example :
I have a vector of IDs :
ids - c( ID1, ID2, ID2, ID3, ID3,ID3, ID5)
I want the function returns the following vector where each term is the
number of replicates for the given id :
c( 1, 2, 2, 3,3,3,1 )
Of course I have a vector of more than 40 000 ID and the function I
wrote (it orders my data and checks on ID:Name of the data if the next
term is the same as the previous one (see below) ) is really slow
(30minutes for 44290 terms). But I don't have time by now to write a C
function.
Thanks a lot for your help,
Laetitia.
Here is the function I have written maybe I have done something not
optimized :
repVector - function(obj){
# order IDName
ord - gif.indexByIDName(obj)
ordobj - obj[ord,]
nspots - nrow(obj)
# vector of spot replicates number
spotrep - rep(NA, nspots )
# function to get ID:Name for a given spot
spotidname - function(ind){
paste(ordobj$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
}
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
__
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Re: [R] Number of replications of a term
?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 [EMAIL PROTECTED] 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$spotrep - spotrep[order(ord)]
obj
}
__
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Jim Holtman
Cincinnati, OH
+1 513 247 0281
What the problem you are trying to solve?
[[alternative HTML version deleted]]
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Re: [R] Number of replications of a term
Ah. It's a bit more complicated than just table(), because you want the
result to be the same length.
tt - table(id)
tt[match(id,names(tt))]
-thomas
On Tue, 24 Jan 2006, Laetitia Marisa wrote:
Hello,
Is there a simple and fast function that returns a vector of the number
of replications for each object of a vector ?
For example :
I have a vector of IDs :
ids - c( ID1, ID2, ID2, ID3, ID3,ID3, ID5)
I want the function returns the following vector where each term is the
number of replicates for the given id :
c( 1, 2, 2, 3,3,3,1 )
Of course I have a vector of more than 40 000 ID and the function I
wrote (it orders my data and checks on ID:Name of the data if the next
term is the same as the previous one (see below) ) is really slow
(30minutes for 44290 terms). But I don't have time by now to write a C
function.
Thanks a lot for your help,
Laetitia.
Here is the function I have written maybe I have done something not
optimized :
repVector - function(obj){
# order IDName
ord - gif.indexByIDName(obj)
ordobj - obj[ord,]
nspots - nrow(obj)
# vector of spot replicates number
spotrep - rep(NA, nspots )
# function to get ID:Name for a given spot
spotidname - function(ind){
paste(ordobj$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@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
[EMAIL PROTECTED] University of Washington, Seattle
__
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Re: [R] Number of replications of a term
It is great! It takes now less than 1 second (with the table function (0.34'), 2 sec with the ave function (1.91') ) with my big data and only two lines of code ;). Thanks a lot every one. Regards, Laetitia. Laetitia Marisa [EMAIL PROTECTED] 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 [[alternative HTML version deleted]] __ 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
Re: [R] Number of replications of a term
Nice. I timed it and its much faster than mine too. On 1/24/06, Barry Rowlingson [EMAIL PROTECTED] 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 __ 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 __ 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
Re: [R] Number of replications of a term
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 [EMAIL PROTECTED] Nice. I timed it and its much faster than mine too. On 1/24/06, Barry Rowlingson [EMAIL PROTECTED] 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 __ 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
Re: [R] Number of replications of a term
Note that that assumes that all occurrences of a value are contiguous. On 1/24/06, Ray Brownrigg [EMAIL PROTECTED] wrote: 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 [EMAIL PROTECTED] Nice. I timed it and its much faster than mine too. On 1/24/06, Barry Rowlingson [EMAIL PROTECTED] 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 __ 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
Re: [R] Number of replications of a term
On Wed, 25 Jan 2006, Ray Brownrigg wrote: There's an even faster one, which nobody seems to have mentioned yet: rep(l - rle(ids)$lengths, l) I considered this but it wasn't clear to me from the initial post that each ID occupied a contiguous section of the vector. Also, lazy evaluation makes code like this rep(l - rle(ids)$lengths, l) a bit worrying. It relies on rep() using the first argument before it uses the second one. In this case, clearly, it works, but it is not a style I would encourage and it's easy to construct functions where it fails. -thomas 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 [EMAIL PROTECTED] Nice. I timed it and its much faster than mine too. On 1/24/06, Barry Rowlingson [EMAIL PROTECTED] 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 __ 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 Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ 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
