Re: [R] average matrices across a list
Gregory Ryslik rsaber at comcast.net writes:
mymats - vector('list', 5)
set.seed(246)
# Generate a list of five 3 x 3 matrices
for(i in 1:5) mymats[[i]] - matrix(sample(1:9), nrow = 3)
mymats[[5]][1,1]-NA
mymats[[4]][2,2]-NA
mymats
matrixadder-function(u,v){
na.u-is.na(u)
na.v-is.na(v)
ifelse(na.u na.v, NA, ifelse(na.u, 0, u)+ ifelse(na.v,0,v))
}
Reduce('matrixadder',mymats)
I was going to suggest that my solution would be faster,
but it turns out to be slower (!) -- 11 seconds vs 6 seconds
for 10,000 replications.
It's cleverer, but I don't know if that's really a virtue.
library(abind)
apply(do.call(abind,c(mymats,list(along=3))),c(1,2),sum,na.rm=TRUE)
system.time(replicate(1,
apply(do.call(abind,c(mymats,list(along=3))),
c(1,2),sum,na.rm=TRUE)))
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Re: [R] average matrices across a list
You can try this also:
Reduce('+', lapply(mymats, function(x)replace(x, is.na(x), 0)))
On Sun, Sep 12, 2010 at 10:36 PM, Gregory Ryslik rsa...@comcast.net wrote:
Hi Everyone,
Thanks to everyone for their help. With your suggestions and some poking
around, the following works for what I need. It basically adds all the
matrices elementwise, and adds nothing if the element is NA. Thanks again!
Code below:
**
mymats - vector('list', 5)
set.seed(246)
# Generate a list of five 3 x 3 matrices
for(i in 1:5) mymats[[i]] - matrix(sample(1:9), nrow = 3)
mymats[[5]][1,1]-NA
mymats[[4]][2,2]-NA
mymats
matrixadder-function(u,v){
na.u-is.na(u)
na.v-is.na(v)
ifelse(na.u na.v, NA, ifelse(na.u, 0, u)+ ifelse(na.v,0,v))
}
Reduce('matrixadder',mymats)
**
Cheers,
Greg
On Sep 12, 2010, at 8:33 PM, Ben Bolker wrote:
My next suggestion (I don't have time to work out or test an example
at the moment):
library(abind)
tmparr - abind(m1,m2,m3,...,along=3)
OR
tmparr - do.call(c(matlist,list(along=3)))
apply(tmparr,c(1,2),mean,na.rm=TRUE)
or something along those lines.
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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Re: [R] average matrices across a list
Hi:
It's certainly fast (0.97s for 1 reps on my box), but doesn't
replacement by zero affect the denominator of the sum, thereby deflating the
means (assuming the contents of the matrices are nonnegative or NA)?
Dennis
On Tue, Sep 14, 2010 at 5:28 AM, Henrique Dallazuanna www...@gmail.comwrote:
You can try this also:
Reduce('+', lapply(mymats, function(x)replace(x, is.na(x), 0)))
On Sun, Sep 12, 2010 at 10:36 PM, Gregory Ryslik rsa...@comcast.net
wrote:
Hi Everyone,
Thanks to everyone for their help. With your suggestions and some poking
around, the following works for what I need. It basically adds all the
matrices elementwise, and adds nothing if the element is NA. Thanks
again!
Code below:
**
mymats - vector('list', 5)
set.seed(246)
# Generate a list of five 3 x 3 matrices
for(i in 1:5) mymats[[i]] - matrix(sample(1:9), nrow = 3)
mymats[[5]][1,1]-NA
mymats[[4]][2,2]-NA
mymats
matrixadder-function(u,v){
na.u-is.na(u)
na.v-is.na(v)
ifelse(na.u na.v, NA, ifelse(na.u, 0, u)+ ifelse(na.v,0,v))
}
Reduce('matrixadder',mymats)
**
Cheers,
Greg
On Sep 12, 2010, at 8:33 PM, Ben Bolker wrote:
My next suggestion (I don't have time to work out or test an example
at the moment):
library(abind)
tmparr - abind(m1,m2,m3,...,along=3)
OR
tmparr - do.call(c(matlist,list(along=3)))
apply(tmparr,c(1,2),mean,na.rm=TRUE)
or something along those lines.
__
R-help@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.
[[alternative HTML version deleted]]
__
R-help@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.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
__
R-help@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.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] average matrices across a list
Hi,
The denominator i compute seperately counting how many observations there were
that were not NA. Thus the I divide each (n,m) cell by the number of counts it
was not NA.
Thanks,
Greg
On Sep 14, 2010, at 9:23 AM, Dennis Murphy wrote:
Hi:
It's certainly fast (0.97s for 1 reps on my box), but doesn't replacement
by zero affect the denominator of the sum, thereby deflating the means
(assuming the contents of the matrices are nonnegative or NA)?
Dennis
On Tue, Sep 14, 2010 at 5:28 AM, Henrique Dallazuanna www...@gmail.com
wrote:
You can try this also:
Reduce('+', lapply(mymats, function(x)replace(x, is.na(x), 0)))
On Sun, Sep 12, 2010 at 10:36 PM, Gregory Ryslik rsa...@comcast.net wrote:
Hi Everyone,
Thanks to everyone for their help. With your suggestions and some poking
around, the following works for what I need. It basically adds all the
matrices elementwise, and adds nothing if the element is NA. Thanks again!
Code below:
**
mymats - vector('list', 5)
set.seed(246)
# Generate a list of five 3 x 3 matrices
for(i in 1:5) mymats[[i]] - matrix(sample(1:9), nrow = 3)
mymats[[5]][1,1]-NA
mymats[[4]][2,2]-NA
mymats
matrixadder-function(u,v){
na.u-is.na(u)
na.v-is.na(v)
ifelse(na.u na.v, NA, ifelse(na.u, 0, u)+ ifelse(na.v,0,v))
}
Reduce('matrixadder',mymats)
**
Cheers,
Greg
On Sep 12, 2010, at 8:33 PM, Ben Bolker wrote:
My next suggestion (I don't have time to work out or test an example
at the moment):
library(abind)
tmparr - abind(m1,m2,m3,...,along=3)
OR
tmparr - do.call(c(matlist,list(along=3)))
apply(tmparr,c(1,2),mean,na.rm=TRUE)
or something along those lines.
__
R-help@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.
[[alternative HTML version deleted]]
__
R-help@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.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
__
R-help@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.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] average matrices across a list
Sorry, I forgot to add that some of the entries in various matrices have NA in them. On Sep 12, 2010, at 3:40 PM, Gregory Ryslik wrote: Hi, I have a list of several hundred 2 dimensional matrices, where each matrix is n x m. What I need to do is that for each n,m I need an average over all the lists. This would collapse it down to just one nxm matrix. Any easy ways to do that? As always, I'd like to avoid a for loop to keep computational time low! Thanks again everyone! Cheers, G __ R-help@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. __ R-help@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.
Re: [R] average matrices across a list
Gregory - Suppose your list is called mymats. Then Reduce(+,mymats) does what you want. - Phil On Sun, 12 Sep 2010, Gregory Ryslik wrote: Hi, I have a list of several hundred 2 dimensional matrices, where each matrix is n x m. What I need to do is that for each n,m I need an average over all the lists. This would collapse it down to just one nxm matrix. Any easy ways to do that? As always, I'd like to avoid a for loop to keep computational time low! Thanks again everyone! Cheers, G __ R-help@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. __ R-help@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.
Re: [R] average matrices across a list
Hi, Doing that I get the following: Browse[2] Reduce[+,results] Error in Reduce[+, results] : object of type 'closure' is not subsettable Thanks again! Kind regards, Greg On Sep 12, 2010, at 3:49 PM, Phil Spector wrote: Gregory - Suppose your list is called mymats. Then Reduce(+,mymats) does what you want. - Phil On Sun, 12 Sep 2010, Gregory Ryslik wrote: Hi, I have a list of several hundred 2 dimensional matrices, where each matrix is n x m. What I need to do is that for each n,m I need an average over all the lists. This would collapse it down to just one nxm matrix. Any easy ways to do that? As always, I'd like to avoid a for loop to keep computational time low! Thanks again everyone! Cheers, G __ R-help@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. __ R-help@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.
Re: [R] average matrices across a list
Gregory Ryslik rsaber at comcast.net writes: Browse[2] Reduce[+,results] Error in Reduce[+, results] : object of type 'closure' is not subsettable You need to use parentheses, not square brackets. __ R-help@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.
Re: [R] average matrices across a list
Gregory - Please provide a reproducible example. I have no idea what results is. - Phil On Sun, 12 Sep 2010, Gregory Ryslik wrote: Hi, Doing that I get the following: Browse[2] Reduce[+,results] Error in Reduce[+, results] : object of type 'closure' is not subsettable Thanks again! Kind regards, Greg On Sep 12, 2010, at 3:49 PM, Phil Spector wrote: Gregory - Suppose your list is called mymats. Then Reduce(+,mymats) does what you want. - Phil On Sun, 12 Sep 2010, Gregory Ryslik wrote: Hi, I have a list of several hundred 2 dimensional matrices, where each matrix is n x m. What I need to do is that for each n,m I need an average over all the lists. This would collapse it down to just one nxm matrix. Any easy ways to do that? As always, I'd like to avoid a for loop to keep computational time low! Thanks again everyone! Cheers, G __ R-help@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. __ R-help@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. __ R-help@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.
Re: [R] average matrices across a list
Hi,
Thanks, I was using the square brackets instead of (. The ( makes it work.
However, some of my matrices have NA for some values. I need those NA's to
basically not be counted. And if all the lists have NA for a specific (n,m), I
want it to remain an (n,m). By using the Reduce('+', mymats), any entries with
NA in at least one of the lists will give me back an NA for the sum (rather
than making it NA if it at least on list has an NA for that element).
Thanks again for everyone's help!
Kind regards,
Greg
On Sep 12, 2010, at 4:54 PM, Dennis Murphy wrote:
Hi:
Here's a more concrete example of Phil's point.
mymats - vector('list', 5)
set.seed(246)
# Generate a list of five 3 x 3 matrices
for(i in 1:5) mymats[[i]] - matrix(sample(1:9), nrow = 3)
# Sum them elementwise
Reduce('+', mymats)
[,1] [,2] [,3]
[1,] 23 33 15
[2,] 25 36 26
[3,] 20 24 23
HTH,
Dennis
On Sun, Sep 12, 2010 at 12:52 PM, Gregory Ryslik rsa...@comcast.net wrote:
Hi,
Doing that I get the following:
Browse[2] Reduce[+,results]
Error in Reduce[+, results] :
object of type 'closure' is not subsettable
You want parentheses there, not brackets; you're asking R to subset a
function, Reduce, which is an object of type closure. Hopefully the error
message makes more sense now.
Thanks again!
Kind regards,
Greg
On Sep 12, 2010, at 3:49 PM, Phil Spector wrote:
Gregory -
Suppose your list is called mymats. Then
Reduce(+,mymats)
does what you want.
- Phil
On Sun, 12 Sep 2010, Gregory Ryslik wrote:
Hi,
I have a list of several hundred 2 dimensional matrices, where each matrix
is n x m. What I need to do is that for each n,m I need an average over
all the lists. This would collapse it down to just one nxm matrix. Any
easy ways to do that? As always, I'd like to avoid a for loop to keep
computational time low! Thanks again everyone!
Cheers,
G
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] average matrices across a list
My next suggestion (I don't have time to work out or test an example at the moment): library(abind) tmparr - abind(m1,m2,m3,...,along=3) OR tmparr - do.call(c(matlist,list(along=3))) apply(tmparr,c(1,2),mean,na.rm=TRUE) or something along those lines. __ R-help@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.
Re: [R] average matrices across a list
Hi Everyone,
Thanks to everyone for their help. With your suggestions and some poking
around, the following works for what I need. It basically adds all the matrices
elementwise, and adds nothing if the element is NA. Thanks again! Code below:
**
mymats - vector('list', 5)
set.seed(246)
# Generate a list of five 3 x 3 matrices
for(i in 1:5) mymats[[i]] - matrix(sample(1:9), nrow = 3)
mymats[[5]][1,1]-NA
mymats[[4]][2,2]-NA
mymats
matrixadder-function(u,v){
na.u-is.na(u)
na.v-is.na(v)
ifelse(na.u na.v, NA, ifelse(na.u, 0, u)+ ifelse(na.v,0,v))
}
Reduce('matrixadder',mymats)
**
Cheers,
Greg
On Sep 12, 2010, at 8:33 PM, Ben Bolker wrote:
My next suggestion (I don't have time to work out or test an example
at the moment):
library(abind)
tmparr - abind(m1,m2,m3,...,along=3)
OR
tmparr - do.call(c(matlist,list(along=3)))
apply(tmparr,c(1,2),mean,na.rm=TRUE)
or something along those lines.
__
R-help@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.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
