Dear all,
I have a list of n matrices which all have the same dimension (r x s). What
would be a fast/elegant way to calculate the element wise average? So result[1,
1] <- mean(c(raw[[1]][1, 1] , raw[[2]][1, 1], raw[[...]][1, 1], raw[[n]][1,
1]))
Here is my attempt.
#create a dummy dataset
n <- 3
r <- 5
s <- 6
raw <- lapply(seq_len(n), function(i){
matrix(rnorm(r * s), ncol = r)
})
#do the calculation
result <- array(dim = c(dim(raw[[1]]), length(raw)))
for(i in seq_along(raw)){
result[,,i] <- raw[[i]]
}
result <- apply(result, 1:2, mean)
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey
* * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en
binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document.
The views expressed in this message and any annex are purely those of the writer
and may not be regarded as stating an official position of INBO, as long as the
message is not confirmed by a duly signed document.
If you don't have any NAs, then one way is:
n <- 3
r <- 5
s <- 6
raw <- lapply(seq_len(n), function(i){
matrix(rnorm(r * s), ncol = r)
})
Reduce("+", raw) / length(raw)
I hope it helps.
Best,
Dimitris
On 11/5/2012 11:32 AM, ONKELINX, Thierry wrote:> Dear all,
>
> I have a list of n matrices which all have the same dimension (r x s). What
would be a fast/elegant way to calculate the element wise average? So result[1,
1] <- mean(c(raw[[1]][1, 1] , raw[[2]][1, 1], raw[[...]][1, 1], raw[[n]][1,
1]))
>
> Here is my attempt.
>
> #create a dummy dataset
> n <- 3
> r <- 5
> s <- 6
> raw <- lapply(seq_len(n), function(i){
> matrix(rnorm(r * s), ncol = r)
> })
>
> #do the calculation
> result <- array(dim = c(dim(raw[[1]]), length(raw)))
> for(i in seq_along(raw)){
> result[,,i] <- raw[[i]]
> }
> result <- apply(result, 1:2, mean)
>
>
> Best regards,
>
> Thierry
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality
Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx at inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say what
the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
> Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver
weer en binden het INBO onder geen enkel beding, zolang dit bericht niet
bevestigd is door een geldig ondertekend document.
> The views expressed in this message and any annex are purely those of the
writer and may not be regarded as stating an official position of INBO, as long
as the message is not confirmed by a duly signed document.
>
> ______________________________________________
> 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.
>
--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
Web: http://www.erasmusmc.nl/biostatistiek/
Hi,
You can also try this:
?apply(simplify2array(raw),c(1,2),mean)
#?????????? [,1]?????? [,2]?????? [,3]??????? [,4]??????? [,5]
#[1,] -0.5457338 -0.2138714 -0.6555012 -0.03926681 -0.61747866
#[2,]? 0.1241875 -0.5987224 -1.6752304? 0.72977962 -0.47794016
#[3,]? 1.0154878 -0.5175063? 0.7309496 -0.57840227? 0.35273184
#[4,]? 0.5954131? 0.8647344 -0.2717948 -0.30062601? 0.73927935
#[5,]? 0.4304302? 0.6012879? 0.1132736? 0.33113125? 0.23399307
#[6,] -0.7745793? 1.0081508? 0.3272952? 0.72818327? 0.07494602
A.K.
----- Original Message -----
From: "ONKELINX, Thierry" <Thierry.ONKELINX at inbo.be>
To: "r-help at r-project.org" <r-help at r-project.org>
Cc:
Sent: Monday, November 5, 2012 5:32 AM
Subject: [R] averaging a list of matrices element wise
Dear all,
I have a list of n matrices which all have the same dimension (r x s). What
would be a fast/elegant way to calculate the element wise average? So result[1,
1] <- mean(c(raw[[1]][1, 1] , raw[[2]][1, 1], raw[[...]][1, 1], raw[[n]][1,
1]))
Here is my attempt.
#create a dummy dataset
n <- 3
r <- 5
s <- 6
raw <- lapply(seq_len(n), function(i){
? matrix(rnorm(r * s), ncol = r)
})
#do the calculation
result <- array(dim = c(dim(raw[[1]]), length(raw)))
for(i in seq_along(raw)){
? result[,,i] <- raw[[i]]
}
result <- apply(result, 1:2, mean)
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey
* * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en
binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document.
The views expressed in this message and any annex are purely those of the writer
and may not be regarded as stating an official position of INBO, as long as the
message is not confirmed by a duly signed document.
______________________________________________
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.