Re: [R] Efficient way to use data frame of indices to initialize matrix
Thanks for the three great answers! For those who are curious, I timed the
three approaches:
nr - 15812
nc - 64636
mymat - matrix(nrow=nr, ncol=nc)
mymat[1,1] - 1 # see note below
# mydf is created elsewhere
dim(mydf)
# 109102633
colnames(mydf)
# x y a
# approach 1:
# mymat[ mydf$x + (mydf$y-1) * nc ] - mydf$a
# approach 2:
# mymat[ as.matrix(mydf[,2:1]) ] - mydf$a
# approach 3:
# mymat[ cbind(mydf$x, mydf$y) ] - mydf$a
system.time( for (i in 1:10) mymat[ mydf$x + (mydf$y-1) * nc ] - mydf$a )
system.time( for (i in 1:10) mymat[ as.matrix(mydf$x, mydf$y) ] - mydf$a )
system.time( for (i in 1:10) mymat[ cbind(mydf$x, mydf$y) ] - mydf$a )
# user system elapsed
# 10.478 3.837 14.317 - #1
# 9.064 1.711 10.777 - #2
# 10.747 2.702 13.450 - #3
So you can see that approach #2 is the fastest. Note that I found that
initializing the new matrix with its first value takes about 8 elapsed seconds
all on its own, which is why I have that initialization line above.
--
Gene
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Tuesday, December 07, 2010 11:00 AM
To: Greg Snow
Cc: Gene; r-help@r-project.org
Subject: Re: [R] Efficient way to use data frame of indices to
initialize matrix
On Dec 7, 2010, at 1:49 PM, Greg Snow wrote:
tmpdf - data.frame( x = c(1,2,3), y=c(2,3,1), a=c(10,20,30) )
mymat - matrix(0, ncol=3, nrow=3)
mymat[ as.matrix(tmpdf[,c('x','y')]) ] - tmpdf$a
cbind is also useful for assembly of arguments to the matrix-`[-`
function:
tmpdf - data.frame( x = c(1,2,3), y=c(2,3,1), a=c(10,20,30) )
mymat - matrix(NA, ncol=max(tmpdf$y), nrow=max(tmpdf$x))
mymat[ cbind(tmpdf$x,tmpdf$y) ] - tmpdf$a
mymat
[,1] [,2] [,3]
[1,] NA 10 NA
[2,] NA NA 20
[3,] 30 NA NA
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Gene
Sent: Tuesday, December 07, 2010 11:31 AM
To: r-help@r-project.org
Subject: [R] Efficient way to use data frame of indices to
initialize
matrix
I have a data frame with three columns, x, y, and a. I want to
create
a matrix from these values such that for matrix m:
m[x,y] == a
Obviously, I can go row by row through the data frame and insert the
value a at the correct x,y location in the matrix. I can make that
slightly more efficient (perhaps), by doing something like this:
for (each.x in unique(df$x)) m[each.x, df$y[df$x == each.x]] -
df$a[df$x == each.x]
But I feel that there must be a more efficient, or at least more
elegant way to do this.
--
Gene
__
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David Winsemius, MD
West Hartford, CT
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Re: [R] Efficient way to use data frame of indices to initialize matrix
index m as a vector and do the assignment in one step i - df$row + (df$col-1)*nrow(m) m[i] - df$a or something along those lines. -Whit On Tue, Dec 7, 2010 at 1:31 PM, Cutler, Gene gcut...@amgen.com wrote: I have a data frame with three columns, x, y, and a. I want to create a matrix from these values such that for matrix m: m[x,y] == a Obviously, I can go row by row through the data frame and insert the value a at the correct x,y location in the matrix. I can make that slightly more efficient (perhaps), by doing something like this: for (each.x in unique(df$x)) m[each.x, df$y[df$x == each.x]] - df$a[df$x == each.x] But I feel that there must be a more efficient, or at least more elegant way to do this. -- Gene __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficient way to use data frame of indices to initialize matrix
tmpdf - data.frame( x = c(1,2,3), y=c(2,3,1), a=c(10,20,30) )
mymat - matrix(0, ncol=3, nrow=3)
mymat[ as.matrix(tmpdf[,c('x','y')]) ] - tmpdf$a
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Cutler, Gene
Sent: Tuesday, December 07, 2010 11:31 AM
To: r-help@r-project.org
Subject: [R] Efficient way to use data frame of indices to initialize
matrix
I have a data frame with three columns, x, y, and a. I want to create
a matrix from these values such that for matrix m:
m[x,y] == a
Obviously, I can go row by row through the data frame and insert the
value a at the correct x,y location in the matrix. I can make that
slightly more efficient (perhaps), by doing something like this:
for (each.x in unique(df$x)) m[each.x, df$y[df$x == each.x]] -
df$a[df$x == each.x]
But I feel that there must be a more efficient, or at least more
elegant way to do this.
--
Gene
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficient way to use data frame of indices to initialize matrix
On Dec 7, 2010, at 1:49 PM, Greg Snow wrote:
tmpdf - data.frame( x = c(1,2,3), y=c(2,3,1), a=c(10,20,30) )
mymat - matrix(0, ncol=3, nrow=3)
mymat[ as.matrix(tmpdf[,c('x','y')]) ] - tmpdf$a
cbind is also useful for assembly of arguments to the matrix-`[-`
function:
tmpdf - data.frame( x = c(1,2,3), y=c(2,3,1), a=c(10,20,30) )
mymat - matrix(NA, ncol=max(tmpdf$y), nrow=max(tmpdf$x))
mymat[ cbind(tmpdf$x,tmpdf$y) ] - tmpdf$a
mymat
[,1] [,2] [,3]
[1,] NA 10 NA
[2,] NA NA 20
[3,] 30 NA NA
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Cutler, Gene
Sent: Tuesday, December 07, 2010 11:31 AM
To: r-help@r-project.org
Subject: [R] Efficient way to use data frame of indices to initialize
matrix
I have a data frame with three columns, x, y, and a. I want to
create
a matrix from these values such that for matrix m:
m[x,y] == a
Obviously, I can go row by row through the data frame and insert the
value a at the correct x,y location in the matrix. I can make that
slightly more efficient (perhaps), by doing something like this:
for (each.x in unique(df$x)) m[each.x, df$y[df$x == each.x]] -
df$a[df$x == each.x]
But I feel that there must be a more efficient, or at least more
elegant way to do this.
--
Gene
__
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.
David Winsemius, MD
West Hartford, CT
__
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.
