Steve Bellan
2014-Jul-03 22:53 UTC
[R] applying operations within() a matrix's environment
I am trying to optimize code for speed and readability for a fairly complex
function inside an MCMC sampler. As of now I have a bunch of variables inside a
function that get iteratively reset inside a loop. Something like this:
set.seed(1)
K <- 10
v1 <- rnorm(K)
v2 <- rnorm(K)
v3 <- rnorm(K)
steps <- 5
row.active <- matrix(rbinom(K*steps, 1, .7), nr = K, nc = steps)
cbind(v1,v2,v3)
for(ii in 1:steps) {
v1[row.active[,ii]] <- 2*v1[row.active[,ii]]
v2[row.active[,ii]] <- 3*v3[row.active[,ii]]^(v1[row.active[,ii]])
v3[row.active[,ii]] <- (v2[row.active[,ii]] + v3[row.active[,ii]] + 3)^2
}
cbind(v1,v2,v3)
Id like to be able to do this more succinctly with something like the following.
This would also allow me to store all the variables in a matrix, which seems
better than having so many variables (I actually have about 50).
v1 <- rnorm(K)
v2 <- rnorm(K)
v3 <- rnorm(K)
vars <- cbind(v1,v2,v3)
for(ii in 1:steps) {
vars[row.active[,ii]] <- within(vars[row.active[,ii]], {
v1 <- 2*v1
v2 <- 3*v3^v1
v3 <- (v2+v3 + 3)^2
})
}
But I get this error because with() & within() don’t work on objects that
aren’t environments such as matrices.
> + . + Error in UseMethod("within") :
no applicable method for 'within' applied to an object of class
"c('double', 'numeric’)"
It’s important that I keep this as a matrix and not a data.frame or list because
I’m trying to optimize for speed. Help is much appreciated. Thanks!
Steve
Steve Bellan, PhD, MPH
Post-doctoral Researcher
Lauren Ancel Meyers Research Group
Center for Computational Biology and Bioinformatics
University of Texas at Austin
http://www.bio.utexas.edu/research/meyers/steve_bellan/
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Hi
Are you 100% sure that you always want select only first item from v1,v2 and v3
and change it in each step of cycle and keep only last value from your cycle in
first item in vectors v1-3?
Because this is what your cycle does.
Petr
From: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org] On
Behalf Of Steve Bellan
Sent: Friday, July 04, 2014 12:53 AM
To: r-help@r-project.org
Subject: [R] applying operations within() a matrix's environment
I am trying to optimize code for speed and readability for a fairly complex
function inside an MCMC sampler. As of now I have a bunch of variables inside a
function that get iteratively reset inside a loop. Something like this:
set.seed(1)
K <- 10
v1 <- rnorm(K)
v2 <- rnorm(K)
v3 <- rnorm(K)
steps <- 5
row.active <- matrix(rbinom(K*steps, 1, .7), nr = K, nc = steps)
cbind(v1,v2,v3)
for(ii in 1:steps) {
v1[row.active[,ii]] <- 2*v1[row.active[,ii]]
v2[row.active[,ii]] <- 3*v3[row.active[,ii]]^(v1[row.active[,ii]])
v3[row.active[,ii]] <- (v2[row.active[,ii]] + v3[row.active[,ii]] + 3)^2
}
cbind(v1,v2,v3)
Id like to be able to do this more succinctly with something like the following.
This would also allow me to store all the variables in a matrix, which seems
better than having so many variables (I actually have about 50).
v1 <- rnorm(K)
v2 <- rnorm(K)
v3 <- rnorm(K)
vars <- cbind(v1,v2,v3)
for(ii in 1:steps) {
vars[row.active[,ii]] <- within(vars[row.active[,ii]], {
v1 <- 2*v1
v2 <- 3*v3^v1
v3 <- (v2+v3 + 3)^2
})
}
But I get this error because with() & within() don�t work on objects that
aren�t environments such as matrices.
> + . + Error in UseMethod("within") :
no applicable method for 'within' applied to an object of class
"c('double', 'numeric�)"
It�s important that I keep this as a matrix and not a data.frame or list because
I�m trying to optimize for speed. Help is much appreciated. Thanks!
Steve
Steve Bellan, PhD, MPH
Post-doctoral Researcher
Lauren Ancel Meyers Research Group
Center for Computational Biology and Bioinformatics
University of Texas at Austin
http://www.bio.utexas.edu/research/meyers/steve_bellan/
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