From: Doran, Harold <HDoran_at_air.org>

Date: Thu 20 Jul 2006 - 22:14:37 EST

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 and provide commented, minimal, self-contained, reproducible code. Received on Thu Jul 20 23:34:56 2006

Date: Thu 20 Jul 2006 - 22:14:37 EST

List:

Thank you for the replies to my post yesterday. Gabor and Phil also gave useful replies on how to improve the function by relying on mapply rather than the explicit for loop. In general, I try and use the family of apply functions rather than the looping constructs such as for, while etc as a matter of practice.

However, it seems the mapply function in this case is slower (in terms of CPU speed) than the for loop. Here is an example.

# data needed for example

items <- list(item1 = c(0,1,2), item2 = c(0,1), item3 = c(0,1,2,3,4),
item4 = c(0,1), item5=c(0,1,2,3,4),

item6=c(0,1,2,3))

score <- c(2,1,3,1,3,2)

theta <- c(-1,-.5,0,.5,1)

# My old function using the for loop

like.mat <- function(score, items, theta){

like.mat <- matrix(numeric(length(items) * length(theta)), ncol = length(theta))

for(i in 1:length(items)) like.mat[i, ] <- pcm(theta, items[[i]], score[[i]])

like.mat

}

system.time(like.mat(score,items,theta)) [1] 0 0 0 NA NA

# Revised using mapply

like.mat <- function(score, items, theta){
matrix(mapply(pcm,rep(theta,length(items)),items,score),ncol=length(thet
a),byrow=TRUE)

}

> system.time(like.mat(score,items,theta)) [1] 0.03 0.00 0.03 NA NA

It is obviously slower to use mapply, but nominaly. So, let's actually look at this within the context of the full program I am working on. For context, I am evaluating an integral using Gaussian quadrature. This is a psychometric problem where the function 'pcm" is Master's partial credit model and 'score' is the student's score on test item i. When an item has two categories (0,1), pcm reduces to the Rasch model for dichotomous data. The dnorm is set at N(0,1) by default, but the parameters of the population distribution are estimated from a separate procedure and are normally input into the function, but this default works for the example.

Here is the full program.

library(statmod)

# Master's partial credit model

pcm <- function(theta,d,score){

exp(rowSums(outer(theta,d[1:score],'-')))/ apply(exp(apply(outer(theta,d, '-'), 1, cumsum)), 2, sum)}

like.mat <- function(score, items, theta){

like.mat <- matrix(numeric(length(items) * length(theta)), ncol = length(theta))

for(i in 1:length(items)) like.mat[i, ] <- pcm(theta, items[[i]], score[[i]])

like.mat

}

# turn this off for now

*#like.mat <- function(score, items, theta){
**#matrix(mapply(pcm,rep(theta,length(items)),items,score),ncol=length(the
*

ta),byrow=TRUE)

*#}
*

class.numer <- function(score,items, prof_cut, mu=0, sigma=1, aboveQ){

gauss_numer <- gauss.quad(49,kind="laguerre") if(aboveQ==FALSE){

mat <- rbind(like.mat(score,items, (prof_cut-gauss_numer$nodes)), dnorm(prof_cut-gauss_numer$nodes, mean=mu, sd=sigma))

} else { mat <- rbind(like.mat(score,items, (gauss_numer$nodes+prof_cut)), dnorm(gauss_numer$nodes+prof_cut,

mean=mu, sd=sigma))

}

f_y <- rbind(apply(mat, 2, prod), exp(gauss_numer$nodes),
gauss_numer$weights)

sum(apply(f_y,2,prod))

}

class.denom <- function(score,items, mu=0, sigma=1){

gauss_denom <- gauss.quad.prob(49, dist='normal', mu=mu, sigma=sigma)
mat <-

rbind(like.mat(score,items,gauss_denom$nodes),gauss_denom$weights)

sum(apply(mat, 2, prod))

}

class.acc <-function(score,items,prof_cut, mu=0, sigma=1, aboveQ=TRUE){

result <- class.numer(score,items,prof_cut, mu,sigma, aboveQ)/class.denom(score,items, mu, sigma)

return(result)

}

# Test the function "class.acc"

items <- list(item1 = c(0,1,2), item2 = c(0,1), item3 = c(0,1,2,3,4),
item4 = c(0,1), item5=c(0,1,2,3,4),

item6=c(0,1,2,3))

score <- c(2,1,3,1,3,2)

# This is the system time when using the for loop for the like.mat

function

system.time(class.acc(score,items,1,aboveQ=T))
[1] 0.04 0.00 0.04 NA NA

# This is the system time using the mapply for the like.mat function

system.time(class.acc(score,items,1,aboveQ=T))
[1] 0.70 0.00 0.73 NA NA

There is a substantial improvement in CPU seconds when the for loop is applied rather than using the mapply function. I experimented with adding more items and varying the quadrature points and it always turned out the for loop was faster.

Given this result, I wonder what advice might be offered. Is there an inherent reason one might opt for the mapply function (such as reliability, etc) even when it compromises computational speed? Or, should the issue of computational speed be considered ahead of common advice to rely on the family of apply functions instead of the explicit loops.

Thanks for your consideration of my question, Harold

orm i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 3.0 year 2006 month 04 day 24 svn rev 37909 language Rversion.string Version 2.3.0 (2006-04-24)

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