Hi all,
I would like to parallelize some R code and would like to use the 'foreach'
package with a foreach loop. However, whenever I call a function from an
enabled package outside of MASS, I get an error message that a number of the
functions aren't recognized (even though the functions should be defined).
For example:
library(foreach)
library(doSMP)
library(survival)
# Create the simplest test data set
test1 <- list(time=c(4,3,1,1,2,2,3),
status=c(1,1,1,0,1,1,0),
x=c(0,2,1,1,1,0,0),
sex=c(0,0,0,0,1,1,1))
# Fit a stratified model
coxph(Surv(time, status) ~ x + strata(sex), test1)
w <- startWorkers()
registerDoSMP(w)
foreach(i=1:3) %dopar% {
# Fit a stratified model
fit<-coxph(Surv(time, status) ~ x + strata(sex), test1)
summary(fit)$coef[i]
}
stopWorkers(w)
####Error message:
Error in { : task 1 failed - "could not find function "coxph""
If I call library(survival) inside the foreach loop, everything runs
properly. I don't think that I should have to call the package iteratively
inside the loop. I would like to use a foreach loop inside code for my own
package, but this is a problem since I can't call my own package in the
source code for the package itself! Any advice would be appreciated.
Thanks,
Stacey
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