Embarrasingly parallel computation of models (practically solved; conceptually still unclear)

Unfortunately I get the same failure with
(1) formulaList[[1]] <- 'y ~ x'
and
(2) formulaList[[1]] <- as.formula('y ~ x')
and
(3) formulaList[[1]] <- as.formula(y ~ x)
and 
(4) formulaList[[1]] <- y ~ x # doesn't make sense to me

All this is puzzling in light of
fit <- lm(sr ~ ., data = LifeCycleSavings)
frml <- as.formula('sr ~ .')
fit <- lm(frml, data = LifeCycleSavings)

and

frml <- vector('list', 4)
frml[[1]] <- as.formula('sr ~ .')
(fit <- lm(frml[[1]], data = LifeCycleSavings))

Call:
lm(formula = frml[[1]], data = LifeCycleSavings)

Coefficients:
(Intercept)        pop15        pop75          dpi         ddpi  
 28.566087    -0.461193    -1.691498    -0.000337     0.409695  

so (2) should work. The problem must be how I use the foreach() function. So instead of

outputList <- foreach(i = 1:4) %dopar% glmer(formulaList, family = binomial, data = selected)

which failed, I tried

outputList <- foreach(i = 1:4) %dopar% glmer(formulaList[[i]], family = binomial, data = selected)

which worked! But that seems to me not to be in spirit of foreach. So how do I tell it where to look for the list over which i is supposed to range?

MK

On Sep 6, 2013, at 9:32 AM, Stephen Weston <stephen.b.weston at gmail.com> wrote:

Hi Michael,

I think the problem is that you're creating a list of strings rather
than a list of formulas.  If you don't use single-quotes around the
formulas, I think it will work.

- Steve

On Fri, Sep 6, 2013 at 7:34 AM, Michael Kubovy <kubovy at virginia.edu> wrote:

Dear HPC people,

I'm trying to leasrn how to run multiple independent models in parrallel. I have succesfully run parallel computations on different sets of data (using 12 of my 24 cores). But there's something (probably trivial) about the nature of formulae that is escaping me. Here is what I tried.

I store my formulae:

formulaList <- vector('list', length = 4)
formulaList[[1]] <- 'resp ~ BAratio +dispDiff + (BAratio + dispDiff | subject)'
formulaList[[2]] <- 'resp ~ BAratio * dispDiff + (BAratio * dispDiff | subject)'
formulaList[[3]] <- 'resp ~ BA3Dratio + dispDiff + (BA3Dratio + dispDiff | subject)'
formulaList[[4]] <- 'resp ~ BA3Dratio * dispDiff + (BA3Dratio * dispDiff | subject)'

I get workers:

require(foreach)
require(doMC)
registerDoMC()
getDoParWorkers()

I try to run:

outputList <- foreach(i = 1:4) %dopar% glmer(formulaList, family = binomial, data = selected)

I get: Error: task 1 failed - "invalid formula"

FYI

sessionInfo()

R version 3.0.1 Patched (2013-09-02 r63805)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines   datasets  utils     stats     graphics  grDevices methods   base

other attached packages:
[1] lme4_0.999999-2   Matrix_1.0-12     lattice_0.20-23   xtable_1.7-1      gamlss_4.2-6      nlme_3.1-111
[7] gamlss.data_4.2-6 gamlss.dist_4.2-0 plyr_1.8          foreach_1.4.1     sos_1.3-7         brew_1.0-6
[13] ggplot2_0.9.3.1   car_2.0-18        nnet_7.3-7        MASS_7.3-29

loaded via a namespace (and not attached):
[1] codetools_0.2-8    colorspace_1.2-2   compiler_3.0.1     dichromat_2.0-0    digest_0.6.3       grid_3.0.1
[7] gtable_0.1.2       iterators_1.0.6    labeling_0.2       munsell_0.4.2      proto_0.3-10       RColorBrewer_1.0-5
[13] reshape2_1.2.2     scales_0.2.3       stats4_3.0.1       stringr_0.6.2      survival_2.37-4    tools_3.0.1