inst/scripts/DDtimes2.R

In Bioconductor/geeni: Parallel implmentation of bounded memory GEE

library(geeni)
data(bigd)

source("engine.R")

library(foreach)
library(doMC)
registerDoMC(cores=12)
library(ff)

choppeddd = function( fmla, src )
   parols( fmla, src, family=gaussian(), binit=c(0,0) )

ww = .dfbychunk$new("dfbychunk", data=bigd[1:1e6,], chunksize=84000L)
dd12c = list()
dd12c$M1M = list()
dd12c$M1M[[1]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M1M[[2]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M1M[[3]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M1M[[4]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M1M[[5]] = unix.time( choppeddd( isT~GCcon, ww ) )

ww = .dfbychunk$new("dfbychunk", data=bigd[1:2e6,], chunksize=167000L)
dd12c$M2M = list()
dd12c$M2M[[1]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M2M[[2]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M2M[[3]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M2M[[4]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M2M[[5]] = unix.time( choppeddd( isT~GCcon, ww ) )

ww = .dfbychunk$new("dfbychunk", data=bigd[1:3e6,], chunksize=250000L)
dd12c$M3M = list()
dd12c$M3M[[1]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M3M[[2]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M3M[[3]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M3M[[4]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M3M[[5]] = unix.time( choppeddd( isT~GCcon, ww ) )

ww = .dfbychunk$new("dfbychunk", data=bigd[1:4e6,], chunksize=334000L)
dd12c$M4M = list()
dd12c$M4M[[1]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M4M[[2]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M4M[[3]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M4M[[4]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M4M[[5]] = unix.time( choppeddd( isT~GCcon, ww ) )

ww = .dfbychunk$new("dfbychunk", data=bigd, chunksize=417000L)
dd12c$M5M = list()
dd12c$M5M[[1]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M5M[[2]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M5M[[3]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M5M[[4]] = unix.time( choppeddd( isT~GCcon, ww ) )
dd12c$M5M[[5]] = unix.time( choppeddd( isT~GCcon, ww ) )

save(dd12c, file="dd12c.rda")