packrat/lib-R/x86_64-w64-mingw32/3.6.1/mgcv/tests/mgcv-parallel.R

In jmcascalheira/LGMIberiaCluster: Research compendium for the paper "Human adaptations and palaeoenvironmental record during the Last Glacial Maximum in the Iberian Peninsula"

## examples that are claimed to be too long in help files
## illustration of multi-threading with gam...

require(mgcv);set.seed(9)
dat <- gamSim(1,n=2000,dist="poisson",scale=.1)
k <- 12;bs <- "cr";ctrl <- list(nthreads=2)

system.time(b1<-gam(y~s(x0,bs=bs)+s(x1,bs=bs)+s(x2,bs=bs,k=k)
            ,family=poisson,data=dat,method="REML"))[3]

system.time(b2<-gam(y~s(x0,bs=bs)+s(x1,bs=bs)+s(x2,bs=bs,k=k),
            family=poisson,data=dat,method="REML",control=ctrl))[3]

## Poisson example on a cluster with 'bam'. 
## Note that there is some overhead in initializing the 
## computation on the cluster, associated with loading 
## the Matrix package on each node. For this reason the 
## sample sizes here are very small to keep CRAN happy, but at
## this low sample size you see little advantage of parallel computation.

k <- 13;set.seed(9)
dat <- gamSim(1,n=6000,dist="poisson",scale=.1)
require(parallel)  
nc <- 2   ## cluster size, set for example portability
if (detectCores()>1) { ## no point otherwise
  cl <- makeCluster(nc) 
  ## could also use makeForkCluster, but read warnings first!
} else cl <- NULL
  
system.time(b3 <- bam(y ~ s(x0,bs=bs,k=7)+s(x1,bs=bs,k=7)+s(x2,bs=bs,k=k)
            ,data=dat,family=poisson(),chunk.size=5000,cluster=cl))

fv <- predict(b3,cluster=cl) ## parallel prediction

if (!is.null(cl)) stopCluster(cl)
b3

## Alternative using the discrete option with bam...

system.time(b4 <- bam(y ~ s(x0,bs=bs,k=7)+s(x1,bs=bs,k=7)+s(x2,bs=bs,k=k)
            ,data=dat,family=poisson(),discrete=TRUE,nthreads=2))