sge.parApply {Rsge}R Documentation

Method used to integrate apply, lapply, sapply fcuntionality with qsub.

Description

applies each row/column of a matrix or each element of a list to a function.

Usage

  sge.apply   (X, MARGIN, FUN, ..., 
               join.method=cbind,
               njobs, batch.size=getOption('sge.block.size'),
               packages=NULL, savelist=NULL,
               cluster =getOption("sge.use.cluster"),
               trace=TRUE, debug=FALSE,
               file.prefix=getOption("sge.file.prefix"))
  sge.parRapply(X, FUN, ..., join.method=cbind, 
               njobs, batch.size=getOption('sge.block.size'),
               packages=NULL, savelist=NULL,
               cluster =getOption("sge.use.cluster"),
               trace=TRUE, debug=FALSE,
               file.prefix=getOption("sge.file.prefix"))
 
  sge.parCapply(X, FUN, ..., join.method=cbind, 
               njobs,batch.size=getOption('sge.block.size'),
               packages=NULL, savelist=NULL,
               cluster =getOption("sge.use.cluster"),
               trace=TRUE, debug=FALSE,
               file.prefix=getOption("sge.file.prefix"))
 
  sge.parLapply(X, FUN, ..., join.method=c, 
               njobs, batch.size=getOption('sge.block.size'),
               packages=NULL, savelist=NULL,
               cluster =getOption("sge.use.cluster"),
               trace=TRUE, debug=FALSE,
               file.prefix=getOption("sge.file.prefix")) 

  sge.parSapply(X, FUN, ...,  
                USE.NAMES=TRUE, simplify=TRUE,
                join.method=c, 
                njobs, batch.size=getOption('sge.block.size'),
                packages=NULL, savelist=NULL,
                cluster=getOption("sge.use.cluster"),
                trace=TRUE, debug=FALSE,
                file.prefix=getOption("sge.file.prefix"))
  sge.parParApply(X, FUN, ...,
               join.method=cbind,
               njobs,
               batch.size=getOption('sge.block.size'),
               trace=TRUE,
               packages=NULL,
               savelist=NULL,
               debug=FALSE,
               file.prefix=getOption('sge.file.prefix'),
               apply.method
              )

Arguments

X Object to be applied to function (matrix, data.frame, list, array, or vector supported)
MARGIN
FUN Function to be applied to object
... Additional arguments to be applied to function
njobs Number of parallel jobs to use
join.method Function used to merge results from each job.
batch.size Number of rows to include in parallel job if njobs is excluded.
savelist Character vector giving the names of local objects that should be copied to each worker process before computation is started.
packages List of library packages to be loaded by each worker process before computation is started.
cluster
trace Prints some information about job submission. (TRUE|FALSE)
file.prefix
debug Prints debug level info about jobs. (TRUE|FALSE)
USE.NAMES Determines if the sapply use names functionality should be used
simplify Detemines if the sapply simplify functionality should be used
apply.method tells apply if it should apply as a list or matrix

Details

sge.parApply applies the function argument to either the rows, or elements of x. (depending on the value of apply.method)

The arguments packages and savelist can be used to properly initialize the worker processes.

sge.parCapply computes the transpose of X and uses it for the arguments of parRapply.

sge.parLapply and sge.parSapply use lapply, sge.parCapply, and sge.parRapply use apply (Margin=1)

Value

Returns an object whose type is determined by the join.method. This object should be equivalent to the object that would be returned by an equivalent call to apply, sapply, or lapply.

Author(s)

Dan Bode dbode@univaud.com


[Package Rsge version 0.4 Index]