\HeaderA{xvalLoop}{Cross-validation in clustered computing environments}{xvalLoop}
\keyword{methods}{xvalLoop}
\begin{Description}\relax
Use cross-validation in a clustered computing environment
\end{Description}
\begin{Usage}
\begin{verbatim}xvalLoop( cluster, ... )\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{cluster}] Any S4-class object, used to indicate how to perform clustered
computations.
\item[\code{...}] Additional arguments used to inform the clustered computation.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Cross-validiation usually involves repeated calls to the same
function, but with different arguments. This provides an obvious
place for using clustered computers to enhance execution. The method
\code{\LinkA{xval}{xval}} is structured to exploit this; \code{xvalLoop}
provides an easy mechanism to change how \code{xval} performs
cross-validation.

The idea is to write an \code{xvalLoop} method that returns a
function. The function is then used to execute the
cross-validation. For instance, the default method returns the
function \code{lapply}, so the cross-validation is performed by using
\code{lapply}. A different method might return a function that
executed lapply-like functions, but sent different parts of the
function to different computer nodes.

An accompanying vignette illustrates the technique in greater
detail. An effective division of labor is for experienced cluster
programmers to write lapply-like methods for their favored clustering
environment. The user then only has to add the cluster object to the
list of arguments to \code{xval} to get clustered calculations.
\end{Details}
\begin{Value}
A function taking arguments like those for \code{\LinkA{lapply}{lapply}}
\end{Value}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
library(golubEsets)
data(Golub_Merge)
smallG <- Golub_Merge[200:250,]

# Evaluation on one node

lk1 <- xval(smallG, "ALL.AML", knnB, xvalMethod="LOO", group=as.integer(0))
table(lk1,smallG$ALL.AML)

# Evaluation on several nodes -- a cluster programmer might write the following...

library(snow)
setOldClass("spawnedMPIcluster")

setMethod("xvalLoop", signature( cluster = "spawnedMPIcluster"),
## use the function returned below to evalutae
## the central cross-validation loop in xval
function( cluster, ... ) {
    clusterExportEnv <- function (cl, env = .GlobalEnv)
    {
        unpackEnv <- function(env) {
            for ( name in ls(env) ) assign(name, get(name, env), .GlobalEnv )
            NULL
        }
        clusterCall(cl, unpackEnv, env)
    }
    function(X, FUN, ...) { # this gets returned to xval
        ## send all visible variables from the parent (i.e., xval) frame
        clusterExportEnv( cluster, parent.frame(1) )
        parLapply( cluster, X, FUN, ... )
    }
})

# ... and use the cluster like this...

cl <- makeCluster(2, "MPI")
clusterEvalQ(cl, library(MLInterfaces))

lk1 <- xval(smallG, "ALL.AML", knnB, xvalMethod="LOO", group=as.integer(0), cluster = cl)
table(lk1,smallG$ALL.AML)
## End(Not run)\end{ExampleCode}
\end{Examples}

