Nothing
bsSCAD <- function(logX,
groupings,
DIR=NULL,
params=NULL) {
#list(seed=123, bstr=100, maxiter=1000,
# maxevals=500, bounds=NULL, saveres=TRUE,
# jitter=FALSE, fs.method="scad")) {
if(is.null(params)) {
#params <- list(seed=123, ncv=5, repeats=10,
# ntree=1000, shrinkage=0.01, interaction.depth=3,
# bag.fraction=0.75, train.fraction=0.75,
# n.minobsinnode=3, n.cores=1, verbose=TRUE,
# jitter=FALSE, saveres=FALSE)
params <- control_params()
}
## introduce some minimal noise to make scaling etc. possible
if(params$jitter) {
logX <- jitter(logX)
}
# output directory
fs.method <- params$fs.method
seed <- params$seed
bstr <- params$bstr
bounds <- params$bounds
maxiter <- params$maxiter
maxevals <- params$maxevals
saveres <- params$saveres
if(!is.null(DIR)) {
SUBDIR <- paste(DIR,fs.method,sep="/")
if(!file.exists(SUBDIR))
dir.create(SUBDIR)
fnames <- paste(SUBDIR, "/", names(groupings), ".pdf", sep="")
} else {
SUBDIR <- NULL
fnames <- rep("-", length(groupings))
saveres <- FALSE
}
# assemble grouping information in one object
X <- lapply(1:length(groupings), function(i,groupings,fnames) list(groupings[[i]], fnames[i]), groupings=groupings, fnames=fnames)
names(X) <- names(groupings)
## use multicores if more than one group is to be classified
useparallel <- length(grep("package:(parallel|multicore)", search())>0)
if(length(X)>1 & useparallel) {
scad_bstr <- mclapply(X, bstr_multi, datX=logX, bstr=bstr, seed=seed, fs.method=fs.method, bounds=bounds, maxiter=maxiter, maxevals=maxevals, mc.preschedule=TRUE, mc.cores=length(X))
} else {
scad_bstr <- lapply(X, bstr_multi, datX=logX, bstr=bstr, seed=seed, fs.method=fs.method, bounds=bounds, maxiter=maxiter, maxevals=maxevals)
}
## set an attribute naming the method used
attr(scad_bstr, "fs.method") <- fs.method
if(saveres) {
## draw an importance graph for the fs
ig <- makeIG(scad_bstr, SUBDIR, prob=0.975)
save(scad_bstr, ig, params, file=paste(SUBDIR, "SCAD_RData.RData", sep="/"))
}
#invisible(list(res=scad_bstr, bstr=bstr, seed=seed, bounds=bounds, maxiter=maxiter, maxeval=maxeval, adj=adj, allsignatures=allsignatures, allprots=allprots))
invisible(scad_bstr)
}
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