Adjustments to pass R CMD check --as-cran

[morpheus.git] / pkg / R / multiRun.R

#' multiRun
#'
#' Estimate N times some parameters, outputs of some list of functions. This method is
#' thus very generic, allowing typically bootstrap or Monte-Carlo estimations of matrices
#' μ or β. Passing a list of functions opens the possibility to compare them on a fair
#' basis (exact same inputs). It's even possible to compare methods on some deterministic
#' design of experiments.
#'
#' @param fargs List of arguments for the estimation functions
#' @param estimParams List of nf function(s) to apply on fargs - shared signature
#' @param prepareArgs Prepare arguments for the functions inside estimParams
#' @param N Number of runs
#' @param ncores Number of cores for parallel runs (<=1: sequential)
#' @param agg Aggregation method (default: lapply)
#' @param verbose TRUE to indicate runs + methods numbers
#'
#' @return A list of nf aggregates of N results (matrices).
#'
#' @examples
#' \dontrun{
#' β <- matrix(c(1,-2,3,1),ncol=2)
#'
#' # Bootstrap + computeMu, morpheus VS flexmix ; assumes fargs first 3 elts X,Y,K
#' io <- generateSampleIO(n=1000, p=1/2, β=β, b=c(0,0), "logit")
#' μ <- normalize(β)
#' res <- multiRun(list(X=io$X,Y=io$Y,optargs=list(K=2,jd_nvects=0)), list(
#'   # morpheus
#'   function(fargs) {
#'     library(morpheus)
#'     ind <- fargs$ind
#'     computeMu(fargs$X[ind,],fargs$Y[ind],fargs$optargs)
#'   },
#'   # flexmix
#'   function(fargs) {
#'     library(flexmix)
#'     ind <- fargs$ind
#'     K <- fargs$optargs$K
#'     dat = as.data.frame( cbind(fargs$Y[ind],fargs$X[ind,]) )
#'     out = refit( flexmix( cbind(V1, 1 - V1) ~ 0+., data=dat, k=K,
#'       model=FLXMRglm(family="binomial") ) )
#'     normalize( matrix(out@@coef[1:(ncol(fargs$X)*K)], ncol=K) )
#'   } ),
#'   prepareArgs = function(fargs,index) {
#'     if (index == 1)
#'       fargs$ind <- 1:nrow(fargs$X)
#'     else
#'       fargs$ind <- sample(1:nrow(fargs$X),replace=TRUE)
#'     fargs
#'   }, N=10, ncores=3)
#' for (i in 1:2)
#'   res[[i]] <- alignMatrices(res[[i]], ref=μ, ls_mode="exact")
#'
#' # Monte-Carlo + optimParams from X,Y, morpheus VS flexmix ; first args n,p,β,b
#' res <- multiRun(list(n=1000,p=1/2,β=β,b=c(0,0),optargs=list(link="logit")),list(
#'   # morpheus
#'   function(fargs) {
#'     library(morpheus)
#'     K <- fargs$optargs$K
#'     μ <- computeMu(fargs$X, fargs$Y, fargs$optargs)
#'     V <- list( p=rep(1/K,K-1), β=μ, b=c(0,0) )
#'     optimParams(V,fargs$optargs)$β
#'   },
#'   # flexmix
#'   function(fargs) {
#'     library(flexmix)
#'     K <- fargs$optargs$K
#'     dat <- as.data.frame( cbind(fargs$Y,fargs$X) )
#'     out <- refit( flexmix( cbind(V1, 1 - V1) ~ 0+., data=dat, k=K,
#'       model=FLXMRglm(family="binomial") ) )
#'     sapply( seq_len(K), function(i) as.double( out@@components[[1]][[i]][,1] ) )
#'   } ),
#'   prepareArgs = function(fargs,index) {
#'     library(morpheus)
#'     io = generateSampleIO(fargs$n, fargs$p, fargs$β, fargs$b, fargs$optargs$link)
#'     fargs$X = io$X
#'     fargs$Y = io$Y
#'     fargs$optargs$K = ncol(fargs$β)
#'     fargs$optargs$M = computeMoments(io$X,io$Y)
#'     fargs
#'   }, N=10, ncores=3)
#' for (i in 1:2)
#'   res[[i]] <- alignMatrices(res[[i]], ref=β, ls_mode="exact")}
#' @export
multiRun <- function(fargs, estimParams,
	prepareArgs = function(x,i) x, N=10, ncores=3, agg=lapply, verbose=FALSE)
{
	if (!is.list(fargs))
		stop("fargs: list")
	# No checks on fargs: supposedly done in estimParams[[i]]()
	if (!is.list(estimParams))
		estimParams = list(estimParams)
	# Verify that the provided parameters estimations are indeed functions
	lapply(seq_along(estimParams), function(i) {
		if (!is.function(estimParams[[i]]))
			stop("estimParams: list of function(fargs)")
	})
	if (!is.numeric(N) || N < 1)
		stop("N: positive integer")

	estimParamAtIndex <- function(index)
	{
		fargs <- prepareArgs(fargs, index)
		if (verbose)
			cat("Run ",index,"\n")
		lapply(seq_along(estimParams), function(i) {
			if (verbose)
				cat("   Method ",i,"\n")
			out <- estimParams[[i]](fargs)
			if (is.list(out))
				do.call(rbind, out)
			else
				out
		})
	}

	if (ncores > 1)
	{
		cl = parallel::makeCluster(ncores, outfile="")
		parallel::clusterExport(cl, c("fargs","verbose"), environment())
		list_res = parallel::clusterApplyLB(cl, 1:N, estimParamAtIndex)
		parallel::stopCluster(cl)
	}
	else
		list_res = lapply(1:N, estimParamAtIndex)

	# De-interlace results: output one list per function
	nf <- length(estimParams)
	lapply( seq_len(nf), function(i) lapply(seq_len(N), function(j) list_res[[j]][[i]]) )
}