Adjustments to pass R CMD check --as-cran

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

diff --git a/pkg/R/multiRun.R b/pkg/R/multiRun.R
index 0a5c843..1cebaab 100644 (file)
--- a/pkg/R/multiRun.R
+++ b/pkg/R/multiRun.R
@@ -11,6 +11,7 @@
 #' @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).
@@ -39,8 +40,11 @@
 #'       model=FLXMRglm(family="binomial") ) )
 #'     normalize( matrix(out@@coef[1:(ncol(fargs$X)*K)], ncol=K) )
 #'   } ),
-#'   prepareArgs = function(fargs) {
-#'     fargs$ind <- sample(1:nrow(fargs$X),replace=TRUE)
+#'   prepareArgs = function(fargs,index) {
+#'     if (index == 1)
+#'       fargs$ind <- 1:nrow(fargs$X)
+#'     else
+#'       fargs$ind <- sample(1:nrow(fargs$X),replace=TRUE)
 #'     fargs
 #'   }, N=10, ncores=3)
 #' for (i in 1:2)
@@ -65,7 +69,7 @@
 #'       model=FLXMRglm(family="binomial") ) )
 #'     sapply( seq_len(K), function(i) as.double( out@@components[[1]][[i]][,1] ) )
 #'   } ),
-#'   prepareArgs = function(fargs) {
+#'   prepareArgs = function(fargs,index) {
 #'     library(morpheus)
 #'     io = generateSampleIO(fargs$n, fargs$p, fargs$β, fargs$b, fargs$optargs$link)
 #'     fargs$X = io$X
@@ -78,7 +82,7 @@
 #'   res[[i]] <- alignMatrices(res[[i]], ref=β, ls_mode="exact")}
 #' @export
 multiRun <- function(fargs, estimParams,
-       prepareArgs = function(x) x, N=10, ncores=3, agg=lapply, verbose=FALSE)
+       prepareArgs = function(x,i) x, N=10, ncores=3, agg=lapply, verbose=FALSE)
 {
        if (!is.list(fargs))
                stop("fargs: list")
@@ -95,7 +99,7 @@ multiRun <- function(fargs, estimParams,
 
        estimParamAtIndex <- function(index)
        {
-               fargs <- prepareArgs(fargs)
+               fargs <- prepareArgs(fargs, index)
                if (verbose)
                        cat("Run ",index,"\n")
                lapply(seq_along(estimParams), function(i) {