improve/fix comments - TODO: debug examples, CSV and after

[epclust.git] / epclust / R / computeSynchrones.R

diff --git a/epclust/R/computeSynchrones.R b/epclust/R/computeSynchrones.R
index 16bf0b4..f8d7a06 100644 (file)
--- a/epclust/R/computeSynchrones.R
+++ b/epclust/R/computeSynchrones.R
@@ -1,10 +1,11 @@
 #' computeSynchrones
 #'
-#' Compute the synchrones curves (sum of clusters elements) from a matrix of medoids,
+#' Compute the synchrones curves (sums of clusters elements) from a matrix of medoids,
 #' using euclidian distance.
 #'
-#' @param medoids matrix of medoids in columns (curves of same length as the series)
-#' @param getSeries Function to retrieve series (argument: 'indices', integer vector)
+#' @param medoids matrix of K medoids curves in columns
+#' @param getSeries Function to retrieve series (argument: 'indices', integer vector),
+#'   as columns of a matrix
 #' @param nb_curves How many series? (this is known, at this stage)
 #' @inheritParams claws
 #'
@@ -12,16 +13,15 @@
 #'
 #' @export
 computeSynchrones <- function(medoids, getSeries, nb_curves,
-       nb_series_per_chunk, ncores_clust=1,verbose=FALSE,parll=TRUE)
+       nb_series_per_chunk, ncores_clust=3, verbose=FALSE, parll=TRUE)
 {
        # Synchrones computation is embarassingly parallel: compute it by chunks of series
        computeSynchronesChunk <- function(indices)
        {
                if (parll)
                {
-                       require("bigmemory", quietly=TRUE)
-                       requireNamespace("synchronicity", quietly=TRUE)
                        require("epclust", quietly=TRUE)
+                       requireNamespace("synchronicity", quietly=TRUE)
                        # The big.matrix objects need to be attached to be usable on the workers
                        synchrones <- bigmemory::attach.big.matrix(synchrones_desc)
                        medoids <- bigmemory::attach.big.matrix(medoids_desc)
@@ -66,7 +66,11 @@ computeSynchrones <- function(medoids, getSeries, nb_curves,
                medoids <- bigmemory::as.big.matrix(medoids)
                medoids_desc <- bigmemory::describe(medoids)
                # outfile=="" to see stderr/stdout on terminal
-               cl <- parallel::makeCluster(ncores_clust, outfile="")
+               cl <-
+                       if (verbose)
+                               parallel::makeCluster(ncores_clust, outfile="")
+                       else
+                               parallel::makeCluster(ncores_clust)
                parallel::clusterExport(cl, envir=environment(),
                        varlist=c("synchrones_desc","m_desc","medoids_desc","getSeries"))
        }