WER distances is a regular matrix, fix doc (weird latex error?)

diff --git a/epclust/R/clustering.R b/epclust/R/clustering.R
index 92adda2..0d37c24 100644 (file)
--- a/epclust/R/clustering.R
+++ b/epclust/R/clustering.R
@@ -18,6 +18,7 @@
 #' @param getContribs Function to retrieve contributions from initial series indices:
 #'   \code{getContribs(indices)} outpus a contributions matrix
 #' @param contribs matrix of contributions (e.g. output of \code{curvesToContribs()})
+#' @param distances matrix of K1 x K1 (WER) distances between synchrones
 #' @inheritParams computeSynchrones
 #' @inheritParams claws
 #'
@@ -77,8 +78,7 @@ clusteringTask2 = function(medoids, K2,
        synchrones = computeSynchrones(medoids,
                getRefSeries, nb_ref_curves, nb_series_per_chunk, ncores_clust, verbose, parll)
        distances = computeWerDists(synchrones, ncores_clust, verbose, parll)
-       # PAM in package 'cluster' cannot take big.matrix in input: need to cast it
-       medoids[ computeClusters2(distances[,],K2,verbose), ]
+       medoids[ computeClusters2(distances,K2,verbose), ]
 }
 
 #' @rdname clustering
@@ -166,7 +166,7 @@ computeSynchrones = function(medoids, getRefSeries,
        }
 
        indices_workers = .spreadIndices(seq_len(nb_ref_curves), nb_series_per_chunk)
-               browser()
+#browser()
        ignored <-
                if (parll)
                        parallel::parLapply(cl, indices_workers, computeSynchronesChunk)
@@ -197,7 +197,7 @@ computeSynchrones = function(medoids, getRefSeries,
 #'   as the series in the initial dataset
 #' @inheritParams claws
 #'
-#' @return A big.matrix of size K1 x K1
+#' @return A matrix of size K1 x K1
 #'
 #' @export
 computeWerDists = function(synchrones, ncores_clust=1,verbose=FALSE,parll=TRUE)
@@ -244,6 +244,7 @@ computeWerDists = function(synchrones, ncores_clust=1,verbose=FALSE,parll=TRUE)
                sqres / max(Mod(sqres))
        }
 
+       # Distance between rows i and j
        computeDistancesIJ = function(pair)
        {
                i = pair[1] ; j = pair[2]
@@ -278,7 +279,9 @@ computeWerDists = function(synchrones, ncores_clust=1,verbose=FALSE,parll=TRUE)
                parallel::stopCluster(cl)
 
        Xwer_dist[n,n] = 0.
-       Xwer_dist
+       distances <- Xwer_dist[,]
+       rm(Xwer_dist) ; gc()
+       distances #~small matrix K1 x K1
 }
 
 # Helper function to divide indices into balanced sets