miga-base 1.2.17.1 → 1.2.17.3

data/utils/enveomics/enveomics.R/R/tribs.R

@@ -36,9 +36,10 @@
 #' selection occur in the same transformed space. However, it's useful to
 #' compare randomly subsampled sets against a selected set of objects. This
 #' is intended to identify overdispersion or overclustering (see
-#' \code{\link{enve.TRIBStest}}) of a subset against the entire collection of objects
-#' with minimum impact of sampling biases. This object can be produced by
-#' \code{\link{enve.tribs}} and supports S4 methods \code{plot} and \code{summary}.
+#' \code{\link{enve.TRIBStest}}) of a subset against the entire collection of
+#' objects with minimum impact of sampling biases. This object can be produced
+#' by \code{\link{enve.tribs}} and supports S4 methods \code{plot} and
+#' \code{summary}.
 #' 
 #' @slot distance \code{(numeric)} Centrality measurement of the distances 
 #' between the selected objects (without subsampling).
@@ -73,9 +74,9 @@ enve.TRIBS <- setClass("enve.TRIBS",
 #' Enveomics: TRIBS Test S4 Class
 #' 
 #' Test of significance of overclustering or overdispersion in a selected
-#' set of objects with respect to the entire set (see \code{\link{enve.TRIBS}}). This
-#' object can be produced by \code{\link{enve.tribs.test}} and supports S4 methods
-#' \code{plot} and \code{summary}.
+#' set of objects with respect to the entire set (see \code{\link{enve.TRIBS}}).
+#' This object can be produced by \code{\link{enve.tribs.test}} and supports S4
+#' methods \code{plot} and \code{summary}.
 #' 
 #' @slot pval.gt \code{(numeric)}
 #' P-value for the overdispersion test.
@@ -101,18 +102,19 @@ enve.TRIBS <- setClass("enve.TRIBS",
 #' 
 #' @exportClass 
 
-enve.TRIBStest <- setClass("enve.TRIBStest",
-                           representation(
-                             pval.gt='numeric',
-                             pval.lt='numeric',
-                             all.dist='numeric',
-                             sel.dist='numeric',
-                             diff.dist='numeric',
-                             dist.mids='numeric',
-                             diff.mids='numeric',
-                             call='call')
-                           ,package='enveomics.R'
-);
+enve.TRIBStest <- setClass(
+  "enve.TRIBStest",
+  representation(
+    pval.gt   = "numeric",
+    pval.lt   = "numeric",
+    all.dist  = "numeric",
+    sel.dist  = "numeric",
+    diff.dist = "numeric",
+    dist.mids = "numeric",
+    diff.mids = "numeric",
+    call      = "call"
+  ), package = "enveomics.R"
+)
 
 #==============> Define S4 methods
 
@@ -125,24 +127,22 @@ enve.TRIBStest <- setClass("enve.TRIBStest",
 #' @param ...
 #' No additional parameters are currently supported.
 #' 
+#' @return No return value.
+#' 
 #' @author Luis M. Rodriguez-R [aut, cre]
 #' 
 #' @method summary enve.TRIBS
-#' @export 
-
-summary.enve.TRIBS <- function
-(object,
- ...
-){
-  cat('===[ enve.TRIBS ]-------------------------\n');
-  cat('Selected',attr(object,'selSize'),'of',
-      attr(object,'spaceSize'),'objects in',
-      attr(object,'dimensions'),'dimensions.\n');
-  cat('Collected',length(attr(object,'subsamples')),'subsamples with',
-      nrow(attr(object,'distances')),'replicates each.\n');
-  cat('------------------------------------------\n');
-  cat('call:',as.character(attr(object,'call')),'\n');
-  cat('------------------------------------------\n');
+#' @export
+summary.enve.TRIBS <- function(object, ...) {
+  cat("===[ enve.TRIBS ]-------------------------\n")
+  cat("Selected", attr(object, "selSize"), "of",
+      attr(object, "spaceSize"), "objects in",
+      attr(object, "dimensions"), "dimensions.\n")
+  cat("Collected", length(attr(object, "subsamples")), "subsamples with",
+      nrow(attr(object, "distances")), "replicates each.\n")
+  cat("------------------------------------------\n")
+  cat("call:", as.character(attr(object, "call")), "\n")
+  cat("------------------------------------------\n")
 }
 
 #' Enveomics: TRIBS Plot
@@ -171,46 +171,57 @@ summary.enve.TRIBS <- function
 #' @param ...
 #' Any additional parameters supported by \code{plot}.
 #' 
+#' @return No return value.
+#' 
 #' @author Luis M. Rodriguez-R [aut, cre]
 #' 
 #' @method plot enve.TRIBS
 #' @export 
 
-plot.enve.TRIBS <- function
-(x,
- new=TRUE,
- type=c('boxplot', 'points'),
- col='#00000044',
- pt.cex=1/2,
- pt.pch=19,
- pt.col=col,
- ln.col=col,
- ...
-){
-  type <- match.arg(type);
-  plot.opts <- list(xlim=range(attr(x,'subsamples'))*attr(x,'selSize'),
-                    ylim=range(attr(x,'distances')), ..., t='n', x=1);
-  if(new) do.call(plot, plot.opts);
-  abline(h=attr(x,'distance'), lty=3, col=ln.col);
-  replicates <- nrow(attr(x,'distances'));
-  if(type=='points'){
-    for(i in 1:ncol(attr(x,'distances')))
-      points(rep(round(attr(x,'subsamples')[i]*attr(x,'selSize')),
-                 replicates), attr(x,'distances')[,i], cex=pt.cex, pch=pt.pch,
-             col=pt.col);
-  }else{
-    stats <- matrix(NA, nrow=7, ncol=ncol(attr(x,'distances')));
-    for(i in 1:ncol(attr(x,'distances'))){
-      b <- boxplot.stats(attr(x,'distances')[,i]);
-      points(rep(round(attr(x,'subsamples')[i]*attr(x,'selSize')),
-                 length(b$out)), b$out, cex=pt.cex, pch=pt.pch, col=pt.col);
-      stats[, i] <- c(b$conf, b$stats[c(1,5,2,4,3)]);
+plot.enve.TRIBS <- function(
+  x,
+  new    = TRUE,
+  type   = c("boxplot", "points"),
+  col    = "#00000044",
+  pt.cex = 1/2,
+  pt.pch = 19,
+  pt.col = col,
+  ln.col = col,
+  ...
+) {
+  type <- match.arg(type)
+  plot.opts <- list(
+    xlim = range(attr(x, "subsamples")) * attr(x, "selSize"),
+    ylim = range(attr(x, "distances")), ..., t = "n", x = 1
+  )
+  if (new) do.call(plot, plot.opts)
+  abline(h = attr(x, "distance"), lty = 3, col = ln.col)
+  replicates <- nrow(attr(x, "distances"))
+  if (type == "points") {
+    for (i in 1:ncol(attr(x, "distances")))
+      points(
+        rep(round(attr(x, "subsamples")[i] * attr(x, "selSize")), replicates),
+        attr(x, "distances")[, i],
+        cex = pt.cex, pch = pt.pch, col = pt.col
+      )
+  } else {
+    stats <- matrix(NA, nrow = 7, ncol = ncol(attr(x, "distances")))
+    for (i in 1:ncol(attr(x, "distances"))) {
+      b <- boxplot.stats(attr(x, "distances")[, i])
+      points(
+        rep(
+          round(attr(x, "subsamples")[i] * attr(x, "selSize")), length(b$out)
+        ),
+        b$out, cex = pt.cex, pch = pt.pch, col = pt.col
+      )
+      stats[, i] <- c(b$conf, b$stats[c(1, 5, 2, 4, 3)])
     }
-    x <- round(attr(x,'subsamples')*attr(x,'selSize'))
-    for(i in c(1,3,5))
-      polygon(c(x, rev(x)), c(stats[i,], rev(stats[i+1,])), border=NA,
-              col=col);
-    lines(x, stats[7,], col=ln.col, lwd=2);
+    x <- round(attr(x, "subsamples") * attr(x, "selSize"))
+    for (i in c(1, 3, 5))
+      polygon(
+        c(x, rev(x)), c(stats[i, ], rev(stats[i + 1, ])), border = NA, col = col
+      )
+    lines(x, stats[7, ], col = ln.col, lwd = 2)
   }
 }
 
@@ -223,37 +234,36 @@ plot.enve.TRIBS <- function
 #' @param ...
 #' No additional parameters are currently supported.
 #' 
+#' @return No return value.
+#' 
 #' @author Luis M. Rodriguez-R [aut, cre]
 #' 
 #' @method summary enve.TRIBStest
-#' @export 
+#' @export
 
-summary.enve.TRIBStest <- function
-(object,
- ...
-){
-  cat('===[ enve.TRIBStest ]---------------------\n');
-  cat('Alternative hypothesis:\n');
-  cat('   The distances in the selection are\n');
-  if(attr(object, 'pval.gt') > attr(object, 'pval.lt')){
-    cat('   smaller than in the entire dataset\n   (overclustering)\n');
-  }else{
-    cat('   larger than in the entire dataset\n   (overdispersion)\n');
+summary.enve.TRIBStest <- function(object, ...) {
+  cat("===[ enve.TRIBStest ]---------------------\n")
+  cat("Alternative hypothesis:\n")
+  cat("   The distances in the selection are\n")
+  if (attr(object, "pval.gt") > attr(object, "pval.lt")) {
+    cat("   smaller than in the entire dataset\n   (overclustering)\n")
+  } else {
+    cat("   larger than in the entire dataset\n   (overdispersion)\n")
   }
-  p.val <- min(attr(object, 'pval.gt'), attr(object, 'pval.lt'));
-  if(p.val==0){
-    diff.dist <- attr(object, 'diff.dist');
-    p.val.lim <- min(diff.dist[diff.dist>0]);
-    cat('\n   P-value <= ', signif(p.val.lim, 4), sep='');
-  }else{
-    p.val.lim <- p.val;
-    cat('\n   P-value: ', signif(p.val, 4), sep='');
+  p.val <- min(attr(object, "pval.gt"), attr(object, "pval.lt"))
+  if (p.val == 0) {
+    diff.dist <- attr(object, "diff.dist")
+    p.val.lim <- min(diff.dist[diff.dist > 0])
+    cat("\n   P-value <= ", signif(p.val.lim, 4), sep = "")
+  } else {
+    p.val.lim <- p.val
+    cat("\n   P-value: ", signif(p.val, 4), sep = "")
   }
-  cat(' ', ifelse(p.val.lim<=0.01, "**", ifelse(p.val.lim<=0.05, "*", "")),
-      '\n', sep='');
-  cat('------------------------------------------\n');
-  cat('call:',as.character(attr(object,'call')),'\n');
-  cat('------------------------------------------\n');
+  cat(" ", ifelse(p.val.lim <= 0.01, "**",
+      ifelse(p.val.lim<=0.05, "*", "")), "\n", sep = "")
+  cat("------------------------------------------\n")
+  cat("call:", as.character(attr(object, "call")), "\n")
+  cat("------------------------------------------\n")
 }
 
 #' Enveomics: TRIBS Plot Test
@@ -263,9 +273,9 @@ summary.enve.TRIBStest <- function
 #' @param x
 #' \code{\link{enve.TRIBStest}} object to plot.
 #' @param type
-#' What to plot. \code{overlap} generates a plot of the two contrasting empirical
-#' PDFs (to compare against each other), \code{difference} produces a plot of the
-#' differences between the empirical PDFs (to compare against zero).
+#' What to plot. \code{overlap} generates a plot of the two contrasting
+#' empirical PDFs (to compare against each other), \code{difference} produces a
+#' plot of the differences between the empirical PDFs (to compare against zero).
 #' @param col
 #' Main color of the plot if type=\code{difference}.
 #' @param col1
@@ -281,48 +291,61 @@ summary.enve.TRIBStest <- function
 #' @param ...
 #' Any other graphical arguments.
 #' 
+#' @return No return value.
+#' 
 #' @author Luis M. Rodriguez-R [aut, cre]
 #' 
 #' @method plot enve.TRIBStest
 #' @export 
 
-plot.enve.TRIBStest <- function
-(x,
- type=c('overlap', 'difference'),
- col='#00000044',
- col1=col,
- col2='#44001144',
- ylab='Probability',
- xlim=range(attr(x, 'dist.mids')),
- ylim=c(0,max(c(attr(x, 'all.dist'), attr(x, 'sel.dist')))),
- ...
-){
-  type <- match.arg(type);
-  if(type=='overlap'){
-    plot.opts <- list(xlim=xlim, ylim=ylim, ylab=ylab, ..., t='n', x=1);
-    do.call(plot, plot.opts);
-    bins <- length(attr(x, 'dist.mids'))
-    polygon(attr(x, 'dist.mids')[c(1, 1:bins, bins)],
-            c(0,attr(x, 'all.dist'),0), col=col1,
-            border=do.call(rgb, as.list(c(col2rgb(col1)/256, 0.5))));
-    polygon(attr(x, 'dist.mids')[c(1, 1:bins, bins)],
-            c(0,attr(x, 'sel.dist'),0), col=col2,
-            border=do.call(rgb, as.list(c(col2rgb(col2)/256, 0.5))));
-  }else{
-    plot.opts <- list(xlim=range(attr(x, 'diff.mids')),
-                      ylim=c(0,max(attr(x, 'diff.dist'))), ylab=ylab, ..., t='n', x=1);
-    do.call(plot, plot.opts);
-    bins <- length(attr(x, 'diff.mids'));
-    polygon(attr(x, 'diff.mids')[c(1, 1:bins, bins)],
-            c(0,attr(x, 'diff.dist'),0), col=col,
-            border=do.call(rgb, as.list(c(col2rgb(col)/256, 0.5))));
+plot.enve.TRIBStest <- function(
+  x,
+  type =c("overlap", "difference"),
+  col  = "#00000044",
+  col1 = col,
+  col2 = "#44001144",
+  ylab = "Probability",
+  xlim = range(attr(x, "dist.mids")),
+  ylim = c(0, max(c(attr(x, "all.dist"), attr(x, "sel.dist")))),
+  ...
+) {
+  type <- match.arg(type)
+  if (type == "overlap") {
+    plot.opts <- list(
+      xlim = xlim, ylim = ylim, ylab = ylab, ..., t = "n", x = 1
+    )
+    do.call(plot, plot.opts)
+    bins <- length(attr(x, "dist.mids"))
+    polygon(
+      attr(x, "dist.mids")[c(1, 1:bins, bins)],
+      c(0, attr(x, "all.dist"), 0), col = col1,
+      border = do.call(rgb, as.list(c(col2rgb(col1) / 256, 0.5)))
+    )
+    polygon(
+      attr(x, "dist.mids")[c(1, 1:bins, bins)],
+      c(0, attr(x, "sel.dist"), 0), col = col2,
+      border = do.call(rgb, as.list(c(col2rgb(col2) / 256, 0.5)))
+    )
+  } else {
+    plot.opts <- list(
+      xlim = range(attr(x, "diff.mids")),
+      ylim = c(0,max(attr(x, 'diff.dist'))),
+      ylab = ylab, ..., t = "n", x = 1
+    )
+    do.call(plot, plot.opts)
+    bins <- length(attr(x, "diff.mids"))
+    polygon(
+      attr(x, "diff.mids")[c(1, 1:bins, bins)],
+      c(0, attr(x, "diff.dist"), 0), col = col,
+      border = do.call(rgb, as.list(c(col2rgb(col) / 256, 0.5)))
+    )
   }
 }
 
 #' Enveomics: TRIBS Merge
 #' 
-#' Merges two \code{\link{enve.TRIBS}} objects generated from the same objects at
-#' different subsampling levels.
+#' Merges two \code{\link{enve.TRIBS}} objects generated from the same objects
+#' at different subsampling levels.
 #' 
 #' @param x
 #' First \code{\link{enve.TRIBS}} object.
@@ -335,35 +358,35 @@ plot.enve.TRIBStest <- function
 #' 
 #' @export 
 
-enve.TRIBS.merge <- function
-(x,
- y
-){
+enve.TRIBS.merge <- function(x, y) {
   # Check consistency
-  if(attr(x,'distance') != attr(y,'distance'))
-    stop('Total distances in objects are different.');
-  if(any(attr(x,'points') != attr(y,'points')))
-    stop('Points in objects are different.');
-  if(attr(x,'spaceSize') != attr(y,'spaceSize'))
-    stop('Space size in objects are different.');
-  if(attr(x,'selSize') != attr(y,'selSize'))
-    stop('Selection size in objects are different.');
-  if(attr(x,'dimensions') != attr(y,'dimensions'))
-    stop('Dimensions in objects are different.');
-  if(nrow(attr(x,'distances')) != nrow(attr(y,'distances')))
-    stop('Replicates in objects are different.');
+  if (attr(x, "distance") != attr(y, "distance"))
+    stop("Total distances in objects are different.")
+  if (any(attr(x, "points") != attr(y, "points")))
+    stop("Points in objects are different.")
+  if (attr(x, "spaceSize") != attr(y, "spaceSize"))
+    stop("Space size in objects are different.")
+  if (attr(x, "selSize") != attr(y, "selSize"))
+    stop("Selection size in objects are different.")
+  if (attr(x, "dimensions") != attr(y, "dimensions"))
+    stop("Dimensions in objects are different.")
+  if (nrow(attr(x, "distances")) != nrow(attr(y, "distances")))
+    stop("Replicates in objects are different.")
+
   # Merge
-  a <- attr(x,'subsamples');
-  b <- attr(y,'subsamples');
-  o <- order(c(a,b));
-  o <- o[!duplicated(c(a,b)[o])] ;
-  d <- cbind(attr(x,'distances'), attr(y,'distances'))[, o] ;
-  z <- new('enve.TRIBS',
-           distance=attr(x,'distance'), points=attr(x,'points'),
-           distances=d, spaceSize=attr(x,'spaceSize'),
-           selSize=attr(x,'selSize'), dimensions=attr(x,'dimensions'),
-           subsamples=c(a,b)[o], call=match.call());
-  return(z) ;
+  a <- attr(x, "subsamples")
+  b <- attr(y, "subsamples")
+  o <- order(c(a, b))
+  o <- o[!duplicated(c(a, b)[o])]
+  d <- cbind(attr(x, "distances"), attr(y, "distances"))[, o]
+  z <- new(
+    "enve.TRIBS",
+    distance = attr(x, "distance"), points = attr(x, "points"),
+    distances = d, spaceSize = attr(x, "spaceSize"),
+    selSize = attr(x, "selSize"), dimensions = attr(x, "dimensions"),
+    subsamples = c(a, b)[o], call = match.call()
+  )
+  return(z)
 }
 
 #==============> Define core functions
@@ -389,44 +412,53 @@ enve.TRIBS.merge <- function
 #' 
 #' @export 
 
-enve.tribs.test <- function
-(dist,
- selection,
- bins=50,
- ...
-){
-  s.tribs <- enve.tribs(dist, selection, subsamples=c(0,1), ...);
-  a.tribs <- enve.tribs(dist,
-                        subsamples=c(0,attr(s.tribs, 'selSize')/attr(s.tribs, 'spaceSize')), ...);
-  s.dist <- attr(s.tribs, 'distances')[, 2];
-  a.dist <- attr(a.tribs, 'distances')[, 2];
-  range <- range(c(s.dist, a.dist));
-  a.f <- hist(a.dist, breaks=seq(range[1], range[2], length.out=bins),
-              plot=FALSE);
-  s.f <- hist(s.dist, breaks=seq(range[1], range[2], length.out=bins),
-              plot=FALSE);
-  zp.f <- c(); zz.f <- 0; zn.f <- c();
-  p.x <- a.f$counts/sum(a.f$counts);
-  p.y <- s.f$counts/sum(s.f$counts);
-  for(z in 1:length(a.f$mids)){
-    zn.f[z] <- 0;
-    zz.f <- 0;
-    zp.f[z] <- 0;
-    for(k in 1:length(a.f$mids)){
-      if(z < k){
-        zp.f[z] <- zp.f[z] + p.x[k]*p.y[k-z];
-        zn.f[z] <- zn.f[z] + p.x[k-z]*p.y[k];
+enve.tribs.test <- function(dist, selection, bins = 50, ...) {
+  s.tribs <- enve.tribs(dist, selection, subsamples = c(0,1), ...)
+  a.tribs <- enve.tribs(
+    dist,
+    subsamples = c(0, attr(s.tribs, "selSize") / attr(s.tribs, "spaceSize")),
+    ...
+  )
+  s.dist <- attr(s.tribs, "distances")[, 2]
+  a.dist <- attr(a.tribs, "distances")[, 2]
+  range <- range(c(s.dist, a.dist))
+  a.f <- hist(
+    a.dist, breaks = seq(range[1], range[2], length.out = bins), plot = FALSE
+  )
+  s.f <- hist(
+    s.dist, breaks = seq(range[1], range[2], length.out = bins), plot = FALSE
+  )
+  zp.f <- c()
+  zz.f <- 0
+  zn.f <- c()
+  p.x <- a.f$counts / sum(a.f$counts)
+  p.y <- s.f$counts / sum(s.f$counts)
+  for (z in 1:length(a.f$mids)) {
+    zn.f[z] <- 0
+    zz.f <- 0
+    zp.f[z] <- 0
+    for (k in 1:length(a.f$mids)) {
+      if (z < k) {
+        zp.f[z] <- zp.f[z] + p.x[k] * p.y[k-z]
+        zn.f[z] <- zn.f[z] + p.x[k-z] * p.y[k]
       }
-      zz.f <- zz.f + p.x[k]*p.y[k];
+      zz.f <- zz.f + p.x[k] * p.y[k]
     }
   }
-  return(new('enve.TRIBStest',
-             pval.gt=sum(c(zz.f, zp.f)), pval.lt=sum(c(zz.f, zn.f)),
-             all.dist=p.x, sel.dist=p.y, diff.dist=c(rev(zn.f), zz.f, zp.f),
-             dist.mids=a.f$mids,
-             diff.mids=seq(diff(range(a.f$mids)), -diff(range(a.f$mids)),
-                           length.out=1+2*length(a.f$mids)),
-             call=match.call()));
+  return(
+    new(
+      "enve.TRIBStest",
+      pval.gt = sum(c(zz.f, zp.f)), pval.lt = sum(c(zz.f, zn.f)),
+      all.dist = p.x, sel.dist = p.y, diff.dist = c(rev(zn.f), zz.f, zp.f),
+      dist.mids = a.f$mids,
+      diff.mids = seq(
+        diff(range(a.f$mids)),
+        -diff(range(a.f$mids)),
+        length.out = 1 + 2 * length(a.f$mids)
+      ),
+      call=match.call()
+    )
+  )
 }
 
 #' Enveomics: TRIBS
@@ -468,8 +500,8 @@ enve.tribs.test <- function
 #' dimensions as columns.
 #' @param pre.tribs
 #' Optional. If passed, the points are recovered from this object (except if
-#' \code{points} is also passed. This should be an \code{\link{enve.TRIBS}} object 
-#' estimated on the same objects (the selection is unimportant).
+#' \code{points} is also passed. This should be an \code{\link{enve.TRIBS}}
+#' object estimated on the same objects (the selection is unimportant).
 #' 
 #' @return Returns an \code{\link{enve.TRIBS}} object.
 #' 
@@ -477,69 +509,87 @@ enve.tribs.test <- function
 #' 
 #' @export
 
-enve.tribs <- function
-(dist,
- selection=labels(dist),
- replicates=1000,
- summary.fx=median,
- dist.method='euclidean',
- subsamples=seq(0,1,by=0.01),
- dimensions=ceiling(length(selection)*0.05),
- metaMDS.opts=list(),
- threads=2,
- verbosity=1,
- points,
- pre.tribs
-){
-  if(!is(dist, 'dist'))
-    stop('`dist` parameter must be a `dist` object.');
+enve.tribs <- function(
+  dist,
+  selection    = labels(dist),
+  replicates   = 1000,
+  summary.fx   = median,
+  dist.method  = "euclidean",
+  subsamples   = seq(0, 1, by = 0.01),
+  dimensions   = ceiling(length(selection) * 0.05),
+  metaMDS.opts = list(),
+  threads      = 2,
+  verbosity    = 1,
+  points,
+  pre.tribs
+) {
+  # Sanity checks
+  if (!is(dist, "dist"))
+    stop("`dist` parameter must be a `dist` object.")
+
   # 1. NMDS
-  if(missing(points)){
-    if(missing(pre.tribs)){
-      if(verbosity > 0)
-        cat('===[ Estimating NMDS ]\n');
-      if(!suppressPackageStartupMessages(
-        requireNamespace("vegan", quietly=TRUE)))
-        stop('Unavailable required package: `vegan`.');
-      mds.args <- c(metaMDS.opts, list(comm=dist, k=dimensions,
-                                       trace=verbosity));
-      points <- do.call(vegan::metaMDS, mds.args)$points;
-    }else{
-      points <- attr(pre.tribs, 'points');
-      dimensions <- ncol(points);
+  if (missing(points)) {
+    if (missing(pre.tribs)) {
+      if (verbosity > 0) cat("===[ Estimating NMDS ]\n")
+      if (!suppressPackageStartupMessages(
+           requireNamespace("vegan", quietly=TRUE))
+         ) stop("Unavailable required package: `vegan`.")
+      mds.args <- c(
+        metaMDS.opts,
+        list(comm = dist, k = dimensions, trace = verbosity)
+      )
+      points <- do.call(vegan::metaMDS, mds.args)$points
+    } else {
+      points <- attr(pre.tribs, "points")
+      dimensions <- ncol(points)
     }
-  }else{
-    points <- as.matrix(points);
-    dimensions <- ncol(points);
+  } else {
+    points <- as.matrix(points)
+    dimensions <- ncol(points)
   }
+
   # 2. Pad ranges
-  if(verbosity > 0) cat('===[ Padding ranges ]\n');
-  dots <- matrix(NA, nrow=nrow(points), ncol=dimensions,
-                 dimnames=list(rownames(points), 1:dimensions));
-  selection <- selection[!is.na(match(selection, rownames(dots)))];
-  for(dim in 1:dimensions){
-    dimRange <- range(points[,dim]) +
-      c(-1,1)*diff(range(points[,1]))/length(selection);
-    dots[, dim] <- (points[,dim]-dimRange[1])/diff(dimRange);
+  if (verbosity > 0) cat("===[ Padding ranges ]\n")
+  dots <- matrix(
+    NA, nrow = nrow(points), ncol = dimensions,
+    dimnames = list(rownames(points), 1:dimensions)
+  )
+  selection <- selection[!is.na(match(selection, rownames(dots)))]
+  for (dim in 1:dimensions) {
+    dimRange <- range(points[, dim]) + c(-1, 1) *
+                diff(range(points[, 1])) / length(selection)
+    dots[, dim] <- (points[, dim] - dimRange[1]) / diff(dimRange)
   }
+
   # 3. Select points and summarize distances
-  if(verbosity > 0) cat('===[ Sub-sampling ]\n');
-  distances <- matrix(NA, nrow=replicates, ncol=length(subsamples),
-                      dimnames=list(1:replicates, as.character(subsamples)));
-  cl <- makeCluster(threads);
-  for(frx in subsamples){
-    if(verbosity > 1) cat('Sub-sampling at ',(frx*100),'%\n',sep='');
-    distances[, as.character(frx)] = parSapply(cl, 1:replicates, enve.__tribs,
-                                               frx, match(selection, rownames(dots)), dimensions, dots, dist.method,
-                                               summary.fx, dist);
+  if (verbosity > 0) cat("===[ Sub-sampling ]\n")
+  distances <- matrix(
+    NA, nrow = replicates, ncol = length(subsamples),
+    dimnames = list(1:replicates, as.character(subsamples))
+  )
+  cl <- makeCluster(threads)
+  for (frx in subsamples) {
+    if (verbosity > 1) cat("Sub-sampling at ", (frx * 100), "%\n", sep = "")
+    distances[, as.character(frx)] <- parSapply(
+      cl, 1:replicates, enve.__tribs, frx,
+      match(selection, rownames(dots)), dimensions, dots, dist.method,
+      summary.fx, dist
+    )
   }
-  stopCluster(cl);
+  stopCluster(cl)
+
   # 4. Build object and return
-  return(new('enve.TRIBS',
-             distance=do.call(summary.fx, list(as.matrix(dist)[selection, selection])),
-             points=points, distances=distances, spaceSize=nrow(points),
-             selSize=length(selection), dimensions=dimensions, subsamples=subsamples,
-             call=match.call()));
+  return(
+    new(
+      "enve.TRIBS",
+      distance = do.call(
+        summary.fx, list(as.matrix(dist)[selection, selection])
+      ),
+      points = points, distances = distances, spaceSize = nrow(points),
+      selSize = length(selection), dimensions = dimensions,
+      subsamples = subsamples, call = match.call()
+    )
+  )
 }
 
 #' Enveomics: TRIBS - Internal Ancillary Function
@@ -555,29 +605,34 @@ enve.tribs <- function
 #' @param summary.fx Summary function
 #' @param dist Distance
 #' 
+#' @return A numeric indicating the \code{summary.fx} value applied to the
+#' distance matrix subset
+#' 
 #' @author Luis M. Rodriguez-R [aut, cre]
 #' 
 #' @export
 
-enve.__tribs <- function
-(rep, frx, selection, dimensions, dots, dist.method, summary.fx, dist){
-  sample <- c();
-  if(frx==0) return(0);
-  for(point in 1:round(frx*length(selection))){
-    rand.point <- runif(dimensions);
-    closest.dot <- '';
-    closest.dist <- Inf;
-    for(dot in selection){
-      dot.dist <- as.numeric(dist(matrix(c(rand.point, dots[dot,]), nrow=2,
-                                         byrow=TRUE), method=dist.method));
-      if(dot.dist < closest.dist){
-        closest.dot <- dot;
-        closest.dist <- dot.dist;
+enve.__tribs <- function(
+  rep, frx, selection, dimensions, dots, dist.method, summary.fx, dist
+) {
+  sample <- c()
+  if (frx == 0) return(0)
+  for (point in 1:round(frx * length(selection))) {
+    rand.point <- runif(dimensions)
+    closest.dot <- ""
+    closest.dist <- Inf
+    for (dot in selection) {
+      dot.dist <- as.numeric(
+        dist(matrix(c(rand.point, dots[dot,]), nrow = 2, byrow = TRUE),
+             method = dist.method)
+      )
+      if (dot.dist < closest.dist) {
+        closest.dot <- dot
+        closest.dist <- dot.dist
       }
     }
-    sample <- c(sample, closest.dot);
+    sample <- c(sample, closest.dot)
   }
-  return( do.call(summary.fx, list(as.matrix(dist)[sample, sample])) );
+  return(do.call(summary.fx, list(as.matrix(dist)[sample, sample])))
 }
 
-