[Vegan-commits] r2154 - in branches/2.0: R inst

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2012-05-06 16:10:15 +0200 (Sun, 06 May 2012)
New Revision: 2154

Modified:
   branches/2.0/R/monoMDS.R
   branches/2.0/R/rrarefy.R
   branches/2.0/inst/ChangeLog
Log:
merge r2149 & r2150: rrarefy, drarefy and monoMDS check their input

Modified: branches/2.0/R/monoMDS.R
===================================================================
--- branches/2.0/R/monoMDS.R	2012-05-06 14:05:36 UTC (rev 2153)
+++ branches/2.0/R/monoMDS.R	2012-05-06 14:10:15 UTC (rev 2154)
@@ -91,6 +91,11 @@
     }
     ## ndis: number dissimilarities
     ndis <- length(dist)
+    ## some people try to use NMDS with too few points and too many
+    ## dimensions
+    if (ndis <= k * nobj)
+        stop(gettextf("Not enough data for NMDS: you have %d dissimilarities,\n  and you ask %d scores (%d dimensions times %d points)",
+                      ndis, k * nobj, k, nobj))
     ## starting configuration
     if (missing(y)) {
         y <- matrix(runif(nobj*k, -1, 1), nobj, k)

Modified: branches/2.0/R/rrarefy.R
===================================================================
--- branches/2.0/R/rrarefy.R	2012-05-06 14:05:36 UTC (rev 2153)
+++ branches/2.0/R/rrarefy.R	2012-05-06 14:10:15 UTC (rev 2154)
@@ -3,6 +3,8 @@
 `rrarefy` <-
     function(x, sample)
 {
+    if (!identical(all.equal(x, round(x)), TRUE)) 
+        stop("function is meaningful only for integers (counts)")
     x <- as.matrix(x)
     if (ncol(x) == 1)
         x <- t(x)
@@ -27,6 +29,8 @@
 `drarefy` <-
     function(x, sample)
 {
+    if (!identical(all.equal(x, round(x)), TRUE)) 
+        stop("function accepts only integers (counts)")
     if (length(sample) > 1 &&  length(sample) != nrow(x))
         stop(gettextf(
              "length of  'sample' and number of rows of 'x' do not match"))

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2012-05-06 14:05:36 UTC (rev 2153)
+++ branches/2.0/inst/ChangeLog	2012-05-06 14:10:15 UTC (rev 2154)
@@ -4,6 +4,11 @@
 
 Version 2.0-4 (opened March 9, 2012)
 
+	* merge r2150: monoMDS checks that the number of dissimilarities
+	is sufficient for the requested analysis. The decostand.Rd fix of
+	r2150 was not yet merged.
+	* merge r2149: drarefy & rrarefy check that input data are
+	integers. 
 	* merge r2148 (partial): format references. However, scoverage()
 	was not merged yet, and its changes have not been merged.
 	* merge r2144: hiersimu and multipart do not assume constant