[Vegan-commits] r1961 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2011-10-28 09:02:28 +0200 (Fri, 28 Oct 2011)
New Revision: 1961

Modified:
   pkg/vegan/R/metaMDSdist.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/metaMDS.Rd
Log:
metaMDS() and metaMDSdist() had inconsistent defaults for 'noshare'

Modified: pkg/vegan/R/metaMDSdist.R
===================================================================
--- pkg/vegan/R/metaMDSdist.R	2011-10-20 14:06:51 UTC (rev 1960)
+++ pkg/vegan/R/metaMDSdist.R	2011-10-28 07:02:28 UTC (rev 1961)
@@ -1,7 +1,7 @@
 `metaMDSdist` <-
-    function (comm, distance = "bray", autotransform = TRUE, noshare = 0.1, 
-              trace = 1, commname, zerodist = "ignore", distfun = vegdist, 
-              ...) 
+    function (comm, distance = "bray", autotransform = TRUE,
+              noshare = TRUE, trace = 1, commname,
+              zerodist = "ignore", distfun = vegdist, ...) 
 {
     ## metaMDSdist should get a raw data matrix, but if it gets a
     ## 'dist' object return that unchanged and quit silently.

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-10-20 14:06:51 UTC (rev 1960)
+++ pkg/vegan/inst/ChangeLog	2011-10-28 07:02:28 UTC (rev 1961)
@@ -7,6 +7,14 @@
 	* opened a new version with the release of vegan 2.0-1 on Oct 20,
 	2011.
 
+	* metaMDSdist: the default value of "noshare" was inconsistent
+	with metaMDS(), and therefore stressplot() could fail for
+	engine="isoMDS". Usually metaMDS() sets the 'noshare' depending on
+	the engine, but metaMDSdist() is called directly from
+	capscale(..., metaMDSdist = TRUE) and metaMDSredist (for
+	stressplot), and now these default to extended dissimilarities.
+	The problem was reported by Falk Hildebrand
+
 	* capscale: could fail if constrained component had zero rank,
 	typically in partial models where constrained component was
 	completely aliased. This was observed when checking an R-News

Modified: pkg/vegan/man/metaMDS.Rd
===================================================================
--- pkg/vegan/man/metaMDS.Rd	2011-10-20 14:06:51 UTC (rev 1960)
+++ pkg/vegan/man/metaMDS.Rd	2011-10-28 07:02:28 UTC (rev 1961)
@@ -37,8 +37,9 @@
     choices = c(1,2), shrink = FALSE, select, ...)
 \method{scores}{metaMDS}(x, display = c("sites", "species"), shrink = FALSE, 
     choices, ...)
-metaMDSdist(comm, distance = "bray", autotransform = TRUE, noshare = 0.1, 
-    trace = 1, commname, zerodist = "ignore", distfun = vegdist, ...)
+metaMDSdist(comm, distance = "bray", autotransform = TRUE, 
+    noshare = TRUE, trace = 1, commname, zerodist = "ignore", 
+    distfun = vegdist, ...)
 metaMDSiter(dist, k = 2, trymax = 20, trace = 1, plot = FALSE, 
     previous.best, engine = "monoMDS", ...)   
 initMDS(x, k=2)