[Vegan-commits] r2336 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2012-12-12 18:45:44 +0100 (Wed, 12 Dec 2012)
New Revision: 2336

Modified:
   pkg/vegan/R/monoMDS.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/monoMDS.Rd
Log:
change default convergence criteria of monoMDS (strickter sfgrmin, slacker smin)

Modified: pkg/vegan/R/monoMDS.R
===================================================================
--- pkg/vegan/R/monoMDS.R	2012-12-12 15:50:22 UTC (rev 2335)
+++ pkg/vegan/R/monoMDS.R	2012-12-12 17:45:44 UTC (rev 2336)
@@ -2,7 +2,7 @@
     function(dist, y, k = 2,
              model = c("global", "local", "linear", "hybrid"),
              threshold = 0.8, maxit = 200, weakties = TRUE, stress = 1,
-             scaling = TRUE, pc = TRUE, smin = 0.00001, sfgrmin = 0.00001,
+             scaling = TRUE, pc = TRUE, smin = 1e-4, sfgrmin = 1e-7,
              sratmax=0.99999, ...) 
 {
     ## Check that 'dist' are distances or a symmetric square matrix

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-12-12 15:50:22 UTC (rev 2335)
+++ pkg/vegan/inst/ChangeLog	2012-12-12 17:45:44 UTC (rev 2336)
@@ -4,9 +4,13 @@
 
 Version 2.1-22 (opened November 19, 2012)
 
-	* monoMDS, metaMDS: scores() ignore now requests to scores beyond
-	those calculated instead of failing. scores.metaMDS() does not
-	drop dimensions.
+	* monoMDS, metaMDS: Default convergence criteria were changed in
+	monoMDS. Most importantly, now scale factor of the gradient is
+	sfgrmin = 1e-7. The former limit 1e-5 was much too slack with
+	large data sets and iterations stopped too early without getting
+	close to the solution. In addition, scores() ignore now requests
+	to scores beyond those calculated instead of failing, and
+	scores.metaMDS() does not drop dimensions.
 
 	* nestednodf: added plot() method modelled after
 	plot.nestedtemp().

Modified: pkg/vegan/man/monoMDS.Rd
===================================================================
--- pkg/vegan/man/monoMDS.Rd	2012-12-12 15:50:22 UTC (rev 2335)
+++ pkg/vegan/man/monoMDS.Rd	2012-12-12 17:45:44 UTC (rev 2336)
@@ -16,7 +16,7 @@
 \usage{
 monoMDS(dist, y, k = 2, model = c("global", "local", "linear", "hybrid"), 
     threshold = 0.8, maxit = 200, weakties = TRUE, stress = 1,
-    scaling = TRUE, pc = TRUE, smin = 0.00001, sfgrmin = 0.00001, 
+    scaling = TRUE, pc = TRUE, smin = 1e-4, sfgrmin = 1e-7, 
     sratmax=0.99999, ...) 
 \method{scores}{monoMDS}(x, choices = NA, ...)
 \method{plot}{monoMDS}(x, choices = c(1,2), type = "t", ...)