[Vegan-commits] r1927 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-10-03 19:30:04 +0200 (Mon, 03 Oct 2011)
New Revision: 1927

Modified:
   pkg/vegan/R/metaMDSiter.R
   pkg/vegan/inst/ChangeLog
Log:
metaMDS did not reset 'tries' when 'previous.best' was from a different model

Modified: pkg/vegan/R/metaMDSiter.R
===================================================================
--- pkg/vegan/R/metaMDSiter.R	2011-10-02 16:43:28 UTC (rev 1926)
+++ pkg/vegan/R/metaMDSiter.R	2011-10-03 17:30:04 UTC (rev 1927)
@@ -30,9 +30,6 @@
             else if (nc < k)
                 for (i in 1:(k-nc))
                     init <- cbind(init, runif(NROW(init), -0.1, 0.1))
-            ## zero 'tries' if started from different no. of dims
-            if (inherits(previous.best, "metaMDS") && nc != k)
-                previous.best$tries <- 0
             if (trace)
                 cat(gettextf("Starting from %d-dimensional configuration\n", nc))
         } else {
@@ -42,6 +39,13 @@
         s0 <- switch(engine,
                      "monoMDS" = monoMDS(dist, y = init, k = k, maxit = 0, ...),
                      "isoMDS" = isoMDS(dist, y = init, k = k, maxit = 0))
+        ## Check whether model changed
+        if (is.list(previous.best) && !is.null(previous.best$stress) &&
+            !isTRUE(all.equal(previous.best$stress, s0$stress))) {
+            if (trace) cat("Stress differs from 'previous.best': reset tries\n")
+            if (inherits(previous.best, "metaMDS"))
+                previous.best$tries <- 0
+        }
     } else {
         ## no previous.best: start with cmdscale
         s0 <- switch(engine,

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-10-02 16:43:28 UTC (rev 1926)
+++ pkg/vegan/inst/ChangeLog	2011-10-03 17:30:04 UTC (rev 1927)
@@ -4,10 +4,14 @@
 
 Version 2.1-2 (opened September 29, 20119
 
+	* metaMDS did not reset 'tries' when the analysis was started from
+	'previous.best' of a different model (except when no. of dims 'k'
+	changed). I think this was a bug(let). Fixed in metaMDSiter.R.
+	
 	* commsimulator is going to be deprecated: it is no longer used in
 	oecosimu() ore elsewhere in other functions. Currently, functions
 	make.commsim(), nullmodel() and simulate.nullmodel() do the same,
-	and more. As the first step, its documenation in oecosimu.Rd is
+	and more. As the first step, its documentation in oecosimu.Rd is
 	moved to vegan-deprecated.Rd.
 	
 	* examples: cut donw some excessively time consuming examples.
@@ -24,7 +28,7 @@
 	without simulations within oecosimu(), and different statistics
 	can be swept out based on the same set of simulated matrices.
 
-	* permatfull/swap is using the new simulate(nullmodel(...)...)
+	* permatfull/swap is using the new simulate.nullmodel(...)
 	infrastructure. permatfull1 and permatswap1 removed from vegan 
 	devel.
 
@@ -143,7 +147,7 @@
 
 	* raupcrick: new function to implement Raup-Crick (dissimilarity/
 	probability) index with unequal sampling probabilities of species.
-	Brian Inouye informed about their paper (Chase et al., Ecospher
+	Brian Inouye informed about their paper (Chase et al., Exosphere
 	2:art24 [doi:10.1890/ES10-00117.1]; 2011) where they showed that
 	Raup & Crick said that we should use sampling probabilities
 	proportional to species frequencies in assessing their index, but
@@ -156,7 +160,7 @@
 
 Version 2.0-0 (released September 8, 2011)
 
-	* opened the release candidate ov vegan_2.0-0 on September 3,
+	* opened the release candidate of vegan_2.0-0 on September 3,
 	2011. 
 
 	* some old functions used attributes(x)$which instead of more