[Vegan-commits] r1932 - in branches/2.0: R inst

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

Author: jarioksa
Date: 2011-10-05 15:18:05 +0200 (Wed, 05 Oct 2011)
New Revision: 1932

Modified:
   branches/2.0/R/metaMDSiter.R
   branches/2.0/R/permutest.cca.R
   branches/2.0/inst/ChangeLog
   branches/2.0/inst/NEWS.Rd
Log:
merge r1927 (reset metaMDS when previous.best changed) and r1982 (permutest.cca result updating)

Modified: branches/2.0/R/metaMDSiter.R
===================================================================
--- branches/2.0/R/metaMDSiter.R	2011-10-05 12:33:34 UTC (rev 1931)
+++ branches/2.0/R/metaMDSiter.R	2011-10-05 13:18:05 UTC (rev 1932)
@@ -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: branches/2.0/R/permutest.cca.R
===================================================================
--- branches/2.0/R/permutest.cca.R	2011-10-05 12:33:34 UTC (rev 1931)
+++ branches/2.0/R/permutest.cca.R	2011-10-05 13:18:05 UTC (rev 1932)
@@ -101,7 +101,9 @@
     ## numerical inaccuracy
     F.0 <- round(F.0, 12)
     F.perm <- round(F.perm, 12)
-    sol <- list(call = match.call(), testcall = x$call, model = model,
+    Call <- match.call()
+    Call[[1]] <- as.name("permutest")
+    sol <- list(call = Call, testcall = x$call, model = model,
                 F.0 = F.0, F.perm = F.perm,  chi = c(Chi.z, Chi.xz),
                 num = num, den = den, df = c(q, r), nperm = permutations,
                 method = x$method, first = first,  Random.seed = seed)

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2011-10-05 12:33:34 UTC (rev 1931)
+++ branches/2.0/inst/ChangeLog	2011-10-05 13:18:05 UTC (rev 1932)
@@ -4,6 +4,9 @@
 
 Version 2.0-1 (opened September 8, 2011)
 
+	* merge r1928: permutest.cca result could not be update()d.
+ 	* merge r1927: reset 'tries' when 'previous.best' was a different
+	model.
 	* merge r1916: ordisurf.Rd references.
 	* merge r1914: example speed-up.
 	* r1897, 1840, 1825, 1823: copy clamtest (at r1897),

Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd	2011-10-05 12:33:34 UTC (rev 1931)
+++ branches/2.0/inst/NEWS.Rd	2011-10-05 13:18:05 UTC (rev 1932)
@@ -34,10 +34,17 @@
       especially when the \code{grouping} was numerical. The problem
       was reported by Dr Miguel Alvarez (Univ. Bonn).
 
+      \item \code{metaMDS} did not reset \code{tries} when a new model
+      was started with a \code{previous.best} solution from a different
+      model. 
+
       \item Function \code{permatswap} for community null models using
       quantitative swap never swapped items in a \eqn{2 \times 2}{2 by 2}
       submatrix if all cells were filled.
 
+      \item The result from \code{permutest.cca} could not be
+      \code{update}d because of a \file{NAMESPACE} issue.
+
     }	
   } % end BUG FIXES
 } % end version 2.0-1
@@ -48,7 +55,7 @@
       
       \item Peter Minchin joins the \pkg{vegan} team.
       
-      \item \pkg{vegan} implements standard \R \code{NAMESPACE}. In
+      \item \pkg{vegan} implements standard \R \file{NAMESPACE}. In
       general, \code{S3} methods are not exported which means that you
       cannot directly use or see contents of functions like
       \code{cca.default}, \code{plot.cca} or \code{anova.ccabyterm}. To