[Vegan-commits] r2475 - in branches/2.0: R inst man

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

Author: jarioksa
Date: 2013-03-08 10:15:18 +0100 (Fri, 08 Mar 2013)
New Revision: 2475

Modified:
   branches/2.0/R/metaMDSiter.R
   branches/2.0/inst/ChangeLog
   branches/2.0/man/metaMDS.Rd
Log:
handcraft r2447: set maxit in metaMDS

Modified: branches/2.0/R/metaMDSiter.R
===================================================================
--- branches/2.0/R/metaMDSiter.R	2013-03-08 08:44:34 UTC (rev 2474)
+++ branches/2.0/R/metaMDSiter.R	2013-03-08 09:15:18 UTC (rev 2475)
@@ -1,6 +1,6 @@
 `metaMDSiter` <-
     function (dist, k = 2, trymax = 20, trace = 1, plot = FALSE, 
-              previous.best, engine = "monoMDS", ...) 
+              previous.best, engine = "monoMDS", maxit = 200, ...) 
 {
     engine <- match.arg(engine, c("monoMDS", "isoMDS"))
     if (engine == "isoMDS")
@@ -49,8 +49,10 @@
     } else {
         ## no previous.best: start with cmdscale
         s0 <- switch(engine,
-                 "monoMDS" = monoMDS(dist, y = cmdscale(dist, k = k), k = k, ...),
-                 "isoMDS" = isoMDS(dist, k = k, trace = isotrace))
+                 "monoMDS" = monoMDS(dist, y = cmdscale(dist, k = k), k = k,
+                 maxit = maxit, ...),
+                 "isoMDS" = isoMDS(dist, k = k, trace = isotrace,
+                 maxit = maxit))
     }
     if (trace) 
         cat("Run 0 stress", s0$stress, "\n")
@@ -58,9 +60,9 @@
     while(tries < trymax) {
         tries <- tries + 1
         stry <- switch(engine,
-                       "monoMDS" = monoMDS(dist, k = k, maxit = 200, ...),
+                       "monoMDS" = monoMDS(dist, k = k, maxit = maxit, ...),
                        "isoMDS" = isoMDS(dist, initMDS(dist, k = k), k = k,
-                       maxit = 200, tol = 1e-07, trace = isotrace))
+                       maxit = maxit, tol = 1e-07, trace = isotrace))
         if (trace) {
             cat("Run", tries, "stress", stry$stress, "\n")
         }

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-03-08 08:44:34 UTC (rev 2474)
+++ branches/2.0/inst/ChangeLog	2013-03-08 09:15:18 UTC (rev 2475)
@@ -12,6 +12,7 @@
 	* merge r2452: plot/text.cca gained axis.bp = TRUE argument. 
 	* merge r2448 (partly), 2449: print.monoMDS clearer about
 	convergence. Only this part merged: metaMDSiter untouched.
+	* handcraft r2447: metaMDSiter gained argument 'maxit'.
 	* merge r2443: edit cca.object.Rd.
 	* merge r2434: return wcmdscale object always with non-default
 	arguments.

Modified: branches/2.0/man/metaMDS.Rd
===================================================================
--- branches/2.0/man/metaMDS.Rd	2013-03-08 08:44:34 UTC (rev 2474)
+++ branches/2.0/man/metaMDS.Rd	2013-03-08 09:15:18 UTC (rev 2475)
@@ -41,7 +41,7 @@
     noshare = TRUE, trace = 1, commname, zerodist = "ignore", 
     distfun = vegdist, ...)
 metaMDSiter(dist, k = 2, trymax = 20, trace = 1, plot = FALSE, 
-    previous.best, engine = "monoMDS", ...)   
+    previous.best, engine = "monoMDS", maxit = 200, ...)   
 initMDS(x, k=2)
 postMDS(X, dist, pc=TRUE, center=TRUE, halfchange, threshold=0.8,
     nthreshold=10, plot=FALSE, ...)
@@ -119,6 +119,11 @@
  \item{distfun}{Dissimilarity function. Any function returning a
    \code{dist} object and accepting argument \code{method} can be used
    (but some extra arguments may cause name conflicts).}
+
+ \item{maxit}{Maximum number of iterations in the single NMDS run;
+   passed to the \code{engine} function \code{\link{monoMDS}} or
+   \code{\link[MASS]{isoMDS}}.}
+
  \item{dist}{Dissimilarity matrix used in multidimensional scaling. }
   \item{pc}{Rotate to principal components. }
   \item{center}{Centre the configuration. }