[Vegan-commits] r1767 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2011-08-28 17:47:50 +0200 (Sun, 28 Aug 2011)
New Revision: 1767

Modified:
   pkg/vegan/R/metaMDSrotate.R
   pkg/vegan/R/monoMDS.R
   pkg/vegan/R/print.monoMDS.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/monoMDS.Rd
Log:
harmonize info on pc rotation between mono/metaMDS and make metaMDSrotate work with monoMDS

Modified: pkg/vegan/R/metaMDSrotate.R
===================================================================
--- pkg/vegan/R/metaMDSrotate.R	2011-08-28 08:59:14 UTC (rev 1766)
+++ pkg/vegan/R/metaMDSrotate.R	2011-08-28 15:47:50 UTC (rev 1767)
@@ -2,10 +2,15 @@
 `metaMDSrotate` <-
     function(object, vec, na.rm = FALSE, ...) 
 {
-    if (!inherits(object, "metaMDS"))
-        stop(gettextf("function works only with 'metaMDS' results"))
+    workswith <- c("metaMDS", "monoMDS")
+    if (!inherits(object, workswith))
+        stop(gettextf("function works only with the results of: %s",
+                      paste(workswith, collapse = ", ")))
     x <- object$points
-    sp <- object$species
+    if (is.null(object$species))
+        sp <- NA
+    else
+        sp <- object$species
     N <- NCOL(x)
     if (N < 2)
         stop(gettextf("needs at least 2 dimensions"))

Modified: pkg/vegan/R/monoMDS.R
===================================================================
--- pkg/vegan/R/monoMDS.R	2011-08-28 08:59:14 UTC (rev 1766)
+++ pkg/vegan/R/monoMDS.R	2011-08-28 15:47:50 UTC (rev 1767)
@@ -109,7 +109,7 @@
     sol$points <- matrix(sol$points, nobj, k)
     if (pc)
         sol$points <- prcomp(sol$points)$x
-    sol$pc <- pc
+    attr(sol$points, "pc") <- pc
     rownames(sol$points) <- nm
     colnames(sol$points) <- paste("MDS", 1:k, sep="")
     class(sol) <- "monoMDS"

Modified: pkg/vegan/R/print.monoMDS.R
===================================================================
--- pkg/vegan/R/print.monoMDS.R	2011-08-28 08:59:14 UTC (rev 1766)
+++ pkg/vegan/R/print.monoMDS.R	2011-08-28 15:47:50 UTC (rev 1767)
@@ -22,7 +22,7 @@
         cat("scaled to unit root mean square")
     else
         cat("unscaled")
-    if (x$pc)
+    if (attr(x$points, "pc"))
         cat(", rotated to principal components")
     cat("\n")
     stoplab <- switch(x$icause,

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-08-28 08:59:14 UTC (rev 1766)
+++ pkg/vegan/inst/ChangeLog	2011-08-28 15:47:50 UTC (rev 1767)
@@ -17,6 +17,8 @@
 	probably this is a user error (but can be intentional and
 	correct).
 
+	* metaMDSrotate: can rotate monoMDS() results.
+	
 	* monoMDS: gained argument 'pc' (defaults TRUE) to rotate the
 	final scores to principal components.
 

Modified: pkg/vegan/man/monoMDS.Rd
===================================================================
--- pkg/vegan/man/monoMDS.Rd	2011-08-28 08:59:14 UTC (rev 1766)
+++ pkg/vegan/man/monoMDS.Rd	2011-08-28 15:47:50 UTC (rev 1767)
@@ -128,6 +128,15 @@
   \code{\link{stressplot}} can be used to display the kind of
   regression in each \code{model}.
 
+  Scaling, orientation and direction of the axes is arbitrary.
+  However, the function always centres the axes, and the default
+  \code{scaling} is to scale the configuration ot unit root mean
+  square and to rotate the axes (argument \code{pc}) to principal
+  components so that the first dimension shows the major variation.
+  It is possible to rotate the solution so that the first axis is
+  parallel to a given environmental variable using fuction
+  \code{\link{metaMDSrotate}}.
+
 }
 
 \value{ Returns an object of class \code{"monoMDS"}. The final scores