[Vegan-commits] r1381 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2010-12-01 11:28:04 +0100 (Wed, 01 Dec 2010)
New Revision: 1381

Modified:
   pkg/vegan/R/fitted.procrustes.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/procrustes.Rd
Log:
predict.procrustes can do truemean = FALSE

Modified: pkg/vegan/R/fitted.procrustes.R
===================================================================
--- pkg/vegan/R/fitted.procrustes.R	2010-11-23 15:58:39 UTC (rev 1380)
+++ pkg/vegan/R/fitted.procrustes.R	2010-12-01 10:28:04 UTC (rev 1381)
@@ -10,15 +10,18 @@
 ## Like above, except when takes 'newata'
 
 `predict.procrustes` <-
-    function(object, newdata, ...)
+    function(object, newdata, truemean = TRUE, ...)
 {
     if (missing(newdata))
-        return(fitted(object, truemean = TRUE))
+        return(fitted(object, truemean = truemean))
     if (object$symmetric)
         stop(gettextf("'predict' not available for symmetric procrustes analysis with 'newdata'"))
     Y <- as.matrix(newdata)
     ## scaling and rotation
     Y <- object$scale * Y %*% object$rotation
     ## translation: always
-    sweep(Y, 2, object$translation, "+")
+    Y <- sweep(Y, 2, object$translation, "+")
+    if (!truemean)
+        Y <- sweep(Y, 2, object$xmean*object$scale, "-")
+    Y
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-11-23 15:58:39 UTC (rev 1380)
+++ pkg/vegan/inst/ChangeLog	2010-12-01 10:28:04 UTC (rev 1381)
@@ -4,6 +4,9 @@
 
 Version 1.18-17 (opened November 17, 2010)
 
+	* predict.procrustes: gained 'truemean' so that new points can be
+	added to the plot.procrustes() graph.
+
 	* alpha release version: preparing release (1.17-5) of
 	vegan. Mainly clean up and checking of functions intended for the
 	release. 

Modified: pkg/vegan/man/procrustes.Rd
===================================================================
--- pkg/vegan/man/procrustes.Rd	2010-11-23 15:58:39 UTC (rev 1380)
+++ pkg/vegan/man/procrustes.Rd	2010-12-01 10:28:04 UTC (rev 1381)
@@ -29,7 +29,7 @@
 \method{lines}{procrustes}(x, type = c("segments", "arrows"), choices = c(1, 2), ...)  
 \method{residuals}{procrustes}(object, ...)
 \method{fitted}{procrustes}(object, truemean = TRUE, ...)
-\method{predict}{procrustes}(object, newdata, ...)
+\method{predict}{procrustes}(object, newdata, truemean = TRUE, ...)
 protest(X, Y, scores = "sites", permutations = 999, strata, ...)
 }
 
@@ -57,7 +57,8 @@
   \item{type}{Combine \code{target} and \code{rotated} points with line
     segments or arrows.}
   \item{truemean}{Use the original range of target matrix instead of
-    centring the fitted values.}
+    centring the fitted values. Function \code{plot.procrustes} needs
+    \code{truemean = FALSE}.}
   \item{newdata}{Matrix of coordinates to be rotated and translated to
      the target.}
   \item{permutations}{Number of permutation to assess the significance