[Vegan-commits] r2363 - in branches/2.0: R inst man

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

Author: jarioksa
Date: 2013-01-12 07:51:40 +0100 (Sat, 12 Jan 2013)
New Revision: 2363

Modified:
   branches/2.0/R/capscale.R
   branches/2.0/R/print.capscale.R
   branches/2.0/inst/ChangeLog
   branches/2.0/man/capscale.Rd
Log:
merge r2357, 2361,2: capscale fixes and enhancements

Modified: branches/2.0/R/capscale.R
===================================================================
--- branches/2.0/R/capscale.R	2013-01-12 06:44:20 UTC (rev 2362)
+++ branches/2.0/R/capscale.R	2013-01-12 06:51:40 UTC (rev 2363)
@@ -88,8 +88,13 @@
     if (is.null(rownames(X$points))) 
         rownames(X$points) <- nm
     X$points <- adjust * X$points
-    if (adjust == 1)
+    ## We adjust eigenvalues to variances, and simultaneously the
+    ## possible negative axes must be adjusted similarly
+    if (adjust == 1) {
         X$eig <- X$eig/k
+        if (!is.null(X$negaxes))
+            X$negaxes <- X$negaxes/sqrt(k)
+    }
     sol <- rda.default(X$points, d$Y, d$Z, ...)
     if (!is.null(sol$CCA) && sol$CCA$rank > 0) {
         colnames(sol$CCA$u) <- colnames(sol$CCA$biplot) <- names(sol$CCA$eig) <-

Modified: branches/2.0/R/print.capscale.R
===================================================================
--- branches/2.0/R/print.capscale.R	2013-01-12 06:44:20 UTC (rev 2362)
+++ branches/2.0/R/print.capscale.R	2013-01-12 06:51:40 UTC (rev 2363)
@@ -3,5 +3,7 @@
 {
     NextMethod("print", x, ...)
     if (!is.null(x$metaMDSdist))
-        cat("metaMDSdist transformed data:", x$metaMDSdist, "\n\n") 
+        cat("metaMDSdist transformed data:", x$metaMDSdist, "\n\n")
+    if (!is.null(x$ac))
+        cat("Constant added to distances:", x$ac, "\n\n")
 }

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-01-12 06:44:20 UTC (rev 2362)
+++ branches/2.0/inst/ChangeLog	2013-01-12 06:51:40 UTC (rev 2363)
@@ -4,6 +4,9 @@
 
 Version 2.0-6 (opened October 8, 2012)
 
+	* merge 2362: doc on r2357 for capscale.
+	* merge 2361: adjust imaginary axes similarly as real eigenvalue. 
+	* merge 2357: print additive constant in capscale.
 	* merge 2350: capscale species score scaling bug fix.
 	* merge 2349: multipart print bug fix.
 	* merge 2345: FAQ update (github, metric NMDS space).

Modified: branches/2.0/man/capscale.Rd
===================================================================
--- branches/2.0/man/capscale.Rd	2013-01-12 06:44:20 UTC (rev 2362)
+++ branches/2.0/man/capscale.Rd	2013-01-12 06:51:40 UTC (rev 2363)
@@ -206,7 +206,8 @@
   \code{squared} is added to the name of distance, unless data were
   square root transformed (argument \code{sqrt.dist = TRUE}). If an
   additive constant was used, keyword \code{euclidified} is added to the
-  the name of inertia (argument \code{add = TRUE}).
+  the name of inertia, and the value of the constant is printed
+ (argument \code{add = TRUE}).
 }