[Vegan-commits] r2365 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2013-01-13 15:35:07 +0100 (Sun, 13 Jan 2013)
New Revision: 2365

Modified:
   pkg/vegan/R/stressplot.wcmdscale.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/stressplot.wcmdscale.Rd
Log:
stressplot implemented for partial capscale and cca

Modified: pkg/vegan/R/stressplot.wcmdscale.R
===================================================================
--- pkg/vegan/R/stressplot.wcmdscale.R	2013-01-13 11:36:48 UTC (rev 2364)
+++ pkg/vegan/R/stressplot.wcmdscale.R	2013-01-13 14:35:07 UTC (rev 2365)
@@ -69,17 +69,14 @@
 `stressplot.cca` <-
     function(object, k = 2, pch, p.col = "blue", l.col = "red", lwd = 2, ...)
 {
-    ## Not yet done for pCCA
-    if (!is.null(object$pCCA))
-        stop("not implemented yet for partial CCA")
     ## Normalized scores to reconstruct data
     u <- cbind(object$CCA$u, object$CA$u)
     sev <- sqrt(c(object$CCA$eig, object$CA$eig))
     w <- sqrt(object$rowsum)
     u <- diag(w) %*% u %*% diag(sev)
     ## Distances
-    dis <- dist(u)
-    odis <- dist(u[,1:k, drop = FALSE])
+    dis <- dist(cbind(u, object$pCCA$Fit))
+    odis <- dist(cbind(u[,seq_len(k), drop = FALSE], object$pCCA$Fit))
     ##odis <- dist(sweep(Xbar, 2, sqrt(object$colsum), "*"))
     ## plot like above
         ## Plot
@@ -97,21 +94,21 @@
 `stressplot.capscale` <-
     function(object, k = 2, pch, p.col = "blue", l.col = "red", lwd = 2, ...)
 {
-    ## Not yet done for pRDA
-    if (!is.null(object$pCCA))
-        stop("not implemented yet for partial analysis")
-    ## Normalized scores to reconstruct data
+    ## Scores to reconstruct data
     u <- cbind(object$CCA$u, object$CA$u)
     ev <- c(object$CCA$eig, object$CA$eig)
-    ## normalizing constant
-    const <- sqrt(ev)
+    u <- u %*% diag(sqrt(ev))
+    if (!is.null(object$pCCA))
+        pFit <- object$pCCA$Fit/sqrt(nrow(object$pCCA$Fit) - 1)
+    else
+        pFit <- NULL
     ## Distances
-    dis <- dist(u %*% diag(const))
+    dis <- dist(cbind(u, pFit))
     if (!is.null(object$CA$imaginary.u.eig))
         dis <- sqrt(dis^2 - dist(object$CA$imaginary.u.eig)^2)
     if (!is.null(object$ac))
         dis <- dis - object$ac
-    odis <- dist(u[,1:k, drop=FALSE] %*% diag(const[1:k], nrow = k))
+    odis <- dist(cbind(u[,seq_len(k), drop=FALSE], pFit))
     ## plot like above
         ## Plot
     if (missing(pch))

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-01-13 11:36:48 UTC (rev 2364)
+++ pkg/vegan/inst/ChangeLog	2013-01-13 14:35:07 UTC (rev 2365)
@@ -21,7 +21,9 @@
 	are found from the full space solution, and in capscale() and
 	wcmdscale() they are correct for the imaginary axes. The weights
 	are used in wcmdscale() and cca() so that their distances differ
-	from plotted ordinations, but agree with eigenvalues.
+	from plotted ordinations, but agree with eigenvalues. Partial
+	models (p-dbRDA, pRDA, pCCA) add the partial component both to the
+	original dissimilarities and the fit.
 
 	* wcmdscale: added method functions print(), plot() and
 	scores(). Now class "wcmdscale" results also retun the function

Modified: pkg/vegan/man/stressplot.wcmdscale.Rd
===================================================================
--- pkg/vegan/man/stressplot.wcmdscale.Rd	2013-01-13 11:36:48 UTC (rev 2364)
+++ pkg/vegan/man/stressplot.wcmdscale.Rd	2013-01-13 14:35:07 UTC (rev 2365)
@@ -60,6 +60,13 @@
   \code{\link{capscale}} with argument \code{add = TRUE} to avoid
   negative eigenvalues, the ordination distances will exceed the
   observed dissimilarities by the additive constant.
+
+  In partial ordination (\code{\link{cca}}, \code{\link{rda}} and
+  \code{\link{capscale}} with \code{Condition} in the formula), the
+  distances in the partial component are included both in the observed
+  distances and in ordination distances.  With \code{k=0}, the
+  ordination distances refer to the partial ordination.
+
 }
 
 \value{