[Vegan-commits] r397 - in branches/1.13: R inst

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

Author: jarioksa
Date: 2008-06-05 05:55:03 +0200 (Thu, 05 Jun 2008)
New Revision: 397

Modified:
   branches/1.13/R/print.cca.R
   branches/1.13/inst/ChangeLog
   branches/1.13/inst/NEWS
Log:
r396 merged to branches/1.13

Modified: branches/1.13/R/print.cca.R
===================================================================
--- branches/1.13/R/print.cca.R	2008-06-05 03:39:30 UTC (rev 396)
+++ branches/1.13/R/print.cca.R	2008-06-05 03:55:03 UTC (rev 397)
@@ -1,35 +1,41 @@
-"print.cca" <-
-  function (x, digits = max(3, getOption("digits") - 3), ...) 
+`print.cca` <-
+    function (x, digits = max(3, getOption("digits") - 3), ...) 
 {
-  cat("\nCall:\n")
-  cat(deparse(x$call), "\n\n")
-  chi <- rbind(x$tot.chi, x$pCCA$tot.chi, x$CCA$tot.chi, x$CA$tot.chi)
-  rnk <- rbind(NA, x$pCCA$rank, x$CCA$rank, x$CA$rank)
-  tbl <- cbind(chi, rnk)
-  tbl <- cbind(chi, rnk)
-  colnames(tbl) <- c("Inertia", "Rank")
-  rn <- c("Total", "Conditional", "Constrained", "Unconstrained")
-  rownames(tbl) <- rn[c(TRUE, !is.null(x$pCCA), !is.null(x$CCA), 
-                        !is.null(x$CA))]
-  printCoefmat(tbl, digits = digits, na.print = "")
-  cat("Inertia is", x$inertia, "\n")
-  if (!is.null(x$CCA$alias))
-    cat("Some constraints were aliased because they were collinear (redundant)\n")
-  if (!is.null(x$CCA)) {
-    cat("\nEigenvalues for constrained axes:\n")
-    print(x$CCA$eig, digits = digits, ...)
-  }
-  if (!is.null(x$CA)) {
-    ax.lim <- 8
-    ax.trig <- 16
-    cat("\nEigenvalues for unconstrained axes:\n")
-    if (x$CA$rank > ax.trig) {
-      print(x$CA$eig[1:ax.lim], digits = digits, ...)
-      cat("(Showed only", ax.lim, "of all", x$CA$rank, 
-          "unconstrained eigenvalues)\n")
+    if (inherits(x, "pcaiv")) {
+        stop("this is an ade4 object which vegan cannot handle")
     }
-    else print(x$CA$eig, digits = digits, ...)
-  }
-  cat("\n")
-  invisible(x)
+    if (x$CCA$rank < x$CCA$QR$rank)
+        warning("rank of constraints higher than the rank of dependent data\nvegan may not handle this -- wait for a bug fix release", call. = FALSE)
+    cat("\nCall:\n")
+    cat(deparse(x$call), "\n\n")
+    chi <- rbind(x$tot.chi, x$pCCA$tot.chi, x$CCA$tot.chi, x$CA$tot.chi)
+    rnk <- rbind(NA, x$pCCA$rank, x$CCA$rank, x$CA$rank)
+    tbl <- cbind(chi, rnk)
+    tbl <- cbind(chi, rnk)
+    colnames(tbl) <- c("Inertia", "Rank")
+    rn <- c("Total", "Conditional", "Constrained", "Unconstrained")
+    rownames(tbl) <- rn[c(TRUE, !is.null(x$pCCA), !is.null(x$CCA), 
+                          !is.null(x$CA))]
+    printCoefmat(tbl, digits = digits, na.print = "")
+    cat("Inertia is", x$inertia, "\n")
+    if (!is.null(x$CCA$alias))
+        cat("Some constraints were aliased because they were collinear (redundant)\n")
+    if (!is.null(x$CCA)) {
+        cat("\nEigenvalues for constrained axes:\n")
+        print(x$CCA$eig, digits = digits, ...)
+    }
+    if (!is.null(x$CA)) {
+        ax.lim <- 8
+        ax.trig <- 16
+        cat("\nEigenvalues for unconstrained axes:\n")
+        if (x$CA$rank > ax.trig) {
+            print(x$CA$eig[1:ax.lim], digits = digits, ...)
+            cat("(Showed only", ax.lim, "of all", x$CA$rank, 
+                "unconstrained eigenvalues)\n")
+        }
+        else print(x$CA$eig, digits = digits, ...)
+    }
+    cat("\n")
+    invisible(x)
 }
+

Modified: branches/1.13/inst/ChangeLog
===================================================================
--- branches/1.13/inst/ChangeLog	2008-06-05 03:39:30 UTC (rev 396)
+++ branches/1.13/inst/ChangeLog	2008-06-05 03:55:03 UTC (rev 397)
@@ -5,6 +5,10 @@
 
 Version 1.13-1 (opened May 22, 2008)
 
+	* merged r396: cca/rda/capscale print issues a warning when rank
+	of constraints+conditions < rank of dependent data, because vegan
+	cannot handle these cases properly.
+
 	* merged mso revisions since r372: now similar as in devel branch
 	at r389. 
 

Modified: branches/1.13/inst/NEWS
===================================================================
--- branches/1.13/inst/NEWS	2008-06-05 03:39:30 UTC (rev 396)
+++ branches/1.13/inst/NEWS	2008-06-05 03:55:03 UTC (rev 397)
@@ -7,6 +7,12 @@
 
     - Helene Wagner joined the vegan team.
 
+    - cca, rda, capscale issue a warning when the rank of the
+      constraints + condition is lower than the rank of the depedent
+      (community) data, because vegan is not prepared to handle these
+      cases properly. This is an ancient issue, but surfaced recently.
+      A real fix is expected in next releases.
+
     - intersetcor and inertcomp now check that input really is from
       constrained ordination instead of giving obscure error messages.