[Vegan-commits] r404 - pkg/R

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

Author: jarioksa
Date: 2008-06-09 06:34:32 +0200 (Mon, 09 Jun 2008)
New Revision: 404

Modified:
   pkg/R/cca.default.R
   pkg/R/print.cca.R
   pkg/R/rda.default.R
Log:
removed warnings of ranks in rda and cca

Modified: pkg/R/cca.default.R
===================================================================
--- pkg/R/cca.default.R	2008-06-09 04:20:30 UTC (rev 403)
+++ pkg/R/cca.default.R	2008-06-09 04:34:32 UTC (rev 404)
@@ -56,8 +56,6 @@
         sol <- svd(Y)
         ## rank of svd can be < qrank
         rank <- min(rank, sum(sol$d > ZERO))
-        if (rank < qrank)
-            warning("rank of QR decomposition > rank of svd: trouble ahead")
         ax.names <- paste("CCA", 1:length(sol$d), sep = "")
         colnames(sol$u) <- ax.names
         colnames(sol$v) <- ax.names

Modified: pkg/R/print.cca.R
===================================================================
--- pkg/R/print.cca.R	2008-06-09 04:20:30 UTC (rev 403)
+++ pkg/R/print.cca.R	2008-06-09 04:34:32 UTC (rev 404)
@@ -5,9 +5,6 @@
         warning("this is an ade4 object which vegan cannot handle")
         x <- ade2vegancca(x)
     }
-    if (!is.null(x$CCA) && x$CCA$rank < x$CCA$qrank) {
-        warning("rank of constraints higher than the rank of dependent data\nvegan may not handle this -- wait for a bug fix release", call. = FALSE)
-    }
     cat("\nCall:\n")
     cat(deparse(x$call), "\n\n")
     chi <- rbind(x$tot.chi, x$pCCA$tot.chi, x$CCA$tot.chi, x$CA$tot.chi)

Modified: pkg/R/rda.default.R
===================================================================
--- pkg/R/rda.default.R	2008-06-09 04:20:30 UTC (rev 403)
+++ pkg/R/rda.default.R	2008-06-09 04:34:32 UTC (rev 404)
@@ -39,8 +39,6 @@
         sol <- svd(Y)
         ## it can happen that rank < qrank
         rank <- min(rank, sum(sol$d > ZERO))
-        if (rank < qrank)
-            warning("rank of QR decomposition > rank of svd: trouble ahead")
         sol$d <- sol$d/sqrt(NR)
         ax.names <- paste("RDA", 1:length(sol$d), sep = "")
         colnames(sol$u) <- ax.names