[Vegan-commits] r403 - in pkg: R inst

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

Author: jarioksa
Date: 2008-06-09 06:20:30 +0200 (Mon, 09 Jun 2008)
New Revision: 403

Modified:
   pkg/R/predict.cca.R
   pkg/R/predict.rda.R
   pkg/inst/ChangeLog
Log:
predict.cca/rda rank fixes for type='lc' and with newdata

Modified: pkg/R/predict.cca.R
===================================================================
--- pkg/R/predict.cca.R	2008-06-08 16:06:53 UTC (rev 402)
+++ pkg/R/predict.cca.R	2008-06-09 04:20:30 UTC (rev 403)
@@ -39,7 +39,8 @@
             }
             E <- sweep(E, 2, c(object$pCCA$envcentre, object$CCA$envcentre), 
                        "-")
-            p1 <- object[[model]]$QR$pivot[1:object[[model]]$qrank]
+            Q <- object[[model]]$QR
+            p1 <- Q$pivot[1:Q$rank]
             u <- E[, p1, drop = FALSE] %*% coef(object)[p1, , 
                          drop = FALSE]
             u <- u[, 1:take, drop = FALSE]

Modified: pkg/R/predict.rda.R
===================================================================
--- pkg/R/predict.rda.R	2008-06-08 16:06:53 UTC (rev 402)
+++ pkg/R/predict.rda.R	2008-06-09 04:20:30 UTC (rev 403)
@@ -44,7 +44,8 @@
                                       object$terminfo$xlev)
                 E <- cbind(d$Z, d$Y)
             }
-            p1 <- object[[model]]$QR$pivot[1:object[[model]]$qrank]
+            Q <- object[[model]]$QR
+            p1 <- Q$pivot[1:Q$rank]
             E <- sweep(E, 2, c(object$pCCA$envcentre, object$CCA$envcentre), 
                        "-")
             u <- E[, p1, drop = FALSE] %*% coef(object)[p1, , 

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-06-08 16:06:53 UTC (rev 402)
+++ pkg/inst/ChangeLog	2008-06-09 04:20:30 UTC (rev 403)
@@ -15,11 +15,14 @@
 	cca objects are handled by many other functions, this may cause
 	trouble in surprising places and the change is unstabilizing.
 
-	* rda.default, cca.default: return now both 'rank' for the
-	ordination, and 'qrank' or the rank of the constrainst. This means
-	following changes in functions using ranks:
+	* rda.default, cca.default: vegan naively used only the rank of
+	the ordination, but indeed, there are three cases of ranks
+	(returned as rank): rank of the ordination or number of axes, rank
+	of the constraints after conditions (now returned as qrank), rank
+	of conditions + constraints (returned in QR$rank). The following
+	changes were made if necessary to cca/rda support functions: 
 
-	* alias.cca: qrank
+	* alias.cca: QR$rank
 	* anova.ccabyaxis: OK 
 	* bstick.cca: OK 
 	* calibrate.cca: stop with error if qrank > rank
@@ -27,7 +30,7 @@
 	* mso: OK (HW confirms)
 	* msoplot: OK (HW cofirms)
 	* permutest.cca: qrank, also fixes anova.ccabyterm
-	* predict.cca/rda: qrank with type = "lc"
+	* predict.cca/rda: QR$rank with type = "lc" & newdata
 	* summary.cca/rda: OK
 	* scores.cca/rda: OK