[Vegan-commits] r1603 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-05-17 13:00:03 +0200 (Tue, 17 May 2011)
New Revision: 1603

Modified:
   pkg/vegan/R/add1.cca.R
   pkg/vegan/R/anova.ccabyaxis.R
   pkg/vegan/R/anova.ccabymargin.R
   pkg/vegan/R/drop1.cca.R
   pkg/vegan/R/model.frame.cca.R
   pkg/vegan/R/model.matrix.cca.R
   pkg/vegan/inst/ChangeLog
Log:
many cca/rda support functions fail with prc results

Modified: pkg/vegan/R/add1.cca.R
===================================================================
--- pkg/vegan/R/add1.cca.R	2011-05-16 20:05:40 UTC (rev 1602)
+++ pkg/vegan/R/add1.cca.R	2011-05-17 11:00:03 UTC (rev 1603)
@@ -2,6 +2,8 @@
     function(object, scope, test = c("none", "permutation"),
              pstep = 100, perm.max = 200, ...)
 {
+    if (inherits(object, "prc"))
+        stop("'step'/'add1' cannot be used for 'prc' objects")
     test <- match.arg(test)
     ## Default add1
     out <- NextMethod("add1", object, test = "none", ...)

Modified: pkg/vegan/R/anova.ccabyaxis.R
===================================================================
--- pkg/vegan/R/anova.ccabyaxis.R	2011-05-16 20:05:40 UTC (rev 1602)
+++ pkg/vegan/R/anova.ccabyaxis.R	2011-05-17 11:00:03 UTC (rev 1603)
@@ -1,6 +1,8 @@
-"anova.ccabyaxis" <-
-function (object, cutoff = 1,  ...) 
+`anova.ccabyaxis` <-
+    function (object, cutoff = 1,  ...) 
 {
+    if(inherits(object, "prc"))
+        stop("anova(..., by = 'axis') cannot be used for 'prc' results")
     cutoff <- cutoff + sqrt(.Machine$double.eps)
     rnk <- object$CCA$rank
     if (!max(rnk, 0)) 

Modified: pkg/vegan/R/anova.ccabymargin.R
===================================================================
--- pkg/vegan/R/anova.ccabymargin.R	2011-05-16 20:05:40 UTC (rev 1602)
+++ pkg/vegan/R/anova.ccabymargin.R	2011-05-17 11:00:03 UTC (rev 1603)
@@ -1,6 +1,8 @@
 `anova.ccabymargin` <-
     function(object, step=100, scope, ...)
 {
+    if(inherits(object, "prc"))
+        stop("anova(..., by = 'margin') cannot be used for 'prc' results")
     if (!missing(scope) && is.character(scope))
         trms <- scope
     else

Modified: pkg/vegan/R/drop1.cca.R
===================================================================
--- pkg/vegan/R/drop1.cca.R	2011-05-16 20:05:40 UTC (rev 1602)
+++ pkg/vegan/R/drop1.cca.R	2011-05-17 11:00:03 UTC (rev 1603)
@@ -2,6 +2,8 @@
     function(object, scope, test = c("none", "permutation"),
              pstep = 100, perm.max = 200, ...)
 {
+    if (inherits(object, "prc"))
+        stop("'step'/'drop1' cannot be used for 'prc' objects")
     test <- match.arg(test)
     out <- NextMethod("drop1", object, test="none", ...)
     cl <- class(out)

Modified: pkg/vegan/R/model.frame.cca.R
===================================================================
--- pkg/vegan/R/model.frame.cca.R	2011-05-16 20:05:40 UTC (rev 1602)
+++ pkg/vegan/R/model.frame.cca.R	2011-05-17 11:00:03 UTC (rev 1603)
@@ -1,6 +1,8 @@
 `model.frame.cca` <-
     function (formula, ...) 
 {
+    if (inherits(formula, "prc"))
+        stop("model.frame does not work with 'prc' results")
     call <- formula$call
     m <- match(c("formula", "data", "na.action", "subset"), names(call), 
         0)

Modified: pkg/vegan/R/model.matrix.cca.R
===================================================================
--- pkg/vegan/R/model.matrix.cca.R	2011-05-16 20:05:40 UTC (rev 1602)
+++ pkg/vegan/R/model.matrix.cca.R	2011-05-17 11:00:03 UTC (rev 1603)
@@ -1,6 +1,8 @@
 `model.matrix.cca` <-
     function (object, ...) 
 {
+    if (inherits(object, "prc"))
+        stop("model.matrix does not work with 'prc' results")
     call <- object$call
     m <- match(c("formula", "data", "na.action", "subset"), names(call), 
         0)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-05-16 20:05:40 UTC (rev 1602)
+++ pkg/vegan/inst/ChangeLog	2011-05-17 11:00:03 UTC (rev 1603)
@@ -16,6 +16,13 @@
 	* scores.cca/rda: failed if user requested only non-existing
 	scores. Now return an empty list of scores instead (with possible
 	attributes). 
+
+	* prc: several support methods did not work with 'prc' results,
+	and these now stop with an informative error instead of an
+	uniformative error. Concerns anova.ccabymargin, anova.ccabyaxis,
+	drop1.cca, add1.cca, model.frame.cca, model.matrix.cca. This was
+	found out after a private user query about having signficance test
+	for the sencond PRC axis.
 	
 Version 1.18-29 (closed April 27, 2011)