[Vegan-commits] r499 - in pkg: R inst man

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

Author: jarioksa
Date: 2008-09-15 17:28:39 +0200 (Mon, 15 Sep 2008)
New Revision: 499

Modified:
   pkg/R/add1.cca.R
   pkg/R/anova.ccabymargin.R
   pkg/R/drop1.cca.R
   pkg/inst/ChangeLog
   pkg/man/anova.cca.Rd
Log:
fixes to remaining issues of add1/drop1 and 'scope' to anova.ccabyterm

Modified: pkg/R/add1.cca.R
===================================================================
--- pkg/R/add1.cca.R	2008-09-15 12:37:26 UTC (rev 498)
+++ pkg/R/add1.cca.R	2008-09-15 15:28:39 UTC (rev 499)
@@ -25,11 +25,7 @@
             else
                 nfit <- update(object,
                                as.formula(paste(". ~ . +", tt)))
-            ## Handle completely aliased terms
-            if (is.null(nfit$CCA))
-                tmp <- matrix(NA, 1, 5)
-            else
-                tmp <- anova(nfit, perm.max = perm.max, ...)
+            tmp <- anova(nfit, perm.max = perm.max, ...)
             adds[i+1,] <- unlist(tmp[1,3:5])
         }
         colnames(adds) <- colnames(tmp)[3:5]

Modified: pkg/R/anova.ccabymargin.R
===================================================================
--- pkg/R/anova.ccabymargin.R	2008-09-15 12:37:26 UTC (rev 498)
+++ pkg/R/anova.ccabymargin.R	2008-09-15 15:28:39 UTC (rev 499)
@@ -1,7 +1,10 @@
 `anova.ccabymargin` <-
-    function(object, step=100,...)
-{ 
-    trms <- drop.scope(object)
+    function(object, step=100, scope, ...)
+{
+    if (!missing(scope) && is.character(scope))
+        trms <- scope
+    else
+        trms <- drop.scope(object, scope)
     alltrms <- labels(terms(object$terminfo))
     keep <- trms %in% alltrms
     trms <- trms[keep]
@@ -11,8 +14,9 @@
         fla <- formula(object)
         ## Put all trms except current into Condition() and update
         ## formula
-        if (ntrms > 1) {
-            updfla <- paste("Condition(",paste(trms[-i], collapse="+"), ")")
+        if (length(alltrms) > 1) {
+            keeptrms <- alltrms[!(alltrms==trms[i])]
+            updfla <- paste("Condition(",paste(keeptrms, collapse="+"), ")")
             fla <- update(fla, paste(". ~ . + ", updfla))
         }
         tmp <- update(object, fla)

Modified: pkg/R/drop1.cca.R
===================================================================
--- pkg/R/drop1.cca.R	2008-09-15 12:37:26 UTC (rev 498)
+++ pkg/R/drop1.cca.R	2008-09-15 15:28:39 UTC (rev 499)
@@ -6,9 +6,13 @@
     out <- NextMethod("drop1", object, test="none", ...)
     cl <- class(out)
     if (test == "permutation") {
-        adds <- anova(object, by = "margin", perm.max = perm.max, ...)
+        rn <- rownames(out)[-1]
+        if (missing(scope))
+            scope <- rn
+        adds <- anova(object, by = "margin", perm.max = perm.max,
+                      scope = scope, ...)
         nr <- nrow(adds)
-        out <- cbind(out, rbind(NA, adds[-nr,3:5]))
+        out <- cbind(out, rbind(NA, adds[rn,3:5]))
         class(out) <- cl
     }
     out

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-09-15 12:37:26 UTC (rev 498)
+++ pkg/inst/ChangeLog	2008-09-15 15:28:39 UTC (rev 499)
@@ -19,6 +19,13 @@
 	impossible. These used to stop with error, but now they return a
 	zeroed result so that things like anova(..., by = "term") and
 	drop1() work. Added function anova.ccanull to handle these cases.
+
+	* anova.cca(..., by = "margin") was handling wrongly 'x' in ~
+	Condition(x) + x + z, or model formulae where same variables were
+	used both as Conditions and (aliased) constraints. 
+
+	* anova.cca(..., by = "margin") or function anova.ccabymargin
+	gained a 'scope' argument which is used in drop.scope(). 
 	
 Version 1.14-11 (closed September 10, 2008)
 

Modified: pkg/man/anova.cca.Rd
===================================================================
--- pkg/man/anova.cca.Rd	2008-09-15 12:37:26 UTC (rev 498)
+++ pkg/man/anova.cca.Rd	2008-09-15 15:28:39 UTC (rev 499)
@@ -109,7 +109,11 @@
   variable). The terms are assessed sequentially from first to last, and
   the order of the terms will influence their significances. Setting
   \code{by = "margin"} will perform separate significance test for each
-  marginal term in a model with all other terms. These are similar to
+  marginal term in a model with all other terms. The marginal test
+  also accepts a \code{scope} argument for the
+  \code{\link{drop.scope}} which can be a character vector
+  of term labels that are analysed, or a fitted model of lower scope. 
+  The marginal effects are also known as
   \dQuote{Type III} effects, but the current function only evaluates
   marginal terms. It will, for instance, ignore main effects that are
   included in interaction terms. In calculating pseudo-\eqn{F}, all
@@ -146,10 +150,16 @@
 data(varespec)
 data(varechem)
 vare.cca <- cca(varespec ~ Al + P + K, varechem)
+## overall test
 anova(vare.cca)
+## Test for axes
 anova(vare.cca, by="axis", perm.max=500)
+## Sequential test for terms
 anova(vare.cca, by="terms", permu=200)
+## Marginal or Type III effects
 anova(vare.cca, by="margin")
+## Marginal test knows 'scope'
+anova(vare.cca, by = "m", scope="P")
 }
 \keyword{ multivariate }
 \keyword{ htest }