[Vegan-commits] r815 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-04-27 09:46:39 +0200 (Mon, 27 Apr 2009)
New Revision: 815

Modified:
   pkg/vegan/R/anova.ccabyaxis.R
   pkg/vegan/R/anova.ccabymargin.R
   pkg/vegan/R/anova.ccabyterm.R
   pkg/vegan/inst/ChangeLog
Log:
anova.cca(..., by = ) name clash if data were indexed with 'i' in fitted model

Modified: pkg/vegan/R/anova.ccabyaxis.R
===================================================================
--- pkg/vegan/R/anova.ccabyaxis.R	2009-04-27 07:19:23 UTC (rev 814)
+++ pkg/vegan/R/anova.ccabyaxis.R	2009-04-27 07:46:39 UTC (rev 815)
@@ -26,20 +26,20 @@
     bigperm <- out$N.Perm[1]
     environment(object$terms) <- environment()
     if (rnk > 1) {
-        for (i in 2:rnk) {
-            zz <- paste(paste("Condition(", axnam[1:(i - 1)], 
+        for (.ITRM in 2:rnk) {
+            zz <- paste(paste("Condition(", axnam[1:(.ITRM - 1)], 
                 ")"), collapse = "+")
             fla <- update(formula(object), paste(". ~ . +", zz))
             sol <- update(object, fla, data = newdata)
             assign(".Random.seed", seed, envir = .GlobalEnv)
-            out[i, ] <- as.matrix(anova(sol, first = TRUE, ...))[1, 
+            out[.ITRM, ] <- as.matrix(anova(sol, first = TRUE, ...))[1, 
                 ]
-            if (out[i, "N.Perm"] > bigperm) {
-                bigperm <- out[i, "N.Perm"]
+            if (out[.ITRM, "N.Perm"] > bigperm) {
+                bigperm <- out[.ITRM, "N.Perm"]
                 bigseed <- get(".Random.seed", envir = .GlobalEnv, 
                   inherits = FALSE)
             }
-            if (out[i, "Pr(>F)"] > cutoff)
+            if (out[.ITRM, "Pr(>F)"] > cutoff)
                 break
         }
     }

Modified: pkg/vegan/R/anova.ccabymargin.R
===================================================================
--- pkg/vegan/R/anova.ccabymargin.R	2009-04-27 07:19:23 UTC (rev 814)
+++ pkg/vegan/R/anova.ccabymargin.R	2009-04-27 07:46:39 UTC (rev 815)
@@ -10,12 +10,12 @@
     trms <- trms[keep]
     ntrms <- length(trms)
     bigperm <- 0
-    for (i in 1:ntrms) {
+    for (.ITRM in 1:ntrms) {
         fla <- formula(object)
         ## Put all trms except current into Condition() and update
         ## formula
         if (length(alltrms) > 1) {
-            keeptrms <- alltrms[!(alltrms==trms[i])]
+            keeptrms <- alltrms[!(alltrms==trms[.ITRM])]
             updfla <- paste("Condition(",paste(keeptrms, collapse="+"), ")")
             fla <- update(fla, paste(". ~ . + ", updfla))
         }
@@ -29,12 +29,12 @@
             bigseed <- get(".Random.seed", envir = .GlobalEnv,
                            inherits = FALSE)
         }
-        if (i == 1) {
+        if (.ITRM == 1) {
             seed <- attr(tmp, "Random.seed")
             sol <- tmp
         }
         else {
-            sol <- rbind(sol[1:(i-1),], as.matrix(tmp[1,]), sol[i,])
+            sol <- rbind(sol[1:(.ITRM-1),], as.matrix(tmp[1,]), sol[.ITRM,])
         }
         assign(".Random.seed", seed, envir = .GlobalEnv)
     }

Modified: pkg/vegan/R/anova.ccabyterm.R
===================================================================
--- pkg/vegan/R/anova.ccabyterm.R	2009-04-27 07:19:23 UTC (rev 814)
+++ pkg/vegan/R/anova.ccabyterm.R	2009-04-27 07:46:39 UTC (rev 815)
@@ -21,21 +21,21 @@
     pchi[ntrm, ] <- sim$num
     df[ntrm:(ntrm + 1)] <- sim$df
     chi[ntrm:(ntrm + 1)] <- sim$chi
-    for (i in ntrm:2) {
+    for (.ITRM in ntrm:2) {
         if (ntrm < 2) 
             break
         assign(".Random.seed", sim$Random.seed, envir = .GlobalEnv)
-        fla <- as.formula(paste(" . ~ . -", trmlab[i]))
+        fla <- as.formula(paste(" . ~ . -", trmlab[.ITRM]))
         object <- update(object, fla)
         if (is.null(object$CCA)) 
             break
         sim <- permutest.cca(object, permutations = step, ...)
-        pchi[i, ] <- pchi[i, ] - sim$num
-        chi[i] <- chi[i] - sim$chi[1]
-        df[i] <- df[i] - sim$df[1]
-        pchi[i - 1, ] <- sim$num
-        chi[i - 1] <- sim$chi[1]
-        df[i - 1] <- sim$df[1]
+        pchi[.ITRM, ] <- pchi[.ITRM, ] - sim$num
+        chi[.ITRM] <- chi[.ITRM] - sim$chi[1]
+        df[.ITRM] <- df[.ITRM] - sim$df[1]
+        pchi[.ITRM - 1, ] <- sim$num
+        chi[.ITRM - 1] <- sim$chi[1]
+        df[.ITRM - 1] <- sim$df[1]
     }
     Fval <- chi/df/(chi[ntrm + 1]/df[ntrm + 1])
     Fval[ntrm + 1] <- NA

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-04-27 07:19:23 UTC (rev 814)
+++ pkg/vegan/inst/ChangeLog	2009-04-27 07:46:39 UTC (rev 815)
@@ -4,6 +4,11 @@
 
 Version 1.16-18 (opened April 21, 2009)
 
+	* anova.cca: there was a name clash and failure in
+	anova.ccabymargin, anova.ccabyaxis and anova.ccabyterm if data
+	were indexed with 'i' in the fitted model. Now the internal
+	indexing uses less likely name (.ITRM) to avoid name clashes.
+
 	* orditkplot: copes with missing or NaN scores (omits them).
 
 	* ordixyplot: failed in constrained ordination (cca, rda,